Basics Manual: Sybyl 7.3 Late 2006

Basics Manual
SYBYL® 7.3
Late 2006
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SYBYL Basics Table of Contents
Chapter 1.
Introduction to SYBYL Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 2.
Quick Introduction to SYBYL Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1 Start the SYBYL Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2 Load Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.3 Change the Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.4 Rotate, Translate, and Scale Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.5 Save a Molecule to a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.6 Clear the Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.7 Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3.
Start/Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1 Start SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.2 Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.3 Get Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.4 Modes for Using SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Menubar Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Command Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Object Picking Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.5 Automatic Command Execution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Chapter 4.
SYBYL’s Main Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4.1 Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Menubar Shortcuts and Comments . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4.2 Toolbox Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3 Textport Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Textport Output Presentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Execute Operating System Commands from within SYBYL . . . . . . 42
Control Characters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.4 Keyboard Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Chapter 5.
Open and Save Files of Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5.1 Open (Read) Molecule File via the Menubar . . . . . . . . . . . . . . . . . . . . . 46
5.2 Save (Write) Molecule File via the Menubar . . . . . . . . . . . . . . . . . . . . . 48
5.3 Open/Save MOL/MOL2 Files via the Command Line . . . . . . . . . . . . . . 50
5.4 Manage Input/Output Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
SLN Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
SMILES Strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
SYBYL 7.3 SYBYL Basics TOC-3

SD/MACCS Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
CSSR files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.5 View and Edit Text Files in SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Chapter 6.
Understand Molecule and Display Areas . . . . . . . . . . . . . . . . . . . . . . .57
6.1 What are Molecule and Display Areas? . . . . . . . . . . . . . . . . . . . . . . . . . 58
6.2 Change the Default Molecule Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
6.3 Copy Between Molecule Areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6.4 Merge Molecule Areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Merge Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Merge Atoms and Associated Data Structures . . . . . . . . . . . . . . . . . 62
Merging Non-Unique Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Chapter 7.
Rotate and Move Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Chapter 8.
Build and Modify Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
8.1 Small Molecule Sketching Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Set Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Enter the Sketching Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Build Piperidine Ring in Chair Conformation . . . . . . . . . . . . . . . . . . 72
Add a Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Add a Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Check Chirality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Clean Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Save the Sketched Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
8.2 Ring Fusion Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Set Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Fuse Two Planar Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Fuse Two Rings to Build a Spiro System . . . . . . . . . . . . . . . . . . . . . 79
Fuse Two Non Planar Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Fuse A Planar Bond With A Non Planar Bond . . . . . . . . . . . . . . . . . 82
8.3 Load Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
8.4 Access the Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Sketching Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Sketcher Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
8.5 Modify Molecules Outside of Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Chirality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
TOC-4 SYBYL Basics SYBYL 7.3

Molecule’s Center of Rotation, Name, Type, etc. . . . . . . . . . . . . . . 109
Combine (Fuse) Two Molecules From Different Molecule Areas . 110
Combine (Join) Two Molecules or Groups in Same Molecule Area 112
Adjust Bond Lengths and Angles to Match Standards . . . . . . . . . . 112
Scan Torsions to Remove van der Waals Contacts . . . . . . . . . . . . . 113
Create Molecule by Averaging Existing Molecules . . . . . . . . . . . . 113
8.6 Create/Modify Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Center of Mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Centroid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Extension Point . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Normal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Renumber Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
UNITY Query Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.7 Markush Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Define a Markush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Delete a Markush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
List Currently Defined Markushes . . . . . . . . . . . . . . . . . . . . . . . . . 125
Load Markush Definitions from a File . . . . . . . . . . . . . . . . . . . . . . 125
Modify a Markush Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Save a Markush Definitions to a File . . . . . . . . . . . . . . . . . . . . . . . . 125
Chapter 9.
Get Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
9.1 Intra-/Intermolecular Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
9.2 Measure the Intramolecular Angle Between Planes . . . . . . . . . . . . . . . 129
9.3 Measurements Specific to UNITY Features . . . . . . . . . . . . . . . . . . . . . 130
9.4 Calculate a Molecule’s Dipole Moment . . . . . . . . . . . . . . . . . . . . . . . . 131
Chapter 10.
Select Atoms, Bonds, or Substructures . . . . . . . . . . . . . . . . . . . . . . 133
10.1 General Description of the Expression Dialogs . . . . . . . . . . . . . . . . . . 135
10.2 Selection How Tos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Individual Objects Using the Cursor . . . . . . . . . . . . . . . . . . . . . . . . 138
Everything in a Molecule Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
By Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
By Residue Conformational State . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Sequence of Residues in a Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
By Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
By Substructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
By Chirality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Within a Radius . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Using Boolean Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
10.3 Atom Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

10.4 Bond Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
10.5 Substructure Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Chapter 11.
Get Information on SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . .161
11.1 Report Information on an Individual Atom, Bond, or Substructure . . 162
11.2 List Coordinates, Distances, or Angles (Same Molecule Area) . . . . . 163
List Information on One or More SYBYL Objects . . . . . . . . . . . . . 164
11.3 Print Information on One or More SYBYL Objects . . . . . . . . . . . . . . 165
Chapter 12.
Clear and Reset the SYBYL Display . . . . . . . . . . . . . . . . . . . . . . . . . .167
Chapter 13.
Use Molecule Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .171
13.1 Database Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
13.2 Open/Close Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Open Database via the Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Open Database via Command Line . . . . . . . . . . . . . . . . . . . . . . . . . 184
Open a New, Empty Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Copy Database Contents to New Database . . . . . . . . . . . . . . . . . . . 185
Define Alias for Database via Command Line . . . . . . . . . . . . . . . . 185
Specify a Default Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Close Database via the Command Line . . . . . . . . . . . . . . . . . . . . . . 186
13.3 Obtain Information on Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
List All Open Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Show Status for Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
List Contents of Open Database . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
List Molecule and Group Information for Open Database . . . . . . . 187
13.4 Retrieve Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Retrieve a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Search for Molecule(s) to Retrieve . . . . . . . . . . . . . . . . . . . . . . . . . 191
Create/Modify a Table of Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
13.5 Managing Database Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Add Molecule(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Delete Molecule(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Organize Molecules into Groups (Sets and Classes) . . . . . . . . . . . . 193
13.6 Save Database Molecules to MOL2 or MOL Files . . . . . . . . . . . . . . . 196
13.7 Connect to External Relational Databases . . . . . . . . . . . . . . . . . . . . . . 197
Define a Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Delete a Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Evaluate a Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
List Query Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Save a Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Define a Reference (Database Connection) . . . . . . . . . . . . . . . . . . . 201

Delete a Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
List Reference Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Save a Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
13.8 DATABASE Command List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Chapter 14.
Manage SYBYL Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
14.1 Save a Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
14.2 Restore a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
14.3 Delete a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
14.4 Record and Play SYBYL Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
Record Session Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Record Output from a Single Command . . . . . . . . . . . . . . . . . . . . . 219
Record Terminal Dialog of Session . . . . . . . . . . . . . . . . . . . . . . . . . 219
Insert a Pause in a Recorded Session File . . . . . . . . . . . . . . . . . . . . 220
Play Recorded Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
Read Command Input From Text File . . . . . . . . . . . . . . . . . . . . . . . 221
Chapter 15.
Objects and Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
15.1 Definitions of SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
15.2 Formats for Specifying Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
Atom Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Bond Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Substructure Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
Set Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
Molecule Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Molecule Area Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Monomer Sequence Specification . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Conformational Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
15.3 Create Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Logical Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Parentheses and Grouping of Operations . . . . . . . . . . . . . . . . . . . . . 239
Chapter 16.
Sets in SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
16.1 Global Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Define a Global Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Modify a Global Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Remove a Global Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Global Sets in the macromol Dictionary . . . . . . . . . . . . . . . . . . . . . 245
16.2 Local Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Modify a Local Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Remove a Local Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
16.3 Dynamic Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

Define a Dynamic Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Dynamic Set Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Manage Dynamic Hydrogen Bonds . . . . . . . . . . . . . . . . . . . . . . . . . 250
16.4 Built-in Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
16.5 Static Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Define a Static Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Manage Static Hydrogen Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
16.6 Working with Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Chapter 17.
Libraries of Chemical Groups and Fragments . . . . . . . . . . . . . . . . .259
17.1 Group Library Structure and Contents . . . . . . . . . . . . . . . . . . . . . . . . . 260
17.2 Fragment Library Structure and Contents . . . . . . . . . . . . . . . . . . . . . . 261

Chapter 1.
Introduction to SYBYL Basics
SYBYL uses computer analysis to assist in the description and prediction of

molecular behavior. SYBYL Base includes the basic tools for molecular
modeling. Topics in this manual include:
• SYBYL Quick Reference
• Quick Introduction to SYBYL Tutorial on page 11
• Start/Exit SYBYL on page 25
• SYBYL’s Main Window on page 35
• Open and Save Files of Molecules on page 45
• Understand Molecule and Display Areas on page 57
• Rotate and Move Molecules on page 67
• Build and Modify Molecules on page 69
• Get Measurements on page 127
• Select Atoms, Bonds, or Substructures on page 133
• Get Information on SYBYL Objects on page 161
• Clear and Reset the SYBYL Display on page 167
• Use Molecule Databases on page 171
• Manage SYBYL Sessions on page 207
• Objects and Expressions on page 223
• Sets in SYBYL on page 241
When combined with SYBYL applications, SYBYL Base provides a completely

integrated environment for computational chemistry and molecular modeling.
License Requirements for SYBYL Basics

Functionality described in the SYBYL Basics manual requires a SYBYL Base
license (“SybylBasic”).
The Substructure Selection tutorial requires the Biopolymer license

(“BioPolymer”).
SYBYL 7.3 SYBYL Basics 9

This page intentionally blank.
Chapter 2. Quick Introduction to SYBYL Tutorial
Chapter 2.
Quick Introduction to SYBYL Tutorial
Run this tutorial to learn some basics operations in SYBYL:

• Start the SYBYL Program on page 12
• Load Molecules on page 15
• Change the Display on page 18
• Rotate, Translate, and Scale Tutorial on page 19
• Save a Molecule to a File on page 21
• Clear the Screen on page 22
• Exit SYBYL on page 23
A Matter of Time: this tutorial requires about 20 minutes of personal time.

Start the SYBYL Program
2.1 Start the SYBYL Program

1. Log into the computer in the normal manner.
2. In a system shell, type:
¾ xterm
Tripos suggests starting SYBYL from an xterm shell.
3. Start the SYBYL program.
¾ Enter SYBYL’s program name at the system prompt.

Example for SYBYL 7.3:
sybyl7.3
Notes:
• SYBYL’s program name can be any name that was defined by the
administrator during installation. The default name for SYBYL 7.3 is
shown in the example. Consult with your system administrator to
determine SYBYL’s program name on your machine.
• See Start/Exit SYBYL on page 25 for more information.
The SYBYL graphical interface is composed of a menubar, toolbox icons,
and display area. The textport is displayed in a separate window.
12 SYBYL Basics SYBYL 7.3

4. Explore the parts of the interface.
Menubar
Active menu options are displayed in black; inactive menu options are
displayed in grey. Additionally, any options for which you do not have a license
are greyed out, except on the Tools menu.
A menu option can be a command (File >>> Exit SYBYL) or a check box
(File >>> Log Commands); it can also lead to submenus (View >>> Color
>>> By Atom Type) or open a dialog (File >>> Read).
Toolbox Icons
Use the icons in the SYBYL toolbox, located on the left edge of the SYBYL
screen, to interact with the graphics.

Descriptions and links to the tutorials for the individual icons can be found in
the Toolbox Icons section of the Graphics Manual. To activate an icon, click it.
You can leave the tool open as you work or you can close it by pressing the Q
button.
Textport Window
Use the textport window to enter any command, including HELP, at the SYBYL
prompt (SYBYL>). For a complete listing of available SYBYL commands, see
the List of SYBYL Commands in the Quick Reference Manual. After entering a
command, the system performs the command operation and redisplays the
SYBYL prompt.
Note: The menubar and command line are available simultaneously.
See SYBYL’s Main Window on page 35 for more in-depth descriptions or the
SYBYL interface.

Load Molecules
2.2 Load Molecules

There are several ways to load molecules in SYBYL: from the menubar, via the
textport, or from the Fragment Library.
Load a Molecule via the Menubar
1. Load methotrexate (mtx.mol2).
¾ File >>> Read
SYBYL opens the Read File dialog.
¾ In File to read text box, type:

$TA_DEMO/mtx.mol2
¾ Press OK.
SYBYL loads methotrexate into D1 (SYBYL’s display area 1). Its default
location is M1 (molecule area 1).
Tip: If you can’t see the molecule, click , verify that the Molecule
Selection area shows m1: ligand, and click Center View (press Close).
A molecule area is a region of memory that holds a particular molecule. The

total number of molecule areas does not have a fixed limit, because the number
depends on your computer’s memory.
Tip: If you have difficulty seeing the molecule against the backdrop, select
View >>> Backdrop >>> Fade.
For more information, see Understand Molecule and Display Areas on page 57.
2. Remove the molecule.
¾ Build/Edit >>> Zap (Delete) Molecule
The system removes the molecule.
For more details on reading files, see Open and Save Files of Molecules on page
45.

Load Molecules
Load a Molecule via the Textport
1. Load dicloxacillin.
¾ In the textport at the SYBYL prompt, type the following script:

take $TA_DEMO/tut.spl
Tip: You may need to position the mouse in the textport and press the Enter
key to display the SYBYL prompt.
If you look at the commands in the textport, you can see that when you ran the
script, SYBYL opened the database, loaded dicloxacillin in M1, and then closed
the database.
2. Change the characteristics of your loaded molecule.
¾ Click the icon.

SYBYL opens the Molecule Display Options tool. Use this tool to modify
the look of the individual molecules.
¾ In the ALL row, click and hold down the button in the Dsp As column
and select Sticks from the popup menu (press Close).
The lines representing your molecule become thicker and the color codes are
more defined.
For more details, see Open and Save Files of Molecules on page 45.
Load Molecules from the Fragment Library
1. Load 1,3-dioxane.
¾ Build/Edit >>> Get Fragment
¾ In the Option dialog, click 1,3-DIOXANE.
SYBYL places 1,3-DIOXANE in the Selection field of the dialog.
¾ Press OK.
SYBYL opens the Molecule Area dialog.
Note: M1 is used by dicloxacillin while the other molecule areas (M2 - M10)
are empty.
2. Choose a molecule area for 1,3-dioxane.
¾ In the Molecule Area dialog, select M2: <empty>.

Load Molecules
¾ Press OK.
SYBYL now displays both 1,3-dioxane and dicloxacillin.
3. Load 1,2,4-Trioxolane
¾ In the Option dialog, click 1,2,4-TRIOXOLANE.
¾ Press OK.
SYBYL opens the Molecule Area dialog.
4. Choose a molecule area for 1,2,4-trioxolane.
¾ In the Molecule Area dialog, select M3: <empty>.
¾ Press OK.
SYBYL now displays 1,3-dioxane, dicloxacillin, and 1,2,4-trioxolane. It is very

hard to distinguish each molecule separately. In the next section, you will learn
how to change the display so that you can see them more clearly.
For more details, see Load Fragments on page 85.

Change the Display
2.3 Change the Display

The three molecules are all displayed in D1, D2, and D3, respectively.
However, since the display option for the screen display is set to Full by
default, all three molecules appear to be in the same molecule area.
1. Toggle the display for each molecule off and on.
¾ Click the icon.
¾ In Molecule Display Options dialog, for row M1, toggle the check box
button in the Mol Vis column off and then on.
Watch the SYBYL screen when you toggle the display off and on. Notice also
that the check box in the cell changes. Likewise, the other molecules can be
displayed and undisplayed using their respective check box buttons.
¾ Press Close.
2. Change the display so you can see each molecule separately.
¾ Click the icon.
¾ In the Display Options dialog, select Quartered.

SYBYL displays the molecules in D1, D2, and D3; D4 is empty.
3. Return the screen display to Full.
¾ Select Full.
¾ Click Q.
For more information, see Understand Molecule and Display Areas on page 57.

Rotate, Translate, and Scale Tutorial
2.4 Rotate, Translate, and Scale Tutorial

Structure rotation is based on the Cartesian coordinate system such that the X
axis is horizontal, the Y axis is vertical, and the Z axis is perpendicular as
viewed in the graphics display.
The mouse focus is set to Global by default when you start a SYBYL session.
All images on the screen — molecules and backgrounds — are affected simulta-
neously by rotations and translations.
This tutorial is for a three-button mouse. To use a two-button mouse, see the
Virtual Dialog Box Tutorial in the Graphics Manual.
1. Rotate molecules along the X-Y axis.
¾ Press the right mouse button and move your mouse in any direction.
Notice that all molecules move. This is because your current mouse focus
setting is G (global).
2. Rotate the molecules along the Z axis.
¾ Simultaneously click the left and right buttons and drag left or right.
Tip: To avoid making a selection (left click) when using multiple mouse buttons
(Z rotation or Z translation), press the middle or right button before the left.
3. Move 1,3-DIOXANE to the upper right corner.
¾ Click the icon.
SYBYL opens the Mouse Focus Options tool.

Rotate, Translate, and Scale Tutorial
Note: The Mouse Focus Options dialog lists the molecules in each molecule
area.
¾ In Mouse Focus Options, click D2.

SYBYL changes the mouse focus to D2. Note that the letter on the button
changed from G to D2. The letter on the button represents the active region
for the mouse focus.
¾ Middle-click and drag 1,3-DIOXANE to the upper right corner.
4. Move 1,2,4-TRIOXOLANE to the upper left corner.
¾ Unselect D2.
¾ Select D3.
SYBYL changes the mouse focus to D3.
¾ Middle-click and drag 1,2,4-TRIOXOLANE to the upper left corner.
Translating the molecules along the Z axis is done using the left and middle
buttons.
You can make three different scaling adjustments to a structure’s display size
with the mouse. When you scale a structure, you can make it display larger or
smaller.
5. Make the molecules appear larger.

¾ Select G and then Q to close the Mouse Focus Options dialog.
¾ Simultaneously click the middle and right mouse buttons and drag
toward the top or right edge of the screen.
6. Make the structure appear smaller.
¾ Simultaneously click the middle and right mouse buttons and drag
toward the bottom or left edge of the screen.
For more information, see Rotate and Move Molecules on page 67.

Save a Molecule to a File
2.5 Save a Molecule to a File

1. File >>> Save as
SYBYL opens the Save Molecule dialog.
2. Verify that m1: dicloxacillin is highlighted; if not, select it.
3. Type dicloxacillin_tut as the file name.
4. Click Save.
SYBYL saves dicloxacillin_tut in the MOL2 format to your current directory.
Note: You can select multiple structures and save them in a specified format.
For more information, see Save (Write) Molecule File via the Menubar on page
48.

Clear the Screen
2.6 Clear the Screen

SYBYL opens the Molecule Expression dialog.
¾ Click the All button.
SYBYL highlights the three listed molecules and enters the number 3 in the
Molecules Selected box.
¾ Press OK.
SYBYL removes all of the molecules.
For more information, see Clear the Screen on page 22.

Exit SYBYL
2.7 Exit SYBYL

¾ File >>> Exit SYBYL
SYBYL closes.
In this tutorial you have already removed your molecules. But at other times, if
you have unsaved molecules or tables, SYBYL gives you the opportunity to
save them before you close the program.
To become more familiar with SYBYL and learn how to use its numerous
features, we suggest that you:
• Refer to your Quick Start Guide brochure that came with the SYBYL
software.
• Use the SYBYL Quick Reference.
• Run other tutorials, see the List of SYBYL Tutorials.

Chapter 3. Start/Exit SYBYL
Chapter 3.
Start/Exit SYBYL
• Start SYBYL on page 26

• Exit SYBYL on page 27
• Get Help on page 28
• Modes for Using SYBYL on page 30
• Automatic Command Execution on page 34

Start SYBYL
3.1 Start SYBYL

1. Log into the computer in the normal manner.
2. In a system shell, type:
¾ xterm
Tripos suggests starting SYBYL from an xterm shell.
3. Start the SYBYL program.
¾ Enter SYBYL’s program name at the system prompt.

The default program name for SYBYL 7.3 is “sybyl7.3”. However, it can be
any name that was defined by the administrator during installation. Consult
with your system administrator to determine SYBYL’s program name on
your machine.
If the default name was specified during installation, you would type the
following to start SYBYL:
sybyl7.3
The computer displays SYBYL’s main window and a textport window. See
SYBYL’s Main Window on page 35 for a complete description.
A SYBYL session begins when SYBYL is started and ends when SYBYL is
exited. The current state of a SYBYL session can be saved and reloaded at a
later time. It is also possible to record commands and arguments that are
executed during the session and replay them later. See Manage SYBYL
Sessions on page 207 for more information.
Notes:
• SYBYL is most commonly operated in a mode called “menubar mode.”
However, there are two other modes available: “command mode” and
“object picking mode.” See Modes for Using SYBYL on page 30 for
more information.
• SYBYL can be configured to execute commands in a file each time it is
started. See Automatic Command Execution on page 34 for more infor-
mation.

Exit SYBYL
3.2 Exit SYBYL

To close SYBYL:
Menubar: File >>> Exit SYBYL

Command Line: QUIT or EXIT [mol_continue] [table_continue]
[NMR_exp_continue] [SPL_col_continue]
• mol_continue—NO/YES, whether to exit even if
unsaved molecules are in the molecule areas. NO
returns control to the program, so you can save the
molecule(s). YES closes SYBYL and returns control
to the operating system.
• table_continue—NO/YES, whether to exit if unsaved
NMR experiments are in memory.
• NMR_exp_continue—NO/YES, whether to exit if
unsaved NMR experiments are in memory.
• SPL_col_continue—NO/YES, whether to exit if
uninstalled SPL column types are in memory.

Get Help
3.3 Get Help

To learn about a specific application or dialog, select Help on the menubar,
type HELP on the command line, or click the Help button present on some
dialogs.
The Tripos Bookshelf is organized by application and contains:
Tutorials What’s New and Release Notes

Quick Reference Guides Tripos web site links
Search functionality References and Related Informa-
tion
Work flow charts PDF library
Detailed descriptions and expla- Index
nations
The table below describes the Menubar and Command Line methods for
accessing help.
Menubar: The Help menu is on the far right side of the menubar.
• Help >>> On Help—Opens this topic.
• Release Notes—Opens SYBYL Release Notes. Links on
this page describe changes and updates for each SYBYL
application.
• Help >>> Tripos Bookshelf—Displays Tripos
Bookshelf’s main page. From here you can view documen-
tation regarding every SYBYL application.
• Tripos Support —Opens Tripos Technical Support
Online (http://www.tripos.com/support) in a browser.
Note: Tripos Bookshelf depends on a browser. To prevent
SYBYL from spawning a browser window, type TAILOR SET
HELP USE_BROWSER NO in the textport, before starting the
help system within SYBYL. This disables all help buttons
within SYBYL. (To always disable the buttons when you log
into SYBYL, modify the .sybylrc file and add:
tailor set help use_browser no ||
Command In the textport, type HELP and press return to activate the Tri-
Line: pos Bookshelf and display information about SYBYL’s help
system.

Get Help
In the textport, type HELP <a SYBYL command/dialog> to dis-

play information on the specified command/dialog. For exam-
ple:
• HELP GRAPHICS—Displays information on the GRAPHICS
command.
• HELP ANNOTATE_DIALOG—Displays information on the
Annotate dialog.
Two subcommands available are:
• ~HISTORY—Displays a numbered list of all help topics
viewed since invoking help. Use these numbers with the
RECALL command.
• ~RECALL {history_number—Redisplays help on any
item in the history list. history_number’s value is obtained
using the HISTORY command.
Type a question mark (?), when prompted by the program for
commands, subcommands, or parameters, to obtain an expla-
nation or more details on the requested input and its acceptable
values.

Modes for Using SYBYL
3.4 Modes for Using SYBYL

There are three basic modes in which you can run SYBYL:
• Menubar Mode on page 30
• Command Mode on page 30
• Object Picking Mode on page 33
The most commonly used mode is menubar and most of the documentation for
SYBYL is written from the perspective of running in this mode. You can use a
mixture of these modes during your SYBYL session.
If you prefer to have SYBYL use a default mode other than menubar, see
Customizing Startup in the Graphics Manual.
3.4.1 Menubar Mode

When in menubar mode, actions are specified using the pull-down menus
available via the SYBYL menubar.
If auto terminal-typing does not work and sets your terminal type to
NOGRAPHICS or if auto terminal-typing is turned off, the menubar can be
activated by typing the menubar command:
MENUBAR
3.4.2 Command Mode

When in command mode, type the commands at the SYBYL prompt in the
textport. (You may also enter commands while in menubar mode.)
• Typing Commands on page 31
• Default Values on page 31
• Special Characters on page 31
• The MODE Command on page 32
• Execute a Command on Multiple Molecules on page 32
• Monitor Performance of SYBYL Command on page 33

Typing Commands
There are three ways you can enter commands:

• Type only the command name and press Enter. SYBYL prompts for the
arguments, one at a time, in the textport or, if the menubar is present, via
dialogs.
• Type the command name and as many arguments as you wish. Any
required command parameters not entered on the command line are
individually requested by the program.
• Type the command name and all arguments on a single line.
Only the shortest unique string needs to be typed to execute a command. The
shortest unique string is sufficient number of characters to resolve any
ambiguity among all other commands which have the same initial character
sequence. For example, since JOIN is the only command in SYBYL, at this
time, which begins with the letter “j,” it is only necessary to type j, although it
is valid to type jo, joi, or join. COLLECT, COLOR, COMPATIBILITY, all begin
with “co” (two also begin with “col”), you must type at least coll, colo, and
comp, respectively, to execute the command. This same principle is true any
time a list of options is presented within the body of a command (e.g., when
asked to reply either YES or NO to some query, you may reply with Y or N).
Note: To return to the command mode from another mode, type: SET PICKING
NO_PICKING. (The SET PICKING command is discussed in the Graphics
Manual.)
Default Values
When you enter a command, the system prompts for the needed arguments.
After each prompt, the system displays a set of angle brackets containing a
word, numeric value, or phrase. This value in brackets is the current default; to
accept the default, press Enter.
Special Characters
?—Use the help character at any time to obtain information about a command,
the legal values of an argument, or the format of a specific parameter.
^ (caret)—In the midst of entering arguments for a command, use the abort
character in response to any prompt to terminate the command operation. No
changes are made to the molecule(s).

| (vertical bar)—Use the end loop character to terminate the entry of parameters
being requested in an indefinitely repeating loop. When you have completed all
the required entries, respond to the next prompt with the end loop character.
SYBYL terminates the request loop and moves on to the next parameter.
The MODE Command
SYBYL has a MODE command that allows repetitive issue of commands to occur
in a particular category without preceding them with the command name.
Categories include: BIOPOLYMER, COMPOSER, DATABASE, MENU, NETBATCH,
NMR, QSAR, STATIC, and TABLE.
MODE category
Other SYBYL commands can be accessed, without leaving a particular mode,

by preceding them with COMMAND. To exit from the mode, issue the ENDMODE
command or type the end-loop character (|).
Execute a Command on Multiple Molecules
Use Default Mole- ALLMOLS sybyl_command

cule Area: The command syntax must include a molecule area (as
a regular argument or as part of an atom or bond
expression). The default is M1. The ALLMOLS com-
mand applies the SYBYL command, substituting the
default area as needed, to every molecule area in turn.
If you do not know the entire command syntax, you are
prompted for information needed to complete the com-
mand.
Use Non-Default ALLMOLS BASE mol_area
Molecule Area: This command must precede the ALLMOLS command
line. It designates the molecule area to substitute in the
loop. You then must include that molecule area in the
ALLMOLS command.
Use Subset of Mol- ALLMOLS GROUP mol_area_expr
ecules: This command must precede the ALLMOLS command
line. It designates the set of molecules to which subse-
quent ALLMOLS commands will apply. Note: The opera-
tion will affect all molecules in the GROUP as well as
the BASE molecule, even if it is not specifically
included in the GROUP.
BASE and GROUP remain in effect until they are changed or until the end of the
session.

The operation you want to perform must be possible on all molecules, otherwise
an error message is issued for every failed attempt. For example, coloring all
alpha helices will fail on molecules that do not contain that secondary structure.
Examples:
The following examples assume four molecules in M1, M2, M3, M4, respec-
tively, all having backbone, heteroatoms, and hydrogen atoms.
Label all heteroatoms in all molecules on the screen. BASE and GROUP are
assumed to have their default values of M1 and *, respectively.
ALLMOLS LABEL HETERO M1(*)
Color backbones in the molecules in M1, M3, and M4 yellow. BASE is assumed
to have its default value of M1. (The molecule in M2 is unchanged.)
ALLMOLS GROUP M1,M3,M4
ALLMOLS COLOR ATOM M1({BACKBONE}) YELLOW
Remove hydrogens from the molecules in M2, M3, and M4. (The molecule in
M1 is unchanged.)
ALLMOLS BASE M2
ALLMOLS GROUP M3,M4
ALLMOLS UNDISPLAY M2(<H>)
Monitor Performance of SYBYL Command

The TIME command monitors the performance of any SYBYL command within
the program. It starts a timer, page fault, and I/O monitor and then re-issues the
command to the program. When the command terminates, SYBYL displays the
elapsed time during the command, time spent in the system, and time spent in
execution of the command (in seconds) in the textport. Use this command to
help optimize program execution and aid in comparison of new algorithms with
existing ones.
TIME command_string
command_string Any single SYBYL command and its arguments.
3.4.3 Object Picking Mode

In this mode, every time the system needs you to select an object (atom, bond,
substructure, or molecule), the system displays a menu or dialog. You may
select that object either from that menu/dialog or from the molecule(s)
displayed on the screen. You may continue your task by using either the textport
command line or menubar pull-down menus.
To use object picking mode, type: SET PICKING OBJECT_ONLY.

Automatic Command Execution
3.5 Automatic Command Execution

By defining and mapping either or both of the logical names TA_USER_STRT
and TA_SYSTEM_STRT to existing files, the commands in these files are
executed each time SYBYL starts.
Use TA_SYSTEM_STRT for commands which are of interest on a group or

system-wide basis. It is defined in the command procedure $TA_ROOT/ lib/
ta_site.sh for sh or ksh users and $TA_ROOT/lib/ta_site.csh for csh users.
The file to which TA_SYSTEM_STRT points typically contains definitions of

global sets, settings of various options such as minimizer parameters, etc. This
file provides system-wide customizing of the SYBYL interface. Below is an
example of the definition of global sets that might be included in this file.
# Define global set CHIRAL_R to identify R centers
DEFINE GLOBAL_SET ATOM {chiral(*,R)}
CHIRAL_R "All R chiral centers"
# Define global set CHIRAL_S to identify S centers
DEFINE GLOBAL_SET ATOM {chiral(*,S)}
CHIRAL_S "All S chiral centers"
Use TA_USER_STRT for commands which are private to each user. It should be
defined in your own login procedure (/$HOME/.profile for sh or ksh users,
/$HOME/.cshrc for csh users). This file provides user-specific customizing of
the SYBYL interface and could typically be used to open the collect (Log
Commands) and the photo (Log Session) files and to set the error reporting
to traceback. See Record and Play SYBYL Sessions on page 217 for a
description of the files and their purpose.

Chapter 4. SYBYL’s Main Window
Chapter 4.
SYBYL’s Main Window
When SYBYL is started, the main window and a textport window are presented.
The main window (sometimes referred to as the SYBYL’s graphical interface)
is composed of a menubar, toolbox icons, and display area. The textport is
displayed in a separate window.
• Menubar on page 36
• Toolbox Icons on page 39
• Textport Window on page 41
• Keyboard Shortcuts on page 44

Menubar
4.1 Menubar
A menu option can be a command (File >>> Exit SYBYL) or a check box
(File >>> Log Commands); it can also lead to submenus (View >>> Color
>>> By Atom Type) or open a dialog (File >>> Read).
Active menu options are displayed in black; inactive menu options are
displayed in grey. Additionally, any options for which you do not have a license
are greyed out, except on the Tools menu. To remove the display of unlicensed
options from the Tools menu, use the environment variable
TA_HIDE_UNLICENSED_PRODS. Before you start SYBYL, set the environment
by typing the following in the textport:
setenv TA_HIDE_UNLICENSED_PRODS TRUE
This and other variables can be set automatically when SYBYL is started. See
Customizing Startup in the Graphics Manual for details.
See SYBYL Menubar to Command Mapping (available online in the Tripos-

Bookshelf) to find a complete listing of options for each menu item, with links
to descriptions and corresponding commands. (Note: This link is also available
as a link directly on the main page of the Tripos Bookshelf.)
File Menu
The File menu primarily contains options for loading information for display in
SYBYL. It also has options for operations such as saving files, creating
Molecular Spreadsheets, editing text files, recording and playing back command
sequences, managing sessions, and exiting SYBYL.
Build/Edit Menu
The Build/Edit menu options focus on creating and modifying structures in the
SYBYL display. It contains options for operations such as clearing the screen,
entering SLN and SMILES strings, loading fragments, sketching, modifying,
copying, merging, and extracting structures, defining aggregates and
constraints.
View Menu
The View menu provides options affecting the visualization of structures in the
SYBYL display. It contains options for operations such as coloring, labeling,
hiding, annotating, managing backgrounds, surfaces, and monitors, accessing
the 2D Viewer, and controlling the backdrop.

Menubar
Compute Menu
The Compute menu is primarily for access to SYBYL’s minimization and

dynamics tools. It contains options for calculating charges, loading force field
parameters, performing distance geometry calculations and conformational
searches.
Analyze Menu
The Analyze menu contains options for analyzing the results of the calcula-
tions setup using the Compute menu. Results of minimization, dynamics,
conformational search jobs are presented using options on this menu. Tools for
measuring, matching, and fitting are also found here.
Options Menu
The Options menu provides access to the interface for setting tailor variables.
The default molecule area and directory can be changed from this menu and
various lists and information can be obtained.
Tools Menu
The Tools menu contains options for accessing the specialized tools and
techniques offered by Tripos for use in SYBYL.
Biopolymer Menu
The Biopolymer menu options concentrate on functionality specific to

biopolymer structures.
UNITY Menu
The UNITY menu provides access to tools for performing various types of
database searches.
Help Menu
The Help menu lists options for accessing the Tripos Bookshelf (HTML
version of the SYBYL documentation). Release notes and other information
about the current version are also available from this menu.

Menubar
4.1.1 Menubar Shortcuts and Comments
Shortcuts
• Type commands at the keyboard while in menubar mode.
• To quickly change the label, click the icon and press Labeling
Options. See Mouse Label Options in the Toolbox Icons section of the
Graphics Manual.)
• Double click an item in a pop-up menu (a single choice list in a dialog)
to select the option and close the dialog.
• For dialogs, press the Tab key to skip to the next field or item in a list.
• Use the arrow keys to move up or down in a list.
Ctrl-click a molecule Selects a molecule to rotate

Ctrl-right-click an atom Labels an atom according to the Tailor vari-
able GRAPHICS MOUSE_LABEL
Click a menu item Keeps pull-down menus visible
Comments
• When you initiate an operation by clicking a menu item, no other
operation is possible until either that operation has finished or until you
cancel it. All menubars are grayed out while the current operation is
active.
• Depending on your X window environment, you can resize the dialogs
to expand the field s.
Restack
If SYBYL seems unresponsive, it may be due to a hidden dialog. It is possible
for one window to cover a dialog waiting for input.
¾ Click to bring that window to the top of the display area.

Toolbox Icons
4.2 Toolbox Icons

Use the icons in the SYBYL toolbox, located on the left edge of the SYBYL
screen, to interact with the graphics. (Note: The following links take you to the
Toolbox Icons section of the Graphics Manual.)
Support Information—Contact information for the Tripos Support

Offices.
Mouse Focus—Select what object(s) are affected by mouse move-

ments.
Display Options—Choose atom and bond representations, the

screen format, and the stereo viewing mode.
Molecule Display Options—Show/hide molecule and background

objects, label atoms and bonds, change display of individual mole-
cules.
General Structure Display—Perform several types of atom and
molecule graphical manipulations.
Graphics Attributes—Set molecule display, labeling, colors and

backdrop options.
Reset—Reset a given display area(s) to its original values of scale,

rotation, and/or translation.
Rotatable Bonds—Manipulate the rotatable bonds in a molecule.
Z-Clipping—View a cross-sectional slice along the Z-axis.
Depth Cue—Enhance three dimensional perception of displayed

objects
Restack—Redisplay all windows associated with SYBYL on top of

all other windows and in their default order.
Stereo (OGLX only)—Make adjustments that can help with view-

ing an image in stereo.

Toolbox Icons
Physical Dial Box (SGI only)—Direct dial control of rotations and

translations, and stereo and Z-clip adjustment.
Virtual Dial Box—Alternative to using the mouse for rotations.
Extents—“Fill” the available space with the molecule(s).
Rate Mode—Rotate a structure continuously about any combina-

tion of the three principal axes.
To activate an icon, click it. You can leave the tool open as you work or you can
close it.

Textport Window
4.3 Textport Window

Use the textport window to enter any command, including HELP, at the SYBYL
prompt (SYBYL>). For a complete listing of available SYBYL commands, see
the List of SYBYL Commands in the Quick Reference Manual. After entering a
command, the system performs the command operation and redisplays the
SYBYL prompt.
Note: The menubar and command line are available simultaneously.

• Textport Output Presentation on page 41
• Execute Operating System Commands from within SYBYL on page 42
• Control Characters on page 43
4.3.1 Textport Output Presentation

Sometimes SYBYL is run from a CRT terminal or other graphical display
device where the amount of textual information which can be presented at one
time is limited. If you want to review this information, change the timeout from
the default of zero to the time you need with the SET CGQ_TIMEOUT
command. SYBYL then monitors the number of lines written to the textport,
and suspends the output when the textport is full.
When the textport is full, the system displays the prompt: “Additional
Output Available [C,G,Q]”:
• C—Continue with output until the textport is once again filled with text,
at which point the prompt is displayed again. Note that instead of typing
the letter C, you can press the Enter key.
• G—Go until the current operation is finished. This is useful when the
output does not warrant close inspection. The system does not redisplay
the prompts, regardless of the number of output lines.
• Q—Quit the current operation and return to the command level.
You can type these single characters in uppercase or lowercase; you do not have
to press the Enter key. If no response is given to the “Additional Output
Available” prompt within your timeout period, the output continues as if you
had pressed the C key.

Textport Window
Tip: You can also run the operation in batch mode.
4.3.2 Execute Operating System Commands from within SYBYL
Single Command
Menubar: File >>> System Window

Command Line: DCL command_string
• command_string—Command and arguments to submit
to operating system.
Any legal operating system command whose arguments can be given in a single
input line can be entered. System output from this command is echoed on the
terminal as usual.
Multiple Commands
Menubar: File >>> System Window

Command Line: SPAWN
SYBYL is suspended in its current state, a new process is created, and the
system shell is entered. Any operating system function, normally available
when outside the program, can be performed. Return to the SYBYL program by
typing EXIT.
This differs from the DCL command by making you explicitly aware of the new
environment and allowing any number of commands to be issued to the system
prior to returning control to SYBYL.

Textport Window
4.3.3 Control Characters

Use these Control Characters when you are in Command mode and typing in the
textport.
Note: ^ is the upper case symbol for the number 6.
^B Move back one word.

^C Kill current input line and terminate search process if active.
^D Delete next word, if at beginning of a word, otherwise delete white
space up to next word or end of line.
Ê Move to end of input buffer.
^F Move forward one word.
^G Redraw current input buffer.
^H Move to beginning of current line.
Î Insert a tab character.
^K Delete from cursor to end of input buffer.
^L Redraw current input buffer.
^N Advance to next line in history list, replacing current input buffer.
Ô Write all output to null device until the next Ô.
^P Advance to previous line in history list, replacing current input
buffer.
^Q Resume output after a Ô or ^S.
^R Search history list for a line matching a given pattern. ^R^R uses
most recent pattern.
^S Suspend output until a ^Q or Ô.
^T List current history list.
Û Delete current input buffer.
^W Toggle more mode on/off.
^X Delete character at the cursor.
^Y Kill current input line and terminate search process if active.
<DEL> Delete character before the cursor.

Keyboard Shortcuts
4.4 Keyboard Shortcuts

Key Action
F1 Toggle between:
• Pushing the textport window back to view the entire
graphics screen
• Returning the textport window to the front.
F5 Toggle between:
• Photo display mode—Expand SYBYL graphics area to fill
entire display. Borders, decorations, controls, and textport
are pushed behind graphics area.
• Normal display mode—Show window border, toolbox,
etc.
F6 Toggle the display of toolbox icons on and off.
F7 Toggle hardware stereo on and off. F7 is active only if neces-
sary hardware is available and OGLX driver is being used.
F8 Toggle between raising and lowering the SYBYL graphics
window. When full screen hardware stereo is active, the
menubar is also raised/lowered.
F9 Toggle between Global and D1.
Up arrow Rotate all displays +90° about the X-axis.
Down arrow Rotate all displays –90° about the X-axis.
Left arrow Rotate all displays +90° about the Y-axis.
Right arrow Rotate all displays –90° about the Y-axis.
Control - Select a molecule or background for object transformation.
click
Control-Right Toggle the display of atom labels on and off; use in conjunc-
click tion with Mouse Labeling Options to display different labels.

Chapter 5. Open and Save Files of Molecules
Chapter 5.
Open and Save Files of Molecules
• Open (Read) Molecule File via the Menubar on page 46

• Save (Write) Molecule File via the Menubar on page 48
• Open/Save MOL/MOL2 Files via the Command Line on page 50
• Manage Input/Output Formats on page 52
• View and Edit Text Files in SYBYL on page 55

Open (Read) Molecule File via the Menubar
5.1 Open (Read) Molecule File via the Menubar

¾ File >>> Read
SYBYL opens the Read File dialog.
Directory Current directory.

Sub-Directories Click one of the sub-directories to select a file from it.
Click [Parent] to go up one level in the directory tree,
then select a directory. This directory becomes the cur-
rent directory and its descendants may be selected.
Note: The number of items visible in the list can be
extended using the Tailor variable DIALOG
NUM_SUBDIR_VISIBLE.)

Open (Read) Molecule File via the Menubar
Other Directo- Lists your current working directory and others speci-
ries fied as follows.
Notes:
• To provide easy access to other directories from this
dialog, add the following line to the .sybylrc file in
your home directory:
setvar OTHER_DIRECTORIES "<space-
separated directory list>"
• The number of items visible in the list can be
extended using the Tailor variable
TAILOR!DIALOG!NUM_OTHERDIR_VISIBLE.
Files Select a file from the list. Its name appears in the Files
to read field.
Files to read The file selected in the list is shown here with its path.
Alternately, type the name (and path) of the desired file
in this field.
File Type Use to list only files of the selected type in the Files
list.
Molecule Select a molecule area from the list. If a molecule area
is needed, SYBYL automatically selects the first avail-
able one. If the file type selected does not require a
molecule area, this field is inactive.
Default Molecule Names
The default molecule name is controlled by the Tailor variable:

TAILOR!MOL!AUTO_NAME. If this variable is set to Yes, unnamed molecules
(single and MultiMol2) are named according to the filename. If the variable is
set to No, unnamed molecules are named “unnamed”.
Note: Tailor variables allow you to customize various parameters affecting

SYBYL operations to suit your needs.

Save (Write) Molecule File via the Menubar
5.2 Save (Write) Molecule File via the Menubar

Use the File >>> Save As option to save one or more molecules. SYBYL
saves the selected molecule(s) in the specified format to the current or selected
directory and file. What is saved with the file depends on the file type. Note that
labels are not saved.
¾ Select File >>> Save As
File You can accept the default, enter a new file name, or navi-
gate via the (...) button to a file.
Default Filename:
For a single selected molecule, the default is the molecule
name. For multiple molecules, the default is the concate-
nated name of the selected molecule (in the lowest num-
bered molecule area), plus “multi” and the number of
molecules being saved.
New Filename:
Acceptable file names:
• 3 to 15 alphanumeric characters
• May include _ (underscore) or a - (hyphen)
• Important - do not include a (.) period in your filename,
unless you are typing the extension.
File Extension:
The default is the extension for the selected file format. If
necessary, you can enter a different extension.

Save (Write) Molecule File via the Menubar
Format Select the file format. Choices include: MOL2, MOL,

FASTA, PIR, PDB, AMBER PDB, DGEOM PDB, CSSR,
SD FILE, and SLN.
Note: The MACCS option is SD FILE. You can save multi-
ple structures in a single file when you use SD FILE. The
MACCS command also has: MULT_IN and MULT_OUT.
Molecule List Use the buttons (Select All, Invert, and Clear) to select
the molecules to save. The dialog reports the total number
of selected molecules and the total number of molecules in
the list.
Important: Use this option to save molecules, not backgrounds. You can not
save molecules and backgrounds in the same file.
Notes:
• If you are saving to a SYBYL MOL2 format, and you have used View
>>> Color >> Color Atoms to color the molecule, these colors are
also saved. Additionally, any defined sets or features are saved to the
mol2 file.
• If you do not enter a path, the file is saved in your current working
directory (wherever you started SYBYL).
• Molecules can be saved to a file via the command line. The command
used depends on the format of the output file. For more information, see:
• Open/Save MOL/MOL2 Files via the Command Line on page 50
• Read and Write PIR and FASTA Files in the Biopolymer manual.
• Read and Write PDB Files in the Biopolymer manual.
• TAILOR SET PDB in the Tailor manual.
• SLN Files on page 52
• CSSR files on page 54
• SD/MACCS Files on page 52
• In the Save Molecule Directory dialog (accessed by pressing (...) button),
you can customize the Other Directories list by adding the following
line to the .sybylrc file in your home directory:.
setvar OTHER_DIRECTORIES "<space-separated directory
list>"
The number of items visible in the list can be extended using the Tailor
variable TAILOR!DIALOG!NUM_OTHERDIR_VISIBLE.

Open/Save MOL/MOL2 Files via the Command Line
5.3 Open/Save MOL/MOL2 Files via the Command

Line
MOL2 direction [mol_area] [filename]
or
MOL direction [mol_area] [filename]

or
MREAD direction [mol_area] [filename]
direction • DIRECTORY—Report if specified file has MOL or MOL2

format, list molecule(s) in the file, plus the number of atoms
and bonds.
• IN—Read file containing a single molecule.
• MULT_IN—Read file containing several molecules, starting at
the specified area and filling subsequent areas thereafter,
until all molecules are read. Use DATABASE ADD to insert
molecules into a new database.
• MULT_OUT—Write file containing several molecules in
several molecule areas.
• OUT—Write file containing a single molecule in specified
area.
• XCOPY—Copy contents of molecule area to X clipboard.
• XPASTE—Copy contents of X clipboard to molecule area.
mol_area Molecule area to receive input data (IN, MULT_IN) or that con-
tains molecule(s) to write to a file (OUT, MULT_OUT) or to the X
clipboard (XCOPY, XPASTE). Contents of molecule areas are
overwritten.
filename File to read/write. When writing a file, if the filename already
exists, it is overwritten.

Open/Save MOL/MOL2 Files via the Command Line
Default Molecule Names
The default molecule names are controlled by the Tailor variable: TAILOR SET
MOL AUTO_NAME. If the variable is set to Yes, unnamed molecules (single and
MultiMol2) are named according to the filename. If No, unnamed molecules are
named “unnamed”.
MOL2
• MOL2 files are ASCII files containing all information necessary to
reconstruct the molecule. The format is based upon the convention of a
keyword for each type of data needed to reconstruct the molecule,
followed by a group of records. (See the MOL2 File Format chapter in
the Toolkit Utilities Manual.)
• SYBYL uses MOL2 files to store molecules resulting from many batch
minimizations (ANNEAL, MAXIMIN2, and MULTIFIT), LATTICE genera-
tions, BIOPOLYMER CONSTRUCT_BACKBONE, and other computations.
• The MOL2 command is functionally equivalent to the MOL command.
However, MOL2 is not affected by the command TAILOR SET MOL
FILE_FORMAT and, therefore, always writes files in MOL2 format.
MOL
• A MOL file does not preserve the complete information available with
molecules in SYBYL 6.x and above. It is provided for compatibility with
existing user programs. Data written to a MOL file include atoms and
bond information, rotatable bond definitions and plane equations. To
preserve the complete molecular description, use the MOL2 file format.
• When reading files, if the file name supplied has no extension, the
system, by default, looks for .mol2 first, then .mol, and lastly a file with
no extension.
• The format of the file written (MOL or MOL2) depends on the variable
set by TAILOR SET MOL FILE_FORMAT (MOL2, by default).
MREAD
The MREAD command is functionally equivalent to the MOL command. It has
been kept for compatibility with previous versions of SYBYL.

Manage Input/Output Formats
5.4 Manage Input/Output Formats

• SLN Files on page 52
• SMILES Strings on page 52
• SD/MACCS Files on page 52
• CSSR files on page 54
5.4.1 SLN Files
Menubar: File >>> Read

File >>> Save As (specify the Format as SLN)
5.4.2 SMILES Strings

Convert the supplied SMILES string into a SYBYL molecule. If Concord is
available, SYBYL uses it to generate a 3D structure. If you do not have
Concord, SYBYL uses an internal SMILES converter to generate 2D coordi-
nates. This structure should be minimized or otherwise converted to 3D for
modeling purposes.
SMILESTOMOL smiles
Reference:
[1] Weininger, D., SMILES, a Chemical Language and Information
Systems. 1. Introduction of Methodology and Encoding Rules, Chem.
Inf. Comput. Sci., 28, 31-36 (1988).
Additional Information:
• CONCORD command description (in the Concord Manual).
• %smiles_to_mol expression generator.
5.4.3 SD/MACCS Files

MACCS is the format used by Molecular Design Ltd. (MLD) and is a trademark
of MDL. It has a default extension of .mac. SD files have a default extension
of .sdf.

Read/Write SD Files

File >>> Save As (Format option should be SD File)
Command Line: MACCS IN|OUT|MULT_IN|MULT_OUT mol_area file-
name(s)
or
FILES MACCS IN|OUT|MULT_IN|MULT_OUT mol_area
filename(s)
• IN—Assign correct atom and bond types (verify that
they are correct before proceeding). Non-recognized
atoms are assigned SYBYL’s type DU (dummy). Files
with more than 999 atoms or bonds cannot be read.
• OUT—Use molecule’s name as MACCS file header
name, and prompt for MACCS header and comment
line. SYBYL aromatic bonds are converted to alter-
nating single and double bonds. SYBYL dummy atoms
(DU) and lone pairs (LP) are removed from the atom list
before file is written in MACCS format. A message is
generated if molecule has more than 255 atoms or 256
bonds to warn that the file is not compatible with the
MACCSII program (however, SYBYL can read it).
• MULT_IN—Read in a file containing more than one
molecule.
• MULT_OUT—Save multiple molecules in the save file.
Note: To include hydrogens when saving to an SD/MACCS file, set the Tailor
variable TABLE MDL_H_HANDLING to KEEP_ALL.
Convert MACCS Files to Molecular Spreadsheet or UNITY Hitlist
MACCS is the format used by Molecular Design Ltd. (MDL) and is a trademark
of MDL. It has a default extension of .mac.
Menubar: File >>> Convert MACCS File

Command Line: MACCS_CONVERT HITLIST|MSS input_file
name_field output_file
• input_file—Name of MACCS file to translate.
• name_field—Registration/Name field to look for in
MACCS file (case sensitive).
• output_file—Name to assign to hitlist file or table
generated.
The UNITY executable dbtranslate is used.

5.4.4 CSSR files

File >>> Save As
Command Line: FILES CSSR IN|OUT mol_area filename
When reading a CSSR (Cambridge Structure Search and Retrieval) file (default
extension .cssr), atom types are converted to SYBYL atom types. Verify all
atom type assignments. Any existing molecule in the designated molecule area
(and all subsequent areas used), is overwritten.

View and Edit Text Files in SYBYL
5.5 View and Edit Text Files in SYBYL

To edit text files using SYBYL’s text editor, select File >>> Edit from the
SYBYL menubar. In the Edit File dialog, select the desired file. (The text editor
can also be displayed using the SPL expression generator, %file_edit.)
Save Save any changes made in the text field to the original
file.
Save As Specify a new location and/or file name in the Save
Text File dialog.
Search Search for the specified string entered in the displayed
dialog.
Again Locate the next occurrence of the search string.
Cut Remove highlighted text and place on the clipboard.
Copy Copy highlighted text to the clipboard.
Paste Paste text on the clipboard at the location of the cursor.
Cancel Ignore any changes made in the text field and closes the
text editor.

Chapter 6. Understand Molecule and Display Areas
Chapter 6.
Understand Molecule and Display Areas
• What are Molecule and Display Areas? on page 58

• Change the Default Molecule Area on page 60
• Copy Between Molecule Areas on page 61
• Merge Molecule Areas on page 62

What are Molecule and Display Areas?
6.1 What are Molecule and Display Areas?

A display area is where your molecule is displayed on the screen. SYBYL has
four unique display areas: D1, D2, D3, and D4.
Click the icon to open the Display Options dialog. Use the Screen
options to change the arrangements. The figure below shows how molecules are
displayed for each Screen option.
Figure 1 Screen Settings for Display Options
A molecule area is a region of memory that holds a particular molecule. The

total number of molecule areas does not have a fixed limit, because the number
depends on your computer’s memory.
Note that molecule areas have rules:

• M1 is always in display area D1.
If you use additional molecule areas, they recycle through the display areas:

What are Molecule and Display Areas?

The figure below demonstrates this pattern.
Figure 2 Display and Molecule Areas

Change the Default Molecule Area
6.2 Change the Default Molecule Area

The default molecule area is M1.
Tip: If you are performing a number of operations on a structure in a different

area (for example, M3), you can change the default to that area (M3), while
working on that structure.
Menubar: Options >>> Set >>> Default Molecule

Command Line: DEFAULT mol_area
UIMS2 Variable: DEFAULT_AREA = Current default molecule area.

Copy Between Molecule Areas
6.3 Copy Between Molecule Areas

When items are copied between molecule areas, the source molecule area
remains unchanged and the target area contains the copy.
Copy Contents of one Molecule Area to Different Molecule Area
Menubar: Build/Edit >>> Copy

Command Line: COPY origin_area target_area
• origin_area—Molecule area to duplicate.
• target_area—Molecule area to receive the duplicate
structures.
Makes an exact copy of all the contents (properties, colors, and associated
displays (backgrounds)) of one work area into another. The origin (source)
molecule is not altered. The previous contents of the target area (if any) are
moved to the recovery stack for that area.
Copy Atoms and Associated Data Structures to Different Molecule Area
Menubar: Build/Edit >>> Extract

Command Line: EXTRACT atom_expr target_mol_area
Copied structures replace the contents of the target area. All local set definitions
associated with the extracted atoms are copied to the new area. The origin
(source) area is left unchanged.
If atom_expr does not specify a work area, the default work area is used.
If atomic charges are present in the target molecule before the extraction, the
atoms still bear same charges after the extraction. However, they are marked
invalid, and will not be used on subsequent SYBYL operations. Validate these
charges manually via the command: CHARGE mol_area VALIDATE YES.

Merge Molecule Areas
6.4 Merge Molecule Areas

Merging combines a copy of the source molecule area with the contents of the
target area.
• Merge Glossary
• Merge Atoms and Associated Data Structures on page 62
• Merging Non-Unique Atoms on page 64
6.4.1 Merge Glossary

Source Area: The molecule area that contains the atoms and molecules to be
merged with another molecule area.
Target Area: The molecule area that is going to receive the atoms and
molecules from the source area in a merge.
Unique Atom: The following scenarios define a unique atom:

• If the coordinates and the atom types in both the source and the target
area are different, an atom is considered to be unique.
• If the coordinates in the source and the target area are the same, but the
atom types are different, an atom is considered to be unique.
• If the atom types in the source and the target are the same, but the
coordinates are different, an atom is considered to be unique.
You can set the distance within which two atoms are considered identical and
whether to keep only unique atoms with the Tailor variable:
TAILOR_SET_MERGE.
Non-unique Atom: An atom in the source area with the same atom type and
coordinates as an atom in the target area.
6.4.2 Merge Atoms and Associated Data Structures

Tip: If molecules have been rotated and/or translated, use FREEZE to transform
the coordinates before merging.
Menubar: Build/Edit >>> Merge

Command Line: MERGE atom_expr target_area
If atom_expr does not specify a work area, the default
work area is used.
Check the output displayed in the textport for messages about the merge.
Special conditions apply when merging non-unique atoms and features.

When you merge atoms and associated data structures, most of the associated
data structures are kept in the merge. These include:
• ATOM
• Atom type
• Atom alternate type (Amber/Kollman/MMFF94 types)
• Atom name
• Charges
• Atom ID is not kept.
• BOND
• Bond type
• Bond ID is not kept.
• SUBSTRUCTURE
• Substructure type
• Substructure name
• Substructure ID is not kept.
• CENTER_OF_MASS
• If a CENTER_OF_MASS in the source area has the same name as
one in the target area, the one in the source area is not merged.
• CENTROID
• If a CENTROID in the source area has the same name as one in the
target area, the one in the source area is not merged.
• Constraints
• FFCON_ANGLE
• FFCON_DIST
• FFCON_MULTI
• FFCON_RANGE
• FFCON_TORSION
• If an atom associated with a constraint is not merged, the constraint
is also not merged.
• PLANE
• If a PLANE in the source area has the same name as one in the target
area, the one in the source area is not merged. Since a plane always
has an associated NORMAL, if that NORMAL is not merged, the
PLANE is not merged.

• NORMAL
• If a NORMAL in the source area has the same name as one in the
target area, the one in the source area is not merged.
• SET
• Any set in the source area with the same name as the set in the target
area will be combined into a single set when merged.
Note: If CENTER_OF_MASS, CENTROID, PLANE, or NORMAL is defined

on a molecule, SYBYL creates dummy atoms representing features (e.g. center
of a centroid). These dummy atoms need to be selected for merging or the
whole feature information is not merged.
The associated data structures that are not merged include:

• ANCHOR_ATOM
• EXTENSION_POINT
• FF_PBC
• RING_CLOSURE
• ROTATABLE_BOND
• U_FEAT
• UNITY_ATOM_ATTR
• UNITY_BOND_ATTR
6.4.3 Merging Non-Unique Atoms

Normally there is nothing to merge if two atoms are “non-unique”. There are
some cases however, where they may be merged.
Non-unique atoms from the source area may be merged into the target area
when both of the following conditions have been met:
• The non-unique atom in the source molecule area has a unique atom
attached to it.
AND
• In the target molecule area there is no open valence on the atom corre-
sponding to the non-unique atom in the source molecule area.
The unique atom carries with it the non-unique atom to preserve the bonding
information.

Example: Merging Non-Unique Atoms

M1 contains a carbon with three hydrogens and a bromine. M2 contains a
methane molecule (CH4). Relative to M2, the carbon and hydrogens in M1 are
non-unique atoms, while the bromine is a unique atom.
Merging M1 into M2 will bring the non-unique carbon and the unique bromine
from the source area to the target area (M2). M2 now contains 7 atoms. To
verify the contents of M2:
¾ Options >>> List >>> Atoms
¾ In the Atom Expression dialog, select M2 (press OK).
¾ In the Option dialog, select BRIEF (press OK).
The textport reports the following:
• TAILOR SET MERGE to alter the characteristics of merging.

Chapter 7. Rotate and Move Molecules
Chapter 7.
Rotate and Move Molecules
Use the mouse to select and manipulate objects. Pressing mouse button combi-
nations and moving the mouse (click and drag) cause various motions of the
objects in the “active” display area. See Rotate, Translate, and Scale Tutorial on
page 19 in this manual and Mouse Focus section in the Graphics Manual.
Tips:
• To avoid making a selection (left click) when using multiple mouse
buttons (Z rotation or Z translation), press the middle or right button
before the left.
• Press the buttons before you start moving the mouse.
3-Button Mouse 2-Button Mouse*
*To access Scaling, Z Rotation, or Z Translation, press and use the

Virtual Dial Box tool.

Chapter 8. Build and Modify Molecules
Chapter 8.
Build and Modify Molecules
Use the options under the Build/Edit menu (in Menubar to Command
Mapping) to sketch and modify molecules. Use the Sketch Molecule menu
option to draw a molecule. The other menu options allow you to add, define,
modify, copy, and delete various molecular components.
• Small Molecule Sketching Tutorial on page 70
• Ring Fusion Tutorial on page 78
• Load Fragments on page 85
• Access the Sketcher on page 87
• Modify Molecules Outside of Sketcher on page 94
• Create/Modify Features on page 115
• Markush Atoms on page 124

Small Molecule Sketching Tutorial
8.1 Small Molecule Sketching Tutorial

Before performing the following tutorial you should be familiar with the
graphics functions of SYBYL. If necessary, refer to the Quick Reference
section in the Graphics Manual for a summary.
• Preface on page 70
• Set Up on page 71
• Enter the Sketching Mode on page 71
• Build Piperidine Ring in Chair Conformation on page 72
• Add a Chain on page 74
• Add a Group on page 75
• Check Chirality on page 75
• Clean Up on page 76
• Save the Sketched Molecule on page 76
8.1.1 Preface
In this tutorial, you will build and minimize Atropine by building the most
complex ring system first and then adding the substituents. Typically, molecular
fragments from the Standard Fragment Library are used to quickly construct
ring systems with good geometry. However, in order to better demonstrate
SYBYL’s sketching capabilities, you will use the Sketch Molecule menu
items to construct and optimize the most complex ring system.
After completing this tutorial, you will be able to:

• Draw a ring
• Minimize a ring system
• Draw a chain
• Add substituent groups

• Check and assign chirality
8.1.2 Set Up
1. Clear the SYBYL screen of all molecules and background images.
¾ Reset everything.
¾ Set the Screen mode to Full.
8.1.3 Enter the Sketching Mode

1. Display the sketch menus and select M1 as the work area in which to build the
molecule.
¾ Build/Edit >>> Sketch Molecule
¾ Select M1:<empty> (press OK).

Both a Sketch Molecule menu and an Atomic Symbol menu appear.
You are automatically placed in Draw mode so you can begin sketching
immediately.
2. Display a grid to aid in building the molecule to scale. The spacing between
grid points is 1.54 Å, the sp3 carbon to sp3 carbon bond length. The grid scales
with the molecule in order to show the correct bond length.
¾ On the Sketch Molecule menu, click Grid

Note: If the grid gets in your way, toggle it off by clicking Grid again in the
Sketch Molecule menu.

8.1.4 Build Piperidine Ring in Chair Conformation

1. Build the ring as follows:
¾ Click in the middle of the screen.

SYBYL displays a highlighted cross or small circle, representing an uncon-
nected atom. The highlighting indicates that this atom is the current atom of
attachment and any subsequent point chosen is attached to this atom. The
atom is number 1 in the figure below.
¾ Click a point above this atom and approximately one grid spacing to
the right (see atom 2 in the figure below).
SYBYL draws a bond to the newly created second atom.
¾ Continue sketching the 6-membered ring by clicking appropriate

points on the screen.
¾ Close the ring by selecting atom 1 again.
When you close the ring by picking atom 1, no atom is highlighted,
indicating that continuous Draw mode is temporarily deactivated.
Continuous mode is always suspended when an existing atom is chosen,
whether it is the current atom of attachment or another atom. In the former
case, no bond is drawn; while in the latter case, a bond is drawn and then
continuous draw mode is deactivated.
Figure 1 Sketched Six Member Ring
2. Change the type of atom 1 to a nitrogen.

¾ On the Atomic Symbol menu, select N.
Tip: Click to bring the Sketching and Atomic Symbol menus to the front.
¾ Click atom 1 on the sketched molecule.

SYBYL displays a label indicating that the type has been successfully
changed and the atom is colored blue (on terminals supporting color).
3. Introduce a third dimension to the molecule.
¾ Use the right mouse button and rotate the molecule about the X axis
until it has an orientation similar to that shown in Figure 2.

Figure 2 Rotated Sketched Six Member Ring
¾ On the Sketch Molecule menu, select Move.
¾ Select N in the ring and then click a spot somewhere above the ring.
N moves to that spot as shown in Figure 3 below.
¾ Select atom 4 and move it below the ring by the same amount.
Figure 3 Sketched Six Member Ring with N and atom 4 Moved
Note: Do not be concerned if the structure sketched is not a perfect chair. You
will optimize the ring later.
4. Add the bridge across the ring.
¾ On the Sketch Molecule menu, select Draw to return to continuous

Draw mode.
¾ Click atom 2 to make it the current attachment atom.
¾ Click a point below atom 2 and then another point diagonal to the
new atom.
¾ Click atom 6 to close the ring.
Figure 4 Sketched Molecule with Bridge Across Ring
5. Clean up the ring system.
¾ On the Sketch Molecule menu, select TAILOR.
¾ Select CLEAN_UP (press OK).

¾ Select 5_QUICK_MINIMIZE (press OK).
¾ On the Option dialog, press End.
¾ On the Sketch Molecule menu, select CLEAN_UP.
There is an initial setup period while the minimizer parameters are being read
from the database. Energy values are then printed in the text window after each
iteration. The molecule display on the screen is not updated until the end of the
minimization in order to reduce execution time. The minimization is complete
when the “Existing atom or new point:” prompt returns in the textport.
8.1.5 Add a Chain

1. Center the molecule on the screen.
¾ On the Sketch Molecule menu, select Center.
¾ Rotate the molecule until its orientation is similar to that shown in the
figure 5.
2. Add a carbon chain to the ring.
¾ Select atom 4 as the current atom of attachment.
¾ Sketch the sidechain by picking (clicking) successive points at

approximate locations on the screen for atoms 9 through 13.
¾ Pick atom 13 again to deactivate continuous Draw mode and end the
chain.
Figure 5 Carbon Chain Added to Piperidine Ring
3. Draw a double bond for the carbonyl group.

¾ Select atom 10 as the new point of attachment and then click (pick) a
point above the atom.
¾ Click atom 10 again.

The double bond appears and continuous Draw mode is deactivated, since
an existing atom was chosen.
Tip: If you can not see the double bond, rotate the molecule.
4. Add a carbon to the nitrogen.
¾ Click atom 1, then a point to its left.
5. Sketch the ester and hydroxyl groups.
¾ Select O from the Atomic Symbol menu and then pick each of the
three atoms.
The atoms are labeled with an O and colored red to reflect the change.
¾ Compare your sketch with atropine.
8.1.6 Add a Group

1. Access a list of predefined chemical groups and add a phenyl ring to the
molecule.
¾ On the Sketch Molecule menu, select GROUP.
¾ Select PHENYL and click atom 11.
2. Center the molecule.
¾ On the Sketch Molecule menu, select CENTER.
8.1.7 Check Chirality

Make sure atom 11 has a chirality of S.
¾ On the Sketch Molecule menu, select CHIRAL and select atom 11.
¾ Select S (press OK).

If atom 11 is already an S chiral center, a message is displayed informing
you of this and nothing else happens. If, however, the R chiral center has
been sketched, the center is inverted to assume the proper stereochemistry.

8.1.8 Clean Up
1. Since the ring system has been already optimized, use the 4_SCAN option,
which involves non ring bonds only, to clean up the model.
Any clean up option from 1 to 6 includes all options preceding it in the list,
therefore, all non-ring bonds have their bond lengths and angles adjusted, and
the torsion angles are scanned and adjusted to relieve bad contacts.
¾ On the Sketch Molecule menu, select TAILOR.
¾ Select CLEAN_UP (press OK).
¾ Select 4_SCAN (press OK).
¾ Press End.
¾ On the Sketch Molecule menu, select CLEAN_UP.
2. Add the necessary hydrogens to all unfilled valences.
¾ On the Sketch Molecule menu, select ADDH.

All atom and bond types are automatically converted to SYBYL types,
based on the connectivity prior to adding hydrogens.
3. Exit from the sketching mode.
¾ On the Sketch Molecule menu, select EXIT.

A final clean up is done automatically every time you exit the Sketch
Molecule menu.
8.1.9 Save the Sketched Molecule

1. Name the molecule.
¾ Build/Edit >>> Name Molecule
¾ Type atropine (press OK).
2. Save the full description of the molecule in a text file.
¾ Select File >>> Save As.
¾ In the Save Molecule dialog, by default, atropine is the Filename.
¾ By default, the Format option menu is set to MOL2.
¾ Press Save.

A file named atropine.mol2 is created in the current directory.
In this tutorial, you built and minimized Atropine by building the most complex
ring system first and then adding the substituents.
When you work on your own research, you can use the same technique to save
your molecules. To view them again, use the Read File dialog.
This concludes the small molecule sketching tutorial. We suggest that you
repeat this tutorial with molecules from your own research.

Ring Fusion Tutorial
8.2 Ring Fusion Tutorial

The following tutorial illustrates several examples of fusions:
• Fuse Two Planar Bonds on page 78
• Fuse Two Rings to Build a Spiro System on page 79
• Fuse Two Non Planar Bonds on page 80
• Fuse A Planar Bond With A Non Planar Bond on page 82
8.2.1 Set Up
2. Set the Screen mode to Quartered.
8.2.2 Fuse Two Planar Bonds

The fusion of two planar systems requires only two pair of atoms. In this
example, furan (M1) is fused to pyridine (M2) and the resulting model appears
in M2.
1. Read in the two fragments, color them by atom type, and label both structures.
¾ Select FURAN (press OK).
¾ Select PYRIDINE (press OK).
¾ Select M2 (press OK).
¾ View >>> Label >>> Atom Id
¾ Highlight M1:furan, click All (press OK).
¾ Select M2:pyridine, click All (press OK).
2. Fuse the two structures.
¾ Build/Edit >>> Other Tools >>> Fuse Rings
¾ Click atom 6 in pyridine (M2), and then atom 2 in furan (M1) to form
the first pair.

¾ Click atom 5 in pyridine (M2), and then atom 3 in furan (M1) to form
another pair.
¾ On Select Atom, press End.
Furan (M1) is fused to pyridine (M2); the resulting model appears in M2.
8.2.3 Fuse Two Rings to Build a Spiro System

You can specify a spiro fusion by first selecting the two atoms that become the
spiro center. The second pair involves a ring atom in one molecule and a
hydrogen in the other.
1. Read in the two molecules.

¾ Select 4H-PYRAN (press OK).
¾ Select PIPERIDINE (press OK).
2. Fuse the two rings.
¾ Click atom 4 in piperidine (M2), and then atom 4 in 4H-pyran (M1) to

form the first pair.
¾ Click atom 12 in piperidine (M2), and then atom 5 in 4H-pyran (M1)to
form another pair.
The two rings are fused with a spiro center; the resulting model appears in M2.

8.2.4 Fuse Two Non Planar Bonds

In the following steps, you will fuse tetrahydropyran (M1) to piperidine. Several
methods are used by providing:
• Two pair of atoms (result in M2),
• Three pair of atoms (result in M3),
• Four pair of atoms (result in M4).
1. Use two pair of atoms to fuse two non planar bonds. SYBYL resolves the
ambiguity automatically by selecting the alternative which gives rise to the best
fusion geometry. The results are displayed in M2.
The selection of two atom pairs is usually insufficient for this type of fusion,
since the resulting fused structure may not have the desired configuration.
¾ Select TETRAHYDROPYRAN (press OK).
¾ Click atom 6 in piperidine (M2), and then atom 3 in tetrahydropyran

(M1) to form the first pair.
(M1) to form another pair.
Two non planar bonds are fused; the resulting model appears in M2.
2. Use three pair of atoms to fuse two non planar bonds. As in the previous steps,
SYBYL automatically resolves the ambiguity. The results are displayed in M3.

¾ Options >>> Set >>> Default Molecule
¾ With M3:piperidine highlighted, press All and then OK.

(M1) to form a pair.
3. Use four pair of atoms to fuse two non planar bonds. The results of the fusion
are displayed in M4.
¾ Options >>> Set >>> Default Molecule
¾ With M4:piperidine highlighted, click All (press OK).
Manual fitting of the two bonds to be fused reveals that the torsional angles of
the four atoms involved are 60° in piperidine and -60° in tetrahydropyran. In
order to produce a geometry better suited for the cis fusion you want to perform,
tetrahydrofuran is inverted first.
¾ Build/Edit >>> Other Tools >>> Invert
¾ Select M1:tetrayhydropyran, click All (press OK).


8.2.5 Fuse A Planar Bond With A Non Planar Bond

1. Fuse benzene (M1) to hexahydroazepine (M2) and the results displayed in M1.
¾ Select HEXAHYDROAZEPINE (press OK).
¾ Select BENZENE (press OK).
¾ Click atom 5 in hexahydroazepine (M1), and then atom 1 in benzene

¾ Click atom 4 in hexahydroazepine (M1), and then atom 2 in benzene
¾ Click atom 16 in hexahydroazepine (M1), and then atom 6 in
benzene (M2) to form a pair.
¾ Click atom 14 in hexahydroazepine (M1), and then atom 3 in
benzene (M2) to form a pair.

The planar bond is fused with a non planar bond. Notice the poor quality of the
geometry at the ring fusion and the fact that extraneous hydrogens are left over
from the hexahydroazepine. Some clean up and minimization would be
necessary before this model could be used.
2. Fuse hexahydroazepine (M3) to benzene (M2) and the results displayed in M2.
¾ Select HEXAHYDROAZEPINE (press OK).
¾ Click atom 1 in benzene (M2), and then atom 5 in hexahydroazepine

¾ Click atom 2 in benzene (M2), and then atom 4 in hexahydroazepine
Notice the poor quality of the geometry at the ring fusion. Here too, a minimi-
zation would be required.
3. A simple strategy to assure the quality of the fusion and reduce the need for
minimization is to determine that the geometry of the bonds to be fused is
identical in both molecules before the fusion occurs.
Fuse benzene (in M3) with tetrahydroazepine (in M4) and display the results in
M4.
¾ Select TETRAHYDROAZEPINE (press OK).
¾ Select BENZENE (press OK).
¾ Click atom 5 in tetrahydroazepine (M4), and then atom 1 in benzene


¾ Click atom 4 in tetrahydroazepine (M4), and then atom 2 in benzene

Notice the quality of the geometry of the atoms at the ring fusion. This
approach, where the bonds to be fused are both planar, gives the best result.
This concludes the Ring Fusion Tutorial.

Load Fragments
8.3 Load Fragments

SYBYL provides a library of fragments from which you can easily build most
molecules. The following table describes information for using the menubar or
command line to select and display fragments contained in the Fragment
Library.
Menubar: Build/Edit >>> Get Fragment

• In the Option dialog, click one of the fragments in
the list.
• If molecule area 1 (M1) is occupied, the Molecule
Area dialog is presented and you must specify the
area in which to display the fragment.
Menu Search Frag- FRAGMENT MENU menu_choices mol_area
ment Library via • menu_choices—Series of numbers, typed at the
Command Line: keyboard, identifying successive menu items.
• mol_area—Area to receive selected fragment,
current contents are overwritten.
Menus are hierarchical and categorize various molecu-
lar fragments according to structure and/or function.
Enter number of menu items to move up or down the
hierarchy until desired molecule is found. Typing the
number of an actual molecule retrieves that molecule.
There are also three words that are valid choices:
• TOP—Return to top level of menu hierarchy, where
the most general categories are displayed.
• UP—Back up one level in the hierarchy to a set of
more general categories.
• QUIT—Exit from search procedure without
choosing a molecule.
Load Single Frag- FRAGMENT NAME name [mol_area]
ment from Library • name—Name (with optional wildcards) of fragment
via Command to retrieve.
Line: • mol_area—Area to receive the fragment.
For example, FRAGMENT NAME BENZENE M1 retrieves
the fragment BENZENE into M1.
FRAGMENT NAME VIT*B2 M1 retrieves the fragment
Vitamin B2 into M1 (because only one fragment satis-
fies the expression VIT*B2).

Load Fragments
Load Multiple FRAGMENT NAME name_expr

Fragments from [QUIT|RETRIEVE|SELECT|UNSELECT]
Library via Com- • name_expr—Name (with optional wildcards) speci-
mand Line: fying multiple fragments to retrieve.
If no fragment is found or if single fragment is
retrieved, no further input necessary (i.e., entering one
of the following items is skipped).
• QUIT—Exit search procedure without choosing a
molecule.
• RETRIEVE [mol_area]—Retrieve multiple
fragments starting with specified mol_area.
• SELECT [name_expr]—Select subset of currently
chosen molecules according to their names.
• UNSELECT—Unselect list of fragments. This undoes
previous SELECT operation, thus allowing a more
flexible search of the library. It can be applied any
number of times.
For example, FRAGMENT NAME BE* RETRIEVE M1
retrieves all fragments starting with the letters BE and
places them in consecutive molecule areas starting with
M1.
• Libraries of Chemical Groups and Fragments on page 259.

Access the Sketcher
8.4 Access the Sketcher

Menubar: Build/Edit >>> Sketch Molecule
See Sketcher Menu Items on page 91.
Command Line: SKETCH mol_area object_type object
• mol_area—Area in which sketching is to occur.
• object_type object—Type of object to select followed
by appropriate object. Choices are:
ATOM atom_id
ATOMIC_SYMBOL atomic_symbol
MENU menu_item
SPACE xyz_coordinates (3 integers in Å)
The above syntax must be used: object type always pre-
cedes actual object identifier.
Molecules are drawn as flat structures until you rotate the structure. Any atoms
added subsequent to a rotation assume the transformed Z-coordinate of the atom
to which it is bonded. Unconnected atoms are always two-dimensional since
there is no reference point.
• Sketching Techniques on page 88
• Sketcher Menu Items on page 91
• CONCORD for fast conversion of 2D coordinates to 3D (in the Concord
Manual).
• TAILOR SET GRID to customize the displayed grid.
Command Line Example:

A sample SKETCH session that draws a ring in command line mode would look
as follows:
MENU DRAW Draw mode is activated.

SPACE 200 200 0 Cross is drawn.
SPACE 250 250 0 Bond drawn from atom1 to new point.
ATOM 1 Ring is closed.
ATOMIC_SYMBOL Cl An atomic symbol is designated.
ATOM 3 Type of atom 3 is changed to chlorine.

Access the Sketcher
MENU CLEAN_UP Ring is “cleaned up”.

MENU ADDH Hydrogens are added to all unfilled
valences.
MENU EXIT SKETCH is exited.
8.4.1 Sketching Techniques

The following sections discuss some basic ideas and helpful techniques for
using the Sketcher.
• Always Review the Sketched Model on page 88
• Atomic Symbols Only on page 89
• Atom Types on page 89
• Branching on page 89
• Edit Existing Molecules on page 90
• Label and Color on page 90
• Multiple Bonds on page 90
• Rings on page 90
• Z Coordinate on page 91
You can start sketching with an atom or a fragment.
Important: You can not start sketching with a chemical group.
Always Review the Sketched Model
Although flexible enough to enable building any structure, the Sketcher does
have enough chemical sense to warn you when you have done something
unnatural. For example, SYBYL displays a message if the valence of an atom is
about to be exceeded. It is your decision to continue or not.
About Continuous Drawing Mode
You can stop the continuous drawing mode (also referred to as “pen up
movement”) by doing one of the following:
• To cancel the selection of a point of attachment, click the last atom
drawn.
You can then move the cursor to another part of the molecule without
drawing a bond. When you pick a new point of attachment, continuous
drawing mode is turned on again.

Access the Sketcher
• Click an existing atom. A bond is drawn from the current atom to this
existing atom and then the pen up movement is initiated.
Atomic Symbols Only
SYBYL designates the atom types with only the atomic symbols, in order to
eliminate the burden of having to decide the proper SYBYL atom type.
Atom Types
You can change the atom types in two different ways:
Method One: Change the default atom type, before adding the new atom to the
model:
1. On the Sketch Molecule menu, select Default_type
2. Pick the desired atomic symbol from the menu.
Subsequent atoms have the new atom type until you select the Default_type
menu option again. Use this technique if you want to draw a chain of atoms,
other than carbons.
Method Two: Modify the type of an existing atom:

1. From the Atomic Symbol menu, select the new atom type.
2. Click the atom whose type you want to change.
SYBYL updates the atom type.
Whenever you select an atom type without being preceded by a Default_type

command, the drawing mode is suspended. This technique allows you to change
the type of as many atoms as necessary. To activate drawing mode again, select
Draw on the Sketch Molecule menu.
Branching
To draw an atom not connected to the last atom displayed, a pen up action must
be signified by choosing this last (highlighted) atom again. SYBYL removes the
highlighting and temporarily turns off the continuous draw mode. When you
choose a new point of attachment, SYBYL automatically turns the continuous
drawing mode on and you can add a new chain of atoms.
If you select a point of attachment in error, click that atom again to initiate the
pen up movement. You can now select a new point of attachment.

Access the Sketcher
Edit Existing Molecules
Existing molecules or fragments can be brought into the sketcher in order to

make quick modifications. When the sketcher is exited or the clean-up option
selected, only the part of the molecule that changed is cleaned up. The rest of
the molecule maintains its current geometry. You can disable this option by
setting TAILOR SET SKETCH AGGREGATES to OFF. With this option, the
whole molecule is considered in the clean up phase.
Label and Color
In order to make different atom types easily identified, heteroatom labeling and
molecule color, coded by atom type, are the sketcher defaults. You can toggle
the labeling On and Off if you “Ctrl- right click” an atom. You can also select a
different coloring scheme via the Color Editor.
Multiple Bonds
Draw the single bond.

• If the last atom drawn is one of the atoms involved in the double bond,
select the target atom and a second line appears between the two atoms
designating the double bond. Since the target atom is an existing atom,
continuous drawing mode is temporarily turned Off and a new point of
attachment must be chosen before drawing commences again.
• If neither atom defining the double bond is currently selected, turn Off
continuous drawing mode by picking the last atom drawn a second time.
Select one of the atoms of interest as the new point of attachment. Pick
the target atom for the double bond and a double line appears between
the two atoms. As mentioned above, since the target atom is an existing
atom, drawing mode is temporarily suspended.
The same strategy can be repeated for sketching triple bonds. Aromatic bonds
are designated by alternating single and double bonds within the ring.
Rings
Sketch the backbone on the ring by picking points at appropriate positions on

the screen. To close the ring select the first atom of the ring again, thereby
causing a bond to be drawn between this atom and the last atom drawn. Since
this ring closure atom is an existing atom, SYBYL temporarily stops the
continuous draw mode, so you can choose a new point of attachment. To add a
bond to the current atom, select that atom again.

Access the Sketcher
Z Coordinate
To add a third dimension to the molecule, apply rotations to the model either
interactively on graphics workstations or via one of the Rotate_85 options on
static terminals. Once an atom has a Z-coordinate, any subsequent atoms
attached to it are drawn in the same Z-plane. For example, if a rotation precedes
the Move option, the atom being moved is drawn in a different plane from the
rest of the molecule. Many different conformations of a molecule can be
achieved with this method, such as chair or boat cyclohexane.
8.4.2 Sketcher Menu Items

You can start sketching with an atom or a fragment.
Important: You can not start sketching with a chemical group.
Draw Activates the continuous drawing mode, the default action,

with the cursor defined as a carbon atom.
To draw a chain of carbons:
1. Click a point on the screen where the first atom
is to be located; a cross appears.
2. Click another point on the screen; that point
appears and SYBYL draws a line (bond)
between the two atoms.
3. Repeat step 2 until you reach the desired chain.
Note that current atom of attachment is always high-
lighted.
Move Prompts you for the atom to move and its new location.
The atom, and all bonds connected to it, are moved to the
new location. This mode remains active until you select
another option. This capability is useful when building a
particular conformer.
Remove_atom Deletes atoms, and any bonds connected to them, from the
molecule being sketched. This mode remains active until
you select another option.
Remove_bond Removes a bond from the drawn structure. You must
select two bonded atoms.
Fragment Accesses the Standard Fragment Library. (Refer to Frag-
ment Library Structure and Contents on page 261 for more
information.)

Access the Sketcher
Group Accesses Group Library. Groups have predefined attach-

ment points. This mode remains active until you select
another option. (Refer to Group Library Structure and
Contents on page 260 for more information.)
Zap Deletes the current sketch molecule.
Center Centers the molecule on the screen.
Chiral Specifies whether a chiral center is R or S.
Default_type Changes the default atom type used for drawing. Select the
new atom type from atomic symbol table. Subsequent
atoms drawn have this new type.
Clean_up Adjusts molecule geometry according to the method speci-
fied via the Tailor button or the TAILOR SET SKETCH
CLEAN_UP command. Also determines the proper atom
hybridization, based upon bond type and atom type of con-
nected atoms. No matter which option is chosen for clean-
up, the atom and bond type conversion is always done.
Addh Adds hydrogens to all unfilled valences.
Undo Undoes the last operation, restoring the molecule to its
previous state. Note: If you want to reverse the effect of
the LABEL command, use UNLABEL.
Tailor Accesses Tailor variables for sketcher (AGGREGATES,
CLEAN_UP, COLOR_BY_TYPE, and LABEL).
Remove_h Removes all hydrogens in the sketched molecule.
Modify_angle Modifies the bond angle of three connected atoms.
Modify_torsion Modifies the torsion angle of four connected atoms.
Grid Toggles the grid on and off. Use the grid to aid sketching.
Spacing between grid points is 1.54 Å, the approximate
length of a carbon-carbon single bond.
Exit Performs clean up procedure and assigns SYBYL atom
types (see description for Clean_Up).
Rotate_X85, Rotates the current molecule in the specified direction on a
Rotate_Y85 static device. Introduces depth (Z-coordinates) to the mol-
ecule. All atoms added to an atom that has a Z-coordinate,
are given the same Z-dimension. On graphics workstations
interactive rotations provide this capability.
Static Accesses the STATIC command. Available on static
devices only.
Reset Resets all rotations. Available on static devices only.

Access the Sketcher
C, N, ... HT, HV Pick one of these atomic symbols at any time to change an
existing atom type. This menu may be extended by adding
to the parameter tables. See Add a Record to a Parameter
Table in the Force Field Manual for details. Any atom
types, with a unique atomic symbol added to the atom def-
inition table, are represented in this menu.

Modify Molecules Outside of Sketcher
8.5 Modify Molecules Outside of Sketcher

• Atoms on page 94
• Bonds on page 101
• Group on page 104
• Substructures on page 105
• Chirality on page 106
• Molecule’s Center of Rotation, Name, Type, etc. on page 109
• Combine (Fuse) Two Molecules From Different Molecule Areas on page
110
• Combine (Join) Two Molecules or Groups in Same Molecule Area on
page 112
• Adjust Bond Lengths and Angles to Match Standards on page 112
• Scan Torsions to Remove van der Waals Contacts on page 113
• Create Molecule by Averaging Existing Molecules on page 113
8.5.1 Atoms
• Add Atom to Existing Structure on page 94
• Add Atom Without Attaching to Any Present Structure on page 95
• Add Chain of Atoms of Same Type on page 95
• Fill Empty Valences on page 96
• Add Pseudoatoms (Centroids) on page 96
• Modify an Atom on page 97
• Remove Atoms or Atom Attributes on page 100
Add Atom to Existing Structure
Menubar: Build/Edit >>> Add >>> Atom

Command Line: ADD ATOM attachment_atom type
• attachment_atom—Atom to which new one is bonded.
• type—New atom’s chemical type and hybridization.
(Type “?” at prompt to list available atom types.)
SYBYL automatically determines the coordinates, based on bond length and

bond angle data from parameter tables.

Add Atom Without Attaching to Any Present Structure
Menubar: Build/Edit >>> Add >>> Raw Atom

Command Line: ADD RAWATOM mol_area name type x y z
• mol_area—Area to receive new atom.
• name—Name for new atom (must start with an alpha-
betic character and contain only alphabetic characters,
digits, and/or the special symbols dollar sign ($), under-
score (_), or apostrophe (')).
• type—Chemical type and hybridization of atom. (Type
“?” at prompt to list available atom types.)
• x, y, z—Coordinates of atom.
Position the atom by specifying coordinates or by using the mouse.
Add Chain of Atoms of Same Type
Menubar: Build/Edit >>> Add >>> Chain

Command Line: ADD CHAIN ATTACH | REPLACE [atom] type
length
• ATTACH—Add new chain to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new chain
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.
• type—Chemical type and hybridization of atoms in
chain. (Type “?” at prompt to list available atom types.)
• length—Length of chain to create, may vary from 1
upward (no upper limit). “1” is equivalent to the ADD
ATOM command.
SYBYL attaches chains to the existing structure with ideal geometry. SYBYL
determines the coordinates of all atoms from the parameter tables.

Fill Empty Valences
Menubar: Build/Edit >>> Other Tools >>> Fill Valences

or
Build/Edit >>> Add >>> Hydrogens
This second menu option checks if molecule is a protein,
nucleic acid, or saccharide, and for a Biopolymer license. If
the license is available, SYBYL first runs BIOPOLYMER
ADDH and then runs FILLVALENCE.
Command Line: FILLVALENCE atom_expr atom_type
• atom_expr—Atoms to have empty valences filled.
• atom_type—Mnemonic type of atom to use in filling
valences.
SYBYL sets bond lengths and angles to standard values determined from the
parameter file.
Add Pseudoatoms (Centroids)
Pseudoatoms (centroids) are added to prochiral, methyl, and phenyl ring groups.
They are often used for defining constraints to the prochiral, methyl, or
aromatic protons. Constraints are needed when you do not have stereospecific
resonance assignments for prochiral atoms (or methyl pairs, such as in leucine
and valine), or when fast motions are present (such as methyl rotors and
aromatic ring flipping).
Menubar: Build/Edit >>> Add >>> NMR Pseudo Atoms

Command Line: ADD_PSEUDOATOMS mol_area
Note: This command is equivalent to BIOPOLYMER
ADD_PSEUDOATOMS and NMR ADD_PSEUDOATOMS.
The dummy atom’s name at the centroid position is defined according to the
nomenclature first presented in Kurt Wüthrich, NMR of Proteins and Nucleic
Acids, J. Wiley and Sons, 1986. For example, the beta methyl group on alanine
is named “QB”.
The algorithm identifies appropriate atom sets, independent of the substructure

and atom names. For example, any pair of protons bonded to a “heavy” atom,
that are not part of a methyl group, will have a pseudoatom added between
them.

Modify an Atom
Menubar: Build/Edit >>> Modify >>> Atom

Change Point MODIFY ATOM CHARGE atom_expr charge
Charge via Com-
mand Line:
Change Coordi- MODIFY ATOM COORDINATES atom_expr
nates: xyz_coord
Changes are not restricted by the bond length table nor
by atoms being in rings. Coordinates are unconditionally
altered.
Update Lone Pairs: MODIFY ATOM LONE_PAIR atom_expr
Lone pair positions may need to be updated after whole
or partial structural changes are made to the molecule,
such as minimizations. Geometry optimizations using
Tripos force field do not affect lone pair positions.
Change Name: MODIFY ATOM NAME atom_expr
APPEND_AUTO|QUERY|SEQUENTIAL_AUTO
• APPEND_AUTO—Supply a single string to concate-
nated with current name for each selected atom.
• QUERY—Prompts for name for each selected atom.
• SEQUENTIAL_AUTO—For each selected atom,
concatenate name of atomic element with the atom
ID number to form new name.
First character of name must be alphabetic. All others
must be alphabetic, numeric, or the apostrophe.
Change Only Type MODIFY ATOM ONLY_TYPE atom_expr {type}
(not Geometry): Prompts for the type for each specified atom. SYBYL
modifies the types of bonds associated with the atoms to
fit the new atom types.
The geometry around atoms or atom names is not
changed, however, this can be a problem when using
LeapFrog. Use TAILOR SET ATOM_TYPE FIX_NAMES
YES to prevent LeapFrog problems.
Recalculate Exten- MODIFY ATOM SYBYL_POINTS atom_expr
sion Points/Lone Use if extension points/lone pairs become distorted dur-
Pairs: ing other calculations.

Change Type and MODIFY ATOM TYPE atom_expr {type}

Geometry: Prompts for the type for each specified atom. After all
new types have been entered, SYBYL modifies the
types of associated bonds to fit the new atom types. For
non-ring atoms, SYBYL also adjusts bond lengths.
Bond lengths and types are taken from
$TA_ASCTABLES/BOND_LENGTHS and
BOND_TYPES. If the bond type is ambiguous (i.e., there
is more than one possible bond type to connect the two
atom types) or unknown, you are prompted.
You can rename atoms by preserving the suffix and
replacing the old atomic symbol with the new one. This
prevents situations such as replacing a carbon labeled
C8 with a nitrogen, and the label is still C8. TAILOR
SET ATOM_TYPE FIX_NAMES sets whether atom names
are affected by changes to an atom’s type.
Assign Alternate MODIFY ATOM OTHER_TYPES set_name ASSIGN
Types SPECIFIC|UNKNOWN
• set_name—Set of alternate atom types: KOLL_ALL,
KOLL_UNI, AMBER7_FF02, AMBER7_FF99,
AMBER95_ALL, or MMFF94.
• SPECIFIC—Specify atoms to assign types to. You
are prompted for the atom types, one at a time, as the
atom is highlighted.
• UNKNOWN—Prompts for atom types for each atom in
molecule which does not have an alternate atom
type.
Kollman and AMBER atom types require a Biopolymer
license (“BioPolymer”).
Assign Alternate MODIFY ATOM OTHER_TYPES set_name
Type via SLN SLN_AUTO_ASSIGN SPECIFIC|UNKNOWN
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL.
• SPECIFIC—Specify atoms to assign types to.
• UNKNOWN
license (“BioPolymer”).
Unassign Alter- MODIFY ATOM OTHER_TYPES set_name UNASSIGN
nate Types atom_expr
SYBYL will use the default (dictionary) value for the
alternate atom type instead of user-assigned value.

Label Alternate MODIFY ATOM OTHER_TYPES set_name LABEL

Types mol_area
To display Kollman atom types enter: MODIFY ATOM
OTHER_TYPES <type> LABEL <mol_area>
Important: Use MODIFY ATOM OTHER_TYPES UNLA-
BEL to remove alternate type labels.
license (“BioPolymer”)
Unlabel Alternate MODIFY ATOM OTHER_TYPES set_name UNLABEL
Types mol_area
List Alternate MODIFY ATOM OTHER_TYPES set_name LIST SPE-
Types CIFIC|UNKNOWN|USER_ASSIGNED
• SPECIFIC—List alternate types of all specified
atoms, including source of alternate type (user-
specified, or default—from macromol dictionary).
• UNKNOWN—List names of all atoms with unknown
alternate atom types.
• USER_ASSIGNED—List types of all atoms with user-
assigned alternate types.
Alternate atom types can come from two sources: the macromol dictionary (also
referred to as the default source) or user input. Alternate atom types are needed
for energy calculations using non-Tripos force fields. MODIFY ATOM
OTHER_TYPES displays or lists alternate atom types from either source, and
allows input of user-assigned alternate types. User-assigned types are stored
with the molecule, and take precedence in force field calculations over
dictionary-supplied alternate atom types. Currently supported alternate atom
type sets are:
• Kollman all-atom (KOLL_ALL) and Kollman united-atom (KOLL_UNI)
force fields. A list of Kollman atom types is provided in the Kollman
Force Field section in the Force Field Manual. Note: Alternate atom
types must be defined for both KOLL_UNI and KOLL_ALL force fields for
energy setup to work. If the atom type is defined for only one, the
ENERGY, MAXIMIN2, and DYNAMICS SETUP commands all fail with an
error condition.

• AMBER7 FF99 (AMBER7_FF99) force field, which is essentially

AMBER95 atom types with a few types added. See the AMBER7_FF99
Force Field section in the Force Field Manual.
• AMBER7 FF02 (AMBER7_FF02) force field, which is essentially
AMBER7 FF99 atom types with different charges and polarization
included See the AMBER7_FF02 Force Field section in the Force Field
Manual.
• AMBER 95 (AMBER95_ALL) force field.
• Changing an atom type to a Kollman or AMBER atom type requires a
Biopolymer license (“BioPolymer”). The same is true for viewing labels
for Kollman or AMBER atom types.
• MMFF94 force field. A list of MMFF94 atom types is provided in the
MMFF94 Force Field theory section in the Force Field Manual.
• The Load Charges section of the Biopolymer Manual to load atomic
charges and alternate atom types from the dictionary.
Remove Atoms or Atom Attributes
Menubar: Build/Edit >>> Delete >>> Atom

Command Line: REMOVE ATOM atom_expr
Removes all bonds involving that atom and any features (normal, plane,
constraint) attached to that atom. SYBYL renumbers atoms and bonds to reflect
the removal of objects from the molecular description. If the removed atom is a
member of a static set, the set membership is updated. (REMOVE ATOM * is
equivalent to ZAP for the molecule.)
Alternatively, the you can use the Split functionality to remove a portion of a
molecule by specifying two bonded atoms:
Menubar: Build/Edit >>> Other Tools >>> Split

Command Line: SPLIT origin_atom target_atom
SYBYL deletes the bond between the specified atoms along with all atoms on
the target side of that bond.
Note: You can not use the Split functionality if the indicated bond is in a ring.
You must first break the ring by removing a bond or an atom.

Attributes can be removed from one or more atoms without deleting the atom
itself.
Command Line: REMOVE ALL_ATOM_ATTRS expression
8.5.2 Bonds
• Add Bonds on page 101
• Modify a Bond on page 102
• Remove a Bond or Bond Attributes on page 103
Add Bonds
Menubar: Build/Edit >>> Add >>> Bond

Command Line: ADD BOND origin_atom target_atom
• origin_atom—Atom at beginning of bond.
• target_atom—Atom at end of bond.
The bond type of the new bond is set by the atom types at its endpoints. If there
is ambiguity regarding the bond type, a prompt asks for the resolution. Atomic
positions are not altered by adding a bond.
Single bonds may also be added using the Quick Bonds functionality. SYBYL
adds a single bond between two atoms if the distance between them is within an
acceptable range. This is particularly useful for PDB files containing discon-
nected HETATM records.
Menubar: Build/Edit >>> Add >>> Quick Bonds

Command Line: QUICKBOND mol_area atom_expr
• mol_area—Work area containing the molecule.
• atom_expr—Atoms between which connectivities must
be identified.

SYBYL adds a bond between two atoms, A and B, if the distance between
them, DISTAB, is within acceptable range:
Ideal_Bond(1-Tol_Neg) < DistAB < Ideal_Bond (1+Tol_Pos) [EQ 1]

where:
• Ideal_Bond—Standard bond length between atom types A and B in
the bond length table.
• Tol_Neg—Tolerance used to determine low end of the distance
range. This Tailor variable has a default of 0.30.
• Tol_Pos—Tolerance used to determine high end of the distance
range. This Tailor variable has a default of 0.10.
The asymmetry of the acceptance window (Tol_Neg > Tol_Pos) allows for
alkynes (Ideal_Bond = ~1.15 Å) and certain short aromatic C-C bonds to be
recognized as bonds without making chemical oddities from non-covalent
intramolecular hydrogen bonding patterns.
By adding only single bonds, molecular connectivity can be determined with a

high degree of accuracy and minimum user intervention. Check all atom and
bond types within the specified atom expression before proceeding with calcula-
tions, where this information is relevant.
• TAILOR SET CONNECT to alter the characteristics of the connectivity
determination.
Modify a Bond
Modify Type via the Build/Edit >>> Modify Bond

Menubar:
Modify Type via MODIFY BOND AUTO_TYPE|TYPE bond_expr
Command Line: {type}
• AUTO_TYPE—Force the automatic determination
of bond type according to types of atoms at each
end of the bond. Only prompts for bonds whose
types are ambiguous.
• TYPE—Prompt for type for each specified bond.
No adjustment of parameters other than type is
attempted for selected bonds.
Modify Length via Build/Edit >>> Modify >>> Distance
the Menubar:
Modify Length via MODIFY DISTANCE atom1 atom2 value
Command Line:

Modify Angle via the Build/Edit >>> Modify >>> Angle

Menubar:
Modify Angle via MODIFY ANGLE atom1 atom2 atom3 angle
Command Line:
Modify Torsion via Build/Edit >>> Modify >>> Torsion
the Menubar:
Modify Torsion via MODIFY TORSION atom1 atom2 atom3 atom4
Command Line: angle
When changing the length, angle, or torsion, SYBYL alters the coordinates of
last specified item and all atoms attached to it. The atoms must be connected to
form a bond, angle, or torsion, respectively. If the bond, angle, or torsion is in a
ring, an error is reported and no alteration is made.
Remove a Bond or Bond Attributes
Menubar: Build/Edit >>> Delete >>> Bond

Command Line: REMOVE BOND bond_expr
Features (rotatable bonds) attached to the deleted bond are removed as well.
Bonds are renumbered to reflect the removal of objects from the molecular
description. If one of the two last atoms in a substructure is a biopolymer (dict)
atom, SYBYL retains the root atom in the substructure and the other atom in the
substructure zero.
Attributes can be removed from one or more bonds without deleting the bond
itself.
Command Line: REMOVE ALL_BOND_ATTRS expression

8.5.3 Group
You can add a chemical group to the molecular structure and have their
geometry determined from the parameter tables. The atoms in the group and
their relative positions are read from the Group Library (refer Group Library
Structure and Contents on page 260).
Menubar: Build/Edit >>> Add >>> Group

Command Line: ADD GROUP group_name ATTACH | REPLACE atom
• group_name—Name of group to add to structure. (Type
“?” at prompt to list available groups.)
• ATTACH—Add new group to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new group
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.
The permission on the Group Library should normally be “read only” to prevent
accidental modification. However, the Group Library is user expandable, and
before adding a group to this library, you must change the permission on the file
$TA_DATA/GROUP to allow writing:
chmod +w $TA_DATA/GROUP
Set the permission back to read only after the group has been added:
chmod -w $TA_DATA/GROUP
See Group Library Structure and Contents on page 260 for details.

8.5.4 Substructures
Modify via the Build/Edit >>> Modify >>> Substructure

Menubar:
Create/Modify MODIFY SUBSTRUCTURE COMMENT
Comment via substructure_expr {comment}
Command Line: • substructure_expr—Substructures to modify.
• comment—Descriptive string. It may contain any
characters and be of arbitrary length. Use double
quotes when entering spaces or special characters
via command line.
Change Name via MODIFY SUBSTRUCTURE NAME
Command Line: substructure_expr {mode name}
• substructure_expr—Substructures to modify.
• mode:
APPEND_AUTO—Single string is supplied and
concatenated with selected substructure’s current
name.
QUERY—Name for each selected substructure is
entered. Each selected substructure is highlighted as
you are prompted for its name.
SEQUENTIAL_AUTO—Element type name is concat-
enated with substructure ID number.
• name—Name or fragment thereof to associate with
the substructure in all but SEQUENTIAL_AUTO
mode. First character must be alphabetic and may
contain alphabetic, numeric, and the apostrophe.
To rename substructures (residues) in a biopolymer, use
the BIOPOLYMER RENUMBER command.
Change Root via MODIFY SUBSTRUCTURE ROOT
Command Line: substructure_expr {atom_sel}
• atom_sel—Atom to be the root of each of the
selected substructures.
Substructures are composed of connected atoms form-
ing a “graph” structure. The graph is traversed from the
“root” to all other atoms in the substructure. All bonds
within the substructures are ordered such that when tra-
versed from origin to terminus, they are directed away
from the root. The original root is selected arbitrarily
by the program. This command alters the root of the
substructure and re-orders the graph.

Change Type via MODIFY SUBSTRUCTURE TYPE

Command Line substructure_expr {type}
• type—DOMAIN, GROUP, PERMANENT, RESIDUE,
TEMPORARY.
All types, which are not temporary, are permanent.
Only RESIDUE has any special meaning. It is used
extensively in the manipulation of macromolecules
where it is synonymous with monomer. Generally you
should not alter the substructure types; they are man-
aged by the system.
Remove via the Build/Edit >>> Delete >>> Substructure
Menubar:
Remove via Com- REMOVE SUBSTRUCTURE expression
mand Line: • expression—Substructure expression indicating
substructure(s) to delete.
8.5.5 Chirality
• Determine Chirality on page 106
• Invert Chirality on page 107
• Reflect Atoms Through a Plane on page 108
• Remove Stereo Attribute from Molecule Description on page 108
Determine Chirality
Menubar: Build/Edit >>> Other Tools >>> Find Chirality

Command Line: • CHIRAL PRO_RS atom_expr—Determine PRO-R or
PRO-S chirality of specified atoms.
• CHIRAL RS atom_expr—Determine R or S chirality
of specified atoms.
• CHIRAL ZE bond_expr—Determine Z or E
isomerism about specified double bonds.
• CHIRAL MARK_RS atom_expr—Determine R or S
chirality of specified atoms and set atom chirality
attribute.
• CHIRAL MARK_ZE bond_expr—Determine Z or E
isomerism about specified double bonds and set bond
stereo attribute.
Both the chirality of an atom and the cis-trans isomerism about a double bond
can be determined by using a set of rules developed by Cahn, Ingold and Prelog
and adopted by IUPAC (See J. Org. Chem., 35, 9, 2849, (1970)). These rules

govern the sequencing of substituents about the chiral atom or double bond.
Once the substituents are assigned a priority, simple geometric algorithms
determine which type of isomerism is present. These same rules are used to
determine the prochirality of an atom.
The system determines the RS isomerism of an atom by positioning a three-

dimensional representation of the atom so that the lowest group in the sequence
is oriented away from the viewer. If the remaining substituents are arranged in a
clockwise manner by priority, the center is designated R, otherwise it is S.
ZE isomerism about a double bond is a more general designation than cis-trans;

it is determined by examining the bond’s substituents and sequencing them in
the manner prescribed by IUPAC (atomic number is the first criterion) which
encompasses the Cahn/Ingold/Prelog sequencing rules. The special relationship
between the higher priority substituent on each end of the double bond is
examined relative to a reference plane, which includes the two double bonded
atoms, and drawn perpendicular to the plane of the four substituents. If the two
higher priority substituents lie on the same side of this reference plane, the
isomerism is denoted as Z; if they lie on opposite side, it is E.
Atom chirality attributes are used by the expression generator %sln() when
converting a SYBYL molecule to an SLN string. The chirality will then be
expressed as [S=N] or [S=I] (see the Tripos SLN Manual for details). The bond
stereo attributes are also used by the expression generator %sln().
Any unfilled valences are assumed to be occupied by hydrogens.
The built-in set {CHIRAL} determines only RS isomerism.
• TAILOR SET CHIRAL to alter the method for calculating chirality.
Invert Chirality
Menubar: Build/Edit >>> Other Tools >>> Invert

Command Line: INVERT atom_expr
If all atoms in the molecule are to be inverted, the entire molecule is inverted by
reflecting the X-coordinate through the YZ plane. Otherwise, each individual
tetrahedral atom is inverted by exchanging two substituents. Note that non-
chiral centers may also be inverted.
Atoms at ring fusions cannot be inverted individually, but only as part of the
inversion of the whole molecule.

No chirality determination is done before or after the inversion. A message is

issued only if a selected center cannot be inverted due to a ring fusion. A count
of the number of tetrahedral centers successfully inverted is given.
If a molecule includes atom chirality attributes, these attributes are inverted as

well as the coordinates of the chosen atoms. Atom chirality attributes are set
either by the CHIRAL_MARK_RS command or by using the expression generator
%sln_to_mol() to convert an SLN string to a SYBYL molecule.
Reflect Atoms Through a Plane
Menubar: Build/Edit >>> Other Tools >>> Reflect

Command Line: REFLECT atom_expr plane_name
• atom_expr—Atoms to reflect through the plane.
• plane_name—Name of plane through which reflection
is done.
The plane must be defined on the molecule. Any arbitrary atoms may be
reflected through the plane. Examine the resulting bonding geometry carefully,
since the program pays no attention to the geometrical arrangement during this
operation.
• DEFINE PLANE to calculate the equation of the plane.
Remove Stereo Attribute from Molecule Description
Chirality Flags: REMOVE STEREO_ATOM_ATTR expres-

sion
Stereo Bond Flags: REMOVE STEREO_BOND_ATTR expres-
sion

8.5.6 Molecule’s Center of Rotation, Name, Type, etc.
Change Center of Build/Edit >>> Center

Rotation via Translates the atom coordinates to center the molecule
Menubar: at 0,0,0. Note that Reset will not restore the original
coordinates.
Or
View >>> Center of Rotation >>> Molecule
Allows rotation and translation using the mouse around
a molecule’s current center. Reset will restore the origi-
nal coordinates. To save the new coordinates, use
FREEZE (in Graphics). See Mouse Focus Options (in
Graphics).
Change Center of MODIFY MOLECULE CENTER_OF_ROTATION area
Rotation via Com- atom_sel
mand Line: • area—Molecule area containing molecule.
• atom_sel—Atom(s) to use as center of rotation.
Create/Modify MODIFY MOLECULE COMMENT area {comment}
Comment via • area—Area(s) containing molecule(s) to modify.
Command Line: • comment—Descriptive string, may contain any
quotes when entering spaces or special characters
via command line.
Create/Modify Build/Edit >>> Name Molecule
Name via
Menubar:
Create/Modify MODIFY MOLECULE NAME area {name}
Name via Com- • area—Area(s) containing molecule(s) to modify.
mand Line: • name—Name to identify molecule and key for its
storage and access in database. If molecules are
saved into a SYBYL Mol2 database, filenames are
generated from molecule names. For database use,
avoid names containing: colon (:), question (?),
backslash (\), and space ( ). If the file and molecule
name are to be manipulated in SPL, avoid:
circumflex (^) and pipe (|).

Change Root via MODIFY MOLECULE ROOT area

Command Line: {substructure_sel comment}
• area—Area(s) containing molecule(s) to modify.
• substructure_sel—Substructure to be the root of the
molecule tree.
• comment—Comment to store with new root.
Molecules may have any number of independent con-
nected fragments, each one composed of at least a sin-
gle substructure. Each fragment has one of its
substructures recorded in the molecule header, i.e., the
“root” of the fragment “tree”.
Change Type via MODIFY MOLECULE TYPE area {type}
Command Line • area—Area(s) containing molecule(s) to modify.
• type—NUCLEIC_ACID_MOLECULE,
SACCHARIDE_MOLECULE, PROTEIN,
SMALL_MOLECULE.
8.5.7 Combine (Fuse) Two Molecules From Different Molecule

Areas
Menubar: Build/Edit >>> Other Tools >>> Fuse Rings

Command Line: FUSE {atom_pairs}
The two structures do not have to be cyclic. At least two atoms must be selected
in each molecule; more atoms help direct fusion of non planar bonds. Terminate
the input list with the end-loop character (|).
SYBYL places the fused structure in the molecule area of the first atom of each
pair. Coordinates of atoms used for the fusion are taken from the first molecule.
The bonds directly connecting fusion atoms in each molecule are discarded. An
attempt is made to retain all other bonds in both molecules. If the atomic
valence of the fusion atom is exceeded, any Hs attached to fusing atoms are
discarded and the fusion rechecked. If the operation still fails, an error is
reported and the command terminated. You must then discard enough atoms to
make fusion legal. If the operation succeeds, Hs are replaced to fill valences of
atoms from which they were removed.
If you specify fusion of two molecules across an aromatic or double bond by

selecting only two atoms, alignment of resulting fragments is unambiguous. If,
however, fusion across a single bond involving tetrahedral atoms is specified by
two atoms, ambiguity arises. The program attempts to select the alternative
which results in the best fusion geometry. If you prefer another alternative
fusion geometry, select three or more atoms to unambiguously establish the
geometry.

Spiro fusions cannot be specified by selecting a single atom pair. They can be
specified by adding Hs and indicating the fusion of an internal bond in one
molecule with the bond involving the H atom.
• Ring Fusion Tutorial on page 78.
• TAILOR SET FUSE to select default parameter set to alter character-
istics of the fusion.

8.5.8 Combine (Join) Two Molecules or Groups in Same Molecule

Area
Menubar: Build/Edit >>> Other Tools >>> Join Molecules

Command Line: JOIN target_atom new_group_atom
• target_atom—Atom to replace with group being added.
• new_group_atom—Atom in joining group being
discarded when group is fused to molecule.
This functionality cannot be used to form a ring closure bond.
The length of the new bond is determined by the type of the atoms being joined
and is taken from a table of standard bond lengths. The two atoms specified are
eliminated by the join operation.
Groups being joined may be in same molecule area or in different areas. In the
latter case, atoms to be joined are copied into the target atom’s molecule area
and then the bond formed.
• Bonds on page 101 to connect two atoms.
• MERGE to move a copy of specified atoms into a new work area.
• TAILOR SET JOIN to customize the parameters for joining.
8.5.9 Adjust Bond Lengths and Angles to Match Standards

The Shaked algorithm iteratively loops through the selected atoms, adjusting
bond lengths and bond angles, to more closely match standard values stored in
the bond length and the Tripos force field bond angle tables.
Corrections are applied to coordinates to satisfy distance constraints:
L ij ≤ D ij ≤ U ij [EQ 2]
Where Lij is the lower bound for the distance (Dij) between atoms i and j, and
Uij is the upper bound. A delta of 0.05 is added to or subtracted from the value
obtained from the parameter tables to derive the upper and lower bounds,
respectively.
This operation is performed until either the maximum number of iterations

(100) is reached or convergence has occurred, that is, all constraints are met.
The algorithm fails when distance constraints are inconsistent or the input
structure is very different from the structure that obeys all distant constraints.

This algorithm is described by I. Haneef, Simon J. Talbot, and Peter G.

Stockley in J. Mol. Graphics, 7, 186-195 (1989).
Menubar: Build/Edit >>> Clean-Up Molecule >>> Shake

Bonds and Angles
Command Line: SHAKED atom_expr
8.5.10 Scan Torsions to Remove van der Waals Contacts
Menubar: Build/Edit >>> Clean-Up Molecule >>> Scan Tor-

sions
Command Line: SCAN bond_expr
The specified torsion angles are scanned, through a full 360°, for positions
which relieve bad steric interactions. Only one bond at a time is altered. After a
position is found, that bond is removed from the set being considered. Scanning
continues until all interactions dependent upon these bonds are relieved or until
no progress is made from one iteration to the next. Interrupt the process by
typing <control> C.
• TAILOR SET SCAN to alter characteristics of the scan.
• The following BIOPOLYMER subcommands: ADD_SIDECHAIN, CHANGE,
INSERT, JOIN, SET CONFORMATION.
8.5.11 Create Molecule by Averaging Existing Molecules

AVERAGE_MOL mol_area_expr mol_area
mol_area_expr Expression indicating location of existing molecules.

Empty molecule areas are ignored.
mol_area Area in which to place new molecule. Default is lowest
numbered empty molecule area.
Assuming the starting set of molecules are different conformations of the same
structure, this command creates another conformation (of the same molecule)
where:
• Coordinates of every atom are the average of the X, Y, Z coordinates of
corresponding atoms in selected molecules.
• All other aspects of the molecule (bonds, substructures, features, etc.)
are taken (arbitrarily) from one of the selected molecules.

If the selected molecules do not all contain the same number of atoms, an error
message is displayed and no molecule is created. Make sure all other aspects of
the molecules are consistent (bonds, substructures, etc.).

Create/Modify Features
8.6 Create/Modify Features

• Center of Mass on page 115
• Centroid on page 116
• Extension Point on page 117
• Line on page 118
• Normal on page 119
• Plane on page 120
• Renumber Atoms on page 121
• UNITY Query Features on page 122
Note:
Whole or partial re-orientation (via FIT, FREEZE, ORIENT, geometrical modifi-

cation or manipulation of rotatable bonds) after defining centers of mass,
centroids, extension points, normals, or planes renders the feature invalid. Use
the EVALUATE command to update the feature’s position.
• VISUALIZE, in the Graphics Manual, to display some of the defined
features.
• List Information on One or More SYBYL Objects on page 164.
8.6.1 Center of Mass

A centroid is a dummy atom at the center of a group of atoms. The center of
mass is a centroid with coordinates weighted by the atomic masses. When
defined, the dummy atom is added to the coordinate list and a feature in the
molecular description. The dummy atom is connected through a dummy bond to
the atom used in the calculation closest to its position. Dummy atoms have the
type Du and are colored magenta.
Note: Atomic weights now (SYBYL 7.1) correlate with the latest accepted
figures from IUPAC and NIST. The average difference is 0.01% of the values in
SYBYL 7.0. For unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem., Vol.75, No.8, pp 1107-1122, 2003.
• National Institutes of Standards and Technology (NIST)
For more information, see $TA_ROOT/sybylbase/tables/metals/ATOM_DEF

Define DEFINE CENTER_OF_MASS atoms center_name comment

Re-Evaluate: EVALUATE CENTER_OF_MASS mol_area name
• mol_area—Area(s) containing center(s) of mass to
evaluate.
• name—Name of center(s) of mass to evaluate. Enter a
question mark (?) to list names. Expression may include
the wildcard character (*) (e.g., to remove both c1 and c2,
enter c*, but the expression c1,c2 is not valid).
The new coordinates are computed and stored in the molecular
definition. In addition, dummy atoms representing the position
of the features are adjusted to reflect the new values.
Remove REMOVE CENTER_OF_MASS mol_area name
• mol_area—Area(s) containing center(s) of mass to delete.
• name—Name of center(s) of mass to delete.
8.6.2 Centroid
A centroid is a dummy atom at the center of a group of atoms. When defined, it
is added to the coordinate list and a feature in the molecular description. The
dummy atom is connected through a dummy bond to the atom used in the calcu-
lation closest to its position. Dummy atoms have the type Du and are colored
magenta. (See TAILOR SET CENTROID to alter the characteristics of the
centroid.)
Define via the Build/Edit >>> Define >>> Centroid

Menubar:
Define via Com- DEFINE CENTROID atom_expr centroid_name com-
mand Line: ment
Re-Evaluate: EVALUATE CENTROID mol_area name
• mol_area—Area(s) containing centroid(s) to evaluate.
• name—Name of centroid(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
The new coordinates are computed and stored in the
molecular definition. In addition, dummy atoms represent-
ing the position of the features are adjusted to reflect the
new values.

Remove: REMOVE CENTROID mol_area name

• mol_area—Area(s) containing centroid(s) to delete.
• name—Name of centroid(s) to delete.
Any features (plane, normal, constraint) attached to that
centroid are removed as well.
8.6.3 Extension Point

An extension point is a dummy atom connected to the molecule that can be used
as a place holder. The extension point can represent a ligand atom or a hydrogen
bond partner. It is added as a dummy atom in the coordinate list and a feature in
the molecular description. It is connected through a dummy bond to atom1.
Define DEFINE EXTENSION_POINT atom1 atom2 atom3 dist

ang tors name comment
• atom1, atom2, atom3—IDs of atoms defining extension
point. If any are lone pairs, use the command MODIFY
ATOM LONE_PAIR first.
• dist—Distance of extension point to atom1.
• ang—Angle for extension point, atom1, and atom2.
• tors—Torsion angle for extension point, atom1, atom2, and
atom3.
• name—Name for extension point.
• comment—Arbitrary string associated with the extension
point.
Re-Evaluate: EVALUATE EXTENSION_POINT mol_area name
• mol_area—Area(s) containing point(s) to evaluate.
• name—Name of point(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
Remove REMOVE EXTENSION_POINT mol_area name
• mol_area—Area(s) containing point(s) to delete.
• name—Name of point(s) to delete.

8.6.4 Line
A line adds a dummy atom at a specified distance along the path between two
atoms.
Define DEFINE LINE origin_atom positive_atom dist name

comment
• origin_atom—Atom defining origin of line.
• positive_atom—Atom defining direction of line from
origin_atom.
• dist—Distance (Å) from origin_atom to dummy atom.
Positive value indicates “towards” positive_atom, a
negative value corresponds to “away from.”
• name—Name for line.
• comment—Arbitrary string associated with line and
dummy atom.
Re-Evaluate: EVALUATE LINE mol_area name
• mol_area—Area(s) containing line(s) to evaluate.
• name—Name of line(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
Remove REMOVE LINE mol_area name
• mol_area—Area(s) containing line(s) to delete.
• name—Name of line(s) to delete.

8.6.5 Normal
A normal is a line normal to a plane through an atom. It is represented by two
dummy atoms on either side of a specified atom. Two dummy bonds connect
them to the midpoint. The bonds are perpendicular to the specified plane.
Distance from the midpoint to the dummy atoms is a variable set at 1 Å by
default. The normal is stored as two dummy atoms, two dummy bonds and a
feature in the molecular description. Dummy atoms have the type Du and are
colored magenta. (See TAILOR SET NORMAL to alter the characteristics of the
normal.)
Note: Plane coordinates and plane normal lines are not updated when you use
FREEZE. Use EVALUATE PLANE mol_area name, then EVALUATE NORMAL
mol_area name to update the plane and normal line.
Define via the Build/Edit >>> Define >>> Normal

Menubar:
Define via Com- DEFINE NORMAL atom_sel plane_name
mand Line: normal_name comment
The two dummy atoms are named “normal_name” fol-
lowed by 1 or 2.
Re-Evaluate: EVALUATE NORMAL mol_area name
• mol_area—Area(s) containing normal(s) to evaluate.
• name—Name of normal(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
new values.
Remove via the Build/Edit >>> Delete >>> Normal
Menubar:
Remove via REMOVE NORMAL mol_area name
Command Line: • mol_area—Area(s) containing normal(s) to delete.
• name—Name of normal(s) to delete.
Any features (e.g., constraints) attached to that normal are
removed as well. If an atom, real or artificial, and involved
in a normal definition, is removed, the normal is removed
automatically.

8.6.6 Plane
A plane is represented by four dummy atoms connected by four dummy bonds
delineating a parallelogram. (See TAILOR SET PLANE to alter the character-
istics of the plane.) The plane is stored as four dummy atoms, four dummy
bonds and a feature in the molecular description.Dummy atoms have the type
Du and are colored magenta.
Note: Plane coordinates and plane normal lines are not updated when you use
FREEZE. Use EVALUATE PLANE mol_area name, then EVALUATE NORMAL
mol_area name to update the plane and normal line.
Define via the Build/Edit >>> Define >>> Plane

Menubar:
Define via Com- DEFINE PLANE atom_expr plane_name comment
mand Line: The four dummy atoms are named “plane_name” followed
by 1, 2, 3, or 4.
Re-Evaluate: EVALUATE PLANE mol_area name
• mol_area—Area(s) containing plane(s) to evaluate.
• name—Name of plane(s) to evaluate. Enter a question
mark (?) to list names. Expression may include the
wildcard character (*) (e.g., to remove both c1 and c2,
enter c*, but the expression c1,c2 is not valid).
new values.
Remove via the Build/Edit >>> Delete >>> Plane
Menubar:
Remove via REMOVE PLANE mol_area name
Command Line: • mol_area—Area(s) containing plane(s) to delete.
• name—Name of plane(s) to delete.
Any features (e.g., constraints) attached to that plane are
removed as well. If an atom, real or artificial, and involved
in a plane definition, is removed, the plane is removed
automatically.

8.6.7 Renumber Atoms

Renumbering atoms imposes an arbitrary order on atoms in a molecule for the
purposes of Z-matrix formation. It is done prior to submitting the molecule to
quantum mechanical calculations.
Menubar: Build/Edit >>> Modify >>> Atom ID Numbers

Command RENUMBER origin_area target_area {atom_sel}
Line: • origin_area—Area containing molecule to renumber.
• target_area—Area to receive renumbered molecule.
• atom_sel—Atoms to renumber, in the new numerical order.
Renumbering atoms causes all defined features to be deleted from the molecule
because there is no automatic translation from the internal representation of the
feature definition to atom numbers. All other information about the molecule is
suitably transformed and restored after renumbering.
You are prompted for the ID number of the atom you want in each position. (To
display current atom numbers, use LABEL ID * before renumbering.) Positions
are given in sequence from 1 to the number of atoms in the molecule. Specifi-
cation can be terminated at any time. Atoms not specified to be renumbered
retain their relative order and are added to the molecule list immediately behind
atoms which were renumbered.

8.6.8 UNITY Query Features

A UNITY geometrical feature or constraint for a structure is used within a
UNITY database query. UNITY features are displayed as background objects
and can be saved as part of the molecular definition. The TAILOR SET UNITY
command can be used to select the color for highlighting constraints, features,
and receptor sites.
For details on defining specific features and constraints, see the “Specifying 3D
Queries” chapter, in the SLN Manual.
Define via the UNITY >>> Features or Constraints

Menubar:
Define via DEFINE UNITY_FEATURE option
Command Line:
• 4_POINT_ANGLE_CONSTR • ACCEPTOR_ATOM
AINT • ANGLE_CONSTRAINT
• ACCEPTOR_SITE • BOND_PATH
• AROMATIC • COLOR
• CENTROID • CONTAINING_VOLUME_CO
NSTRAINT
• DISTANCE_CONSTRAINT • DONOR_ATOM
• DONOR_SITE • EXCLUDED_VOLUME_CONS
• EXTENSION_POINT TRAINT
• HYDROPHOBIC • FRAGMENT
• LINE
• LP_ANGLE_CONSTRAINT • NEGATIVE_CENTER
• NORMAL_POINT • PARTIAL_MATCH_CONSTR
• PLANE AINT
• RECEPTOR_SITE • POSITIVE_N
• SPATIAL_CAP
• SPATIAL_LINE • SPATIAL_PLANE
• SPATIAL_POINT • STERIC_FEATURE
• SURFACE_VOLUME • TETRAHEDRAL
• TORUS
Delete Non- UNITY >>> Delete >>> Atoms not in the Query
Query Atoms The list of atoms to remove is displayed in the atom
via the expression dialog and highlighted on the molecule.
Menubar: Changes to the atom expression may be made before
pressing OK to remove the atoms.

Delete Non- REMOVE NON_QUERY_ATOMS mol_area

Query Atoms • mol_area—Area containing the UNITY query.
via Command A list of atoms to remove is displayed in the atom expres-
Line: sion dialog and highlighted in the molecule. Changes to
the atom expression may be made before pressing OK to
remove the atoms. If the molecule area does not contain
any UNITY features or constraints, no action is taken.
Modify via the UNITY >>> Manage Features >>> Define
Menubar:
Modify via MODIFY UNITY_FEATURE mol_area feature/con-
Command Line: straint [{attribute value}] [COLOR]
• mol_area—Molecule area containing feature or
constraint.
• feature/constraint—Feature or constraint to modify.
• attribute—Name of an attribute. Modifiable attributes
are type-specific, and depend on feature or constraint
selected.
• value—Value for the attribute.
• COLOR—Optional for UNITY features only.
Remove via the UNITY >>> Delete >>> Features
Menubar:
Remove via REMOVE UNITY_FEATURE mol_area name
Command Line: • mol_area—Area containing feature or constraint.
• name—Name of UNITY feature or constraint to
delete. Type ALL instead of a single name to delete all
features and constraints.
Any constraints based on that feature are removed as well.
If an atom, real or artificial, and involved in a feature or
constraint definition, is removed, the feature or constraint
is removed automatically.

Markush Atoms
8.7 Markush Atoms

Markushes are lists of groups of atoms which can provide constrained
variability in a pattern or structure. For example, a markush atom that represents
all halogens would be:
Hal:F|CL|BR|I
SYBYL has predefined Markushes that are made available by default when a
SYBYL is started. They are loaded from $TA_ROOT/tables/markush.defs.
However, using the methods discussed below, you can create your own set of
Markush definitions, save them to a file, and load them instead.
(The Markush functionality in SYBYL presented below is identical to the

UNITY MARKUSH command, except that it does not start the server and,
therefore, does not require a UNITY license.)
• Define a Markush on page 124
• Delete a Markush on page 124
• List Currently Defined Markushes on page 125
• Load Markush Definitions from a File on page 125
• Modify a Markush Definition on page 125
• Save a Markush Definitions to a File on page 125
8.7.1 Define a Markush

Note: A newly defined Markush is only available during the current SYBYL
session, unless it is saved to a file and then loaded.
Menubar: UNITY >>> Markush >>> Define

Command Line: MARKUSH DEFINE name definition
• name—Name for new Markush atom.
• definition—SLN defining the Markush (refer
to the SLN Manual).
8.7.2 Delete a Markush
Menubar: UNITY >>> Markush >>> Delete

Command Line: MARKUSH DELETE name

Markush Atoms
8.7.3 List Currently Defined Markushes

The contents of the file of Markushes that is currently loaded is listed in the
textport (by default this is $TA_ROOT/tables/markush.defs). Any
Markushes that have been defined during the current SYBYL session are
included in the list as well.
Menubar: UNITY >>> Markush >>> List

Command Line: MARKUSH LIST
8.7.4 Load Markush Definitions from a File
Menubar: UNITY >>> Markush >>> Load

Command Line: MARKUSH LOAD filename
8.7.5 Modify a Markush Definition

Any modifications to Markush definitions will not exist beyond the current
SYBYL session unless they are saved to a file.
Menubar: UNITY >>> Markush >>> Modify

Command Line: MARKUSH MODIFY name definition
• name—Name of Markush to modify.
• definition—New SLN defining the Markush.
8.7.6 Save a Markush Definitions to a File

For any user-defined Markushes to be available during subsequent SYBYL
sessions, they must be saved to a file and then loaded during that session.
Menubar: UNITY >>> Markush >>> Save

Command Line: MARKUSH SAVE filename

Chapter 9. Get Measurements
Chapter 9.
Get Measurements
• Intra-/Intermolecular Measurements on page 128

• Measure the Intramolecular Angle Between Planes on page 129
• Measurements Specific to UNITY Features on page 130
• Calculate a Molecule’s Dipole Moment on page 131
• BIOPOLYMER MEASURE to measure omega and zeta angles.
• TAILOR SET GENERAL ANGLE_RANGE to specify how an angle range
should be displayed.

Intra-/Intermolecular Measurements
9.1 Intra-/Intermolecular Measurements

Angles
Menubar: Analyze >>> Measure >>> Angle
Command Line: MEASURE ANGLE {atom1 atom2 atom3}
Loops until you type the end-loop character (|).
UIMS Variable: measure_angle
Distances
Menubar: Analyze >>> Measure >>> Distance
Command Line: MEASURE DISTANCE {atom1 atom2}
UIMS Variable: measure_distance
Height of Atoms Above Plane
Menubar: Analyze >>> Measure >>> Height Above Plane
Command Line: MEASURE HEIGHT atom_expr plane_name
• atom_expr—Atoms whose height is to be measured.
• plane_name—Name of plane, in default work area, to
use. Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS Variable: measure_height
Torsion Angles
Menubar: Analyze >>> Measure >>> Torsion
Command Line: MEASURE TORSION {atom1 atom2 atom3 atom4}
UIMS Variable: measure_torsion

Measure the Intramolecular Angle Between Planes
9.2 Measure the Intramolecular Angle Between

Planes
Menubar: Analyze >>> Measure >>> Plane Angle
Command Line: MEASURE PLANE_ANGLE mol_area plane_name1
plane_name2
Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS Variable: measure_plane_angle

Measurements Specific to UNITY Features
9.3 Measurements Specific to UNITY Features

MEASURE UNITY_MEASUREMENTS mol_area option
Option:
ANGLE atom1 atom2 atom3 Measure angle of atoms.

DISTANCE atom1, atom2 Measure distance between atoms.
HEIGHT atom_expr plane_name Measure height of atom above plane.
PLANE_ANGLE plane_name1 Measure angle between planes in
plane_name2 same work area.
TORSION atom1 atom2 atom3 Measure torsion angle of atoms.
atom4

Calculate a Molecule’s Dipole Moment
9.4 Calculate a Molecule’s Dipole Moment

Menubar: Compute >>> Dipole
Command Line: DIPOLE mol_area options
• mol_area—Molecule area containing molecule.
• options:
DISPLAY_DIPOLE—Create annotation arrow
centered on geometric center of molecule.
EXIT—Exit DIPOLE command and return to
SYBYL prompt.
SCALE_CHARGES scale_factor—Scale charges
by specified factor (real number multiplied with
current charges), update molecule data structure
with new charges, and recompute dipole moment.
SPECIFY_DIPOLE total_dipole—Scale atomic
charges to produce specified value (Debyes), and
update molecule data structure with new charges.
Only applicable to molecules with a non-zero dipole
moment. Only magnitude is affected, with a
possible direction reversal (if negative value is
specified).
The dipole moment (Debyes) is based on point charge distribution in the

molecule (using atomic charges currently associated with the molecule). The
dipole’s origin is at the molecule’s center, and is guaranteed to coincide with
coordinates X=0, Y=0, Z=0 only if the molecule has been centered on the
screen via the CENTER * command. The magnitude and X,Y,Z components of
the dipole moment are reported.
UIMS2 Variables:
The following variables are assigned values:
DIPOLE_X DIPOLE_Y DIPOLE_Z

DIPOLE_TOTAL DIPOLE_CHARGE
If you have unsaved molecules or tables, SYBYL gives you the opportunity to
save them before you close the program.

Chapter 10. Select Atoms, Bonds, or Substructures
Chapter 10.
Select Atoms, Bonds, or Substructures
Selection of atoms, bonds, or substructures (such as residues in a protein) can be

as simple as clicking on the desired objects in the SYBYL display area.
However, selection may need to be based on a particular type, a defined set, or
even on Boolean operations.
SYBYL’s various Expression dialogs, used for selecting objects such as atoms,
bonds, substructures, etc., are designed to allow as much flexibility as possible.
They are activated by other dialogs whenever an activity requires an expression
as an argument. For example, the menu item View >>> Color >>> Atoms (or
the command: COLOR ATOM) displays the Atom Expression dialog.
As selections are made by clicking on objects in SYBYL’s display area or using

the various buttons, an expression is formed in the bottom field of the dialog.
The expression itself shows the molecule area and current “formula” that the
program will use to select the objects for the action being performed. As you
become familiar with expressions, you may find it more convenient to enter
them directly in the field. (Note, however, that no atoms will be highlighted
until you press Apply.)

For additional information about the Expression field and the formulas that
you can use to select objects, see Objects and Expressions on page 223.
• General Description of the Expression Dialogs on page 135
• Selection How Tos on page 138
• Tutorials:
• Atom Selection Tutorial on page 143
• Bond Selection Tutorial on page 153
• Substructure Selection Tutorial on page 156

General Description of the Expression Dialogs
10.1 General Description of the Expression Dialogs

The Expression dialog was designed to be an all-purpose selection tool. It is
presented in SYBYL under several different titles: Atom Expression, Bond
Expression, Substructure Expression, Sequence Expression, Molecule Expression.
Which dialog is displayed depends on the type of selection that is required by
the present activity. Although the various Expression dialogs are very similar to
each other in layout, there are a few differences. In the dialog description
below, these differences are noted.
Atoms, Bonds, Indicates the selection mode, the type of object on

Monomers which to base the expression formula. For example, if
Atoms is chosen, clicking an atom highlights just that
atom and the formula will contain the atom ID. If
Monomers is chosen, clicking an atom highlights the
entire monomer to which the selected atom belongs and
the formula will contain the residue number. (Note: The
Substructure Expression, and Sequence Expression dia-
logs only have the Monomer option available, and the
Molecule Expression dialog does not have this pull-
down menu.)
Selected Displays the number of objects that are selected in the
currently active molecule area. This field is nonedit-
able.
Highlight Turn on to highlight the selected objects in the SYBYL
window. (The check box is on by default.)
Union The Boolean operator to use when combining two
groups of selected objects.
• Union—Add subsequent selections. The remaining
highlighted objects are in either of the two groups
of selected objects.
• Difference—Subtract subsequent selections. The
remaining highlighted objects are those found in the
first group of selected objects, but not the second.
• Intersection—Find the common objects between
current selection and subsequent selections. The
remaining highlighted objects are those found in
both groups of selected objects.
(Note: This pull-down menu is not available in the Mol-
ecule Expression dialog.)

Sets Displays the Sets dialog for choosing defined sets to

include in the selection. Chirality or a radius can also
be defined in this dialog. The option menu selection
determines the options that are available in the Sets dia-
log.
(Note: This button is not available in the Molecule
Expression dialog.)
Atom Types, Displays the Atom Types, Bond Types*, Monomer Types
Bond Types, dialog, respectively, for selecting by available type.
Monomer Types Notes:
• For the Atom Types dialog, turning on a check box
for a chemical element highlights all atom types
involving this element in the list.
• When bonds are being selected based on atom
types, all bonds connected to specified atoms are
highlighted.
• The Types button is not available in the Molecule
Expression dialog.
Substructures Displays the Substructures dialog for selecting by resi-
due, water, or other defined substructure. (Note: This
button is not available in the Molecule Expression dia-
log.)
All Selects all objects in the area specified in the Mole-
cules field.
Clear Unselects all objects.
Undo Undoes the last action. Useful when experimenting
with selections.
Invert Inverts the current selection.
Molecules Lists molecule area and name of all displayed mole-
cules. Click a molecule area in the list to highlight it
and make it the active one. (Note: The number of items
visible in the list can be extended using the Tailor vari-
able DIALOG NUM_MOL_VISIBLE.)
Expression Displays the current formula/expression to use for
selecting objects. If this field is edited directly, you
must press Apply to update the highlighted atoms in
the display area.
Apply Selects the objects as defined by the formula shown in
the Expression field.

Create Set Defines a new set containing the selected atoms speci-
fied in the Expression field. Specify a name for the set.
This new set is added to the list of predefined sets in
the Sets dialog. (Note: The new set is temporary unless
you save the molecule. Otherwise, it is lost once the
molecule is deleted from the display)
*Definitions for bond types are:
1—Single ar—Aromatic
2—Double du—Dummy
3—Triple un—Unknown (cannot determine from parameter tables)
am—Amide nc—Not connected

Selection How Tos
10.2 Selection How Tos

Selection of objects can be accomplished in many ways. This section attempts
to walk through several mechanisms that are available via the Expression
dialogs. The topics specifically covered include how to select...
• Individual Objects Using the Cursor on page 138
• Everything in a Molecule Area on page 138
• By Sets on page 139
• By Residue Conformational State on page 139
• Sequence of Residues in a Chain on page 139
• By Type on page 140
• By Substructure on page 140
• By Chirality on page 141
• Within a Radius on page 141
• Using Boolean Operators on page 141
10.2.1 Individual Objects Using the Cursor

To select an object:
¾ With the Expression dialog displayed, move the cursor over the
display area and click:
- the atom(s), or
- the two atoms that form the bond(s), or
- an atom in the desired residue(s), substructure(s), or molecule(s).
Note: If you are working from the Bond Expression dialog, all bonds connected
to the atom(s) picked are selected.
10.2.2 Everything in a Molecule Area

To select all objects in a molecule area:
¾ Select the desired molecule area from the list in the Expression dialog.
¾ Press All.

Selection How Tos
10.2.3 By Sets
To select objects using a molecule’s built-in sets or currently defined sets:
¾ In the Expression dialog, press Sets.
¾ In the Sets dialog:

- Click one or more sets that are currently defined for the
molecule, which are shown in the Sets list. (The list changes
from molecule to molecule and depending on what is specified in
the option menu at the top of the Expression dialog.)
- If Atoms or Bonds is chosen in the Expression dialog’s option
menu, built-in sets are available for selection. Turn on one or
more check boxes to include members of those sets.
¾ Press OK.
For more details on sets, see Sets in SYBYL on page 241.
10.2.4 By Residue Conformational State

To select objects by a residue’s conformational state:
¾ In the Expression dialog, select Monomer from the option menu.
¾ Press Sets.
¾ In the Sets dialog, click one or more conformational states in the

Conformations list. This list contains residue conformational states
as defined in the macromol dictionary.
¾ Press OK.
10.2.5 Sequence of Residues in a Chain

To select a sequence of residues in a chain:
¾ In the Expression dialog, select Monomer from the option menu.
¾ In the new field that shows the chain(s), press the left mouse button
and drag the cursor over the desired residue name(s).
Tip: As long as any portion of the residue’s name in the list is highlighted, it
is considered to be chosen.
For large proteins (e.g., > 530 residues), we recommend using the
Substructure Selection dialog instead.

Selection How Tos
10.2.6 By Type
To select objects by type (i.e., atom type, bond type, or residue type):
¾ In the Expression dialog, select the appropriate item from the option
menu (Atom, Bond, or Monomer).
¾ Press the Atom (Bond or Monomer) Types button.
¾ In the Types dialog, click one or more types in the list.
¾ For atom types, you can choose chemical elements by turning on the
corresponding check box. All atom types that include this element are
automatically selected in the list of available types.
¾ Press OK.
Note: If you are working from the Bond Expression dialog, all bonds connected
to the atom(s) picked are selected.
10.2.7 By Substructure
To select objects by substructure (i.e., residues, waters, or other substructures):
¾ In the Expression dialog, press Substructure.
¾ In the Substructures dialog, click one or more items in the lists of

available residues, waters and other substructures.
Note: For Linux users, to select more than one item from a list, Ctrl-
click each item. For UNIX users, click each item.
¾ Use the corresponding All, Invert, and Clear buttons to manipulate

the objects selected in a list.
¾ To apply selection to more than one chain in a protein, press Apply
Selection to All Chains.
¾ Press OK.

Selection How Tos
10.2.8 By Chirality
To select objects by chirality:
¾ In the Expression dialog, select Atoms from the option menu.
¾ Press Sets.
¾ In the Sets dialog, turn on one or more check boxes for the desired
type(s) of chirality to use in the selection.
¾ Press OK.
10.2.9 Within a Radius

To select objects within a given radius:
¾ In the Expression dialog, select Atoms or Monomers from the option

menu.
¾ Identify the center of the sphere, either by clicking an atom(s) in the
display area or using the tools in the Expression dialog to highlight an
atom(s).
¾ Press Sets.
¾ In the Sets dialog, turn on the Sphere check box and enter a radius
(Å).
¾ Press OK.
10.2.10 Using Boolean Operators

To select objects by combining sets:
¾ In the Expression dialog, choose the objects for the first set (set 1).
¾ Select one of the Boolean operators from the pull-down menu:

- Union to add the members of the two sets.
- Difference to subtract set 2 members from set 1.
- Intersection to retain only members that are in both sets.
¾ Use the Sets, Types, or Substructures tools in the dialog, choose

the objects in the second set.
¾ Press OK in the dialog to return to the Expression dialog.

Selection How Tos
When OK is pressed, the Boolean operation is performed and the objects that
remain highlighted in the display area are the result.

Atom Selection Tutorial
10.3 Atom Selection Tutorial

• Simple Atom Selection on page 143
• Atom Expression Field on page 145
• Select By Atom Types on page 146
• Select via Built-In Sets on page 147
• Select by Substructure on page 148
• Select by Monomer/Residue on page 149
• Select via Currently Defined Sets for Proteins on page 150
Setup
Clear the SYBYL screen of all molecules and background images.
¾ If there are more than one molecule on the screen, click All, then OK
in the Molecule Expression dialog.
¾ View >>> Delete All Backgrounds
¾ In the textport, type: take $TA_DEMO/tut.spl to load a dicloxacillin

molecule.
Simple Atom Selection
¾ Select View >>> Color >>> Atoms to open the Atom Expression
dialog.
The option button in the upper left corner is set to Atoms, by default. Use
this button to select various portions of a molecule (atoms or monomers).

¾ Click any five atoms in the work area.

Since the Highlight toggle button is On (the default), selected atoms are
highlighted in green.
¾ In the Atom Expression dialog, click All.
All atoms are selected (and highlighted); the Selected Atoms information
box at the top of the Atom Expression dialog shows that 49 atoms are
selected.
Tip: If the Atom Expression dialog is hidden from view, click the
icon.
¾ Click Clear.
The 49 atoms are no longer selected; Selected Atoms displays 0.
¾ Select three atoms.
¾ Click Undo to unselect the last selected item.

The Undo button enables you to “take back” the last operation.
¾ Click Invert to deselect atoms that were selected and select all
others.
Selected Atoms displays 47.
¾ Click Clear.

Atom Expression Field
For the Atom Expression field to be useful, you must first understand atom
ID numbers and how SYBYL defines them.
¾ Click the icon and, in the M1 row, set the button in the Atm Lbl
column to Id (press Close).
SYBYL identifies all atoms with a unique Atom ID number.
¾ Click one atom in the display area to select it.
SYBYL displays a green selection marker on the atom. The Atom
Expression field echoes the atom’s ID number. If you continue to select
atoms, each atom’s corresponding ID number is echoed within the paren-
theses.
¾ Click Clear.
¾ Click All to select all atoms in the molecule.

An asterisk (*) appears between the parentheses, which represents all atoms
in the molecule.
You can also type atom ID numbers, types, Boolean operators, and defined sets
directly into the field.
¾ Replace * with 1+2+3.
¾ Click Apply.

Nothing happens until you press Apply. Three atoms are highlighted, since
you asked for atoms that had the SYBYL ID # 1, 2, and 3. The ‘+’ signifies
the “AND” (Union) Boolean.
¾ Click Clear.
Select By Atom Types
column to Type (press Close).
¾ In the Atom Expression dialog, click Atom Types to display a
predefined list of atom types.
¾ Check the N check box.
Several lines, representing all nitrogen atom types within SYBYL, are
selected within the list.
¾ Click OK to return to the Atom Expression dialog.

The three nitrogens are highlighted. There are two types of nitrogens in this
molecule: 2 N.am and 1 N.2.
So far, you have been able to add atoms to your selection because the Union
operator is selected in the Atom Expression dialog.
Use the Difference operator, a subtraction Boolean, to keep the N.am atoms
and turn off the N.2 atom.
¾ Change the Union operator to Difference (click to open the drop

down options).
¾ Click Atom Types.
¾ In the Atom Types dialog, select N.2 in the list (press OK).
The N.2 atom is no longer selected, since the Difference operator was used
to remove all N.2 atoms.
¾ Click Clear.

Select via Built-In Sets
SYBYL also has a wide variety of unique “Sets” available. Use sets to highlight
unique characteristics of a molecule. Various built-in sets exist, including:
Aromatic, H-bonds, Backbone, Sidechain, Rings, and Bumps.
A built-in set is a rule-based set, such as {AROMATIC}. For any molecule,

SYBYL identifies the atoms belonging to this set when they are needed.
You are also able to select chirality sets and specify a sphere to select the
molecules that are within the radius of the sphere.
1. Select all atoms that are aromatic.

¾ In the Atom Expression dialog, click Sets to open the Sets dialog.
¾ Check the Aromatic check box (press OK).

All carbons in the phenyl ring are selected and the Atom Expression field
has a defined argument to locate all (*) aromatic atoms, which is expressed
as: {AROMATIC(*)}. (Set names must always be surrounded by braces.)
¾ Click Clear.
2. Locate all rings within this molecule.
¾ If necessary, on the Atom Expression dialog change the drop down

option from Difference to Union.
¾ Click Sets.
¾ In the Sets dialog, check the Rings check box (press OK).
Four rings are identified and the Atom Expression field has a defined
argument to locate all atoms within a ring.
3. Find all nitrogen atoms in rings.
¾ In the Atom Expression dialog, change the drop down option from
Union to Intersection.
The Intersection operator can be thought of as a true “AND” filter that
must have both operations in common with one another. You have already
selected Rings in the Atom Types dialog, now select another criteria.
¾ Click Atom Types.
¾ In the Atom Types dialog, check N (press OK).

Two nitrogen atoms are now selected. This is because two (of the three)
atoms matched the intersection criteria (i.e., the atom has to be a nitrogen
and be part of a ring).
¾ In the Atom Expression dialog, click Cancel.
Clear all molecules.
Select by Substructure
In the following steps load the crambin protein into SYBYL and color some of
the substructures.
Note: There are many ways to display the Atom Expression dialog. Coloring
atoms is the one used in this example.
¾ In the textport window, type take $TA_DEMO/tut_big.spl
column to Substructure (press Close).
For biopolymers, each residue is a substructure. In the SYBYL window, the

alpha carbon of each residue bears the label consisting of the amino acid name
and ID number in the protein sequence.
¾ View >>> Color >>> Atoms
¾ Click Substructures to open the Substructures dialog.

All substructures in the protein are listed.
¾ In the Residues list, select both A/THR1 and A/PRO41.
Note: For Linux users, to select more than one item from a list, Ctrl-
click each item. For UNIX users, click each item.
Tip: You may need to scroll down the list to find A/PRO41.

¾ Press OK.
All atoms that are part of the two substructures are selected (green markers).
¾ In the Atom Expression dialog, click Clear.
Select by Monomer/Residue
Atoms to Monomers.
An additional field is displayed in the Atom Expression dialog, just above
the molecule list.
¾ In the new field that shows the chain, highlight CYS3-CYS4-PRO5.

Tip: As long as any portion of the residue’s name in the list is highlighted, it
is considered to be selected.
All atoms in the 3 selected residues are displayed with the green selection
marker.
Note: You can also select residues via the Monomer Types button.
¾ If necessary, toggle Atoms to Monomers.
¾ Click Monomer Types.
¾ Click TYR in the list (press OK).

All tyrosines are selected.

Monomers back to Atoms.
Select via Currently Defined Sets for Proteins
1. Color atoms that are in a helix and in the backbone.
¾ In the Atom Expression dialog, click Sets.
¾ In the Sets dialog, select HELIX_H1_PDB and HELIX_H2_PDB.

(press OK)
¾ In the Atom Expression dialog, toggle Union to Intersection.
¾ Click Sets.
¾ In the Sets dialog, click the Backbone check box (press OK).
Only atoms that are part of the protein’s backbone and in one of the two
helices are highlighted.
¾ In the Atom Expression dialog, press OK.
¾ In the Option dialog, select MAGENTA (press OK).

All selected atoms are displayed in magenta.
2. Highlight the sheet in the protein.
¾ View >>> Color >>> Atoms
¾ In the Sets dialog, select SHEET_S1_PDB (press OK).
¾ If necessary, toggle the operator to Intersection.
¾ Click Sets.
¾ In the Sets dialog, click Backbone (press OK).
¾ In the Option dialog, select GREEN (press OK)

The sheet is green.

3. Undisplay sidechains to have a better view of the protein backbone.
¾ View >>> Undisplay Atoms
¾ In the Sets dialog, click the Sidechain check box (press OK).
4. List the sets you have made.
¾ Options >>> List >>> Sets
¾ Click CHAIN_HEAD.
¾ For Listing Mode, select BRIEF (press OK).
SYBYL selects the molecules in the chain head.

¾ Options >>> List >>> Sets
¾ Explore the other sets with the Select All, Invert, and Clear buttons.
¾ Click Clear (press OK).
5. Modify a set
¾ Build/Edit >>> Modify >>> Set
¾ In the Option dialog, select NAME (press OK).
¾ Select CHAIN_HEAD
¾ For the new name, enter: CHAIN_HEAD_tut (press OK).

6. Delete a set.
¾ Build/Edit >>> Delete >>> Set
¾ Select CHAIN_TAIL (press OK).
SYBYL removes the molecules in the CHAIN_TAIL set.
7. When finished, reset the atom colors and Atom Expression dialog.
¾ View >>> Display Atoms
¾ Click the All button (press OK).
¾ View >>> Color >>> By Atom Type
This concludes the Atom Selection Tutorial.
Crambin Protein Exercise
Using what you learned in this tutorial, clear the screen, load crambin, and do
the following:
1. Color all atoms in external rings (sulfur) magenta.
2. Color all bonds connected to the sulfur atoms yellow.
3. Undisplay all external rings.
4. Change the remaining atoms to sticks.

Bond Selection Tutorial
10.4 Bond Selection Tutorial

• Simple Bond Selection on page 153
• Select via Bond Sets on page 154
• Select by Bond Types on page 154
• Select by Substructure on page 155
• Clear the Bond Color on page 155
Setup
Clear the SYBYL screen of all molecules and background images.
¾ Type: take $TA_DEMO/tut_big.spl in the textport to load the

structure for crambin.
Simple Bond Selection
¾ View >>> Color >>> Bonds
SYBYL opens the Bond Expression dialog.
¾ In the Bond Expression dialog, select two atoms that are bonded.

The entire bond is highlighted in green and the bond number appears in the
Bond Expression field.
¾ Click Clear.
Select via Bond Sets
¾ In the Bond Expression dialog, click Sets to open the Sets dialog.
¾ From the list of defined sets (in the macromol dictionary), select
ACIDIC (press OK).
All bonds in residues of type ASP, GLU, and TYR are selected (highlighted)
and the equation in the Bond Expression field states: M2({ACIDIC}).
¾ Click Clear.
Select by Bond Types
¾ In the Bond Expression dialog, click Bond Types to open the Bond
Types dialog.
All possible bonds in the molecule are listed. Highlighting one or more of the
bond types and clicking OK selects all bonds in the molecule of the selected
type(s).
¾ In the Bond Types dialog, click Cancel.

Select by Substructure
¾ Click Substructures to open the Substructure dialog.
Use the Substructures dialog to select all bonds within selected substructures.
¾ Click Cancel.
You can also display a list of bonds by selecting Atoms or Monomers in the
option menu (upper left corner of the Bond Expression dialog).
¾ On Bond Expression, select Atoms from the option menu.
Important: Although it appears identical to the Atom Expression dialog, the

Bond Expression dialog selections relate to bonds.
¾ Select three atoms in the crambin protein.
¾ Press OK.
¾ In the Color Bonds dialog, select magenta (press OK).
All bonds directly connected to the selected atoms are magenta.
Clear the Bond Color
Because atom coloring can only be done by also coloring the lines between
atoms, bond themselves are usually not colored. It is a good idea, at this point,
to reset the bond coloring.
¾ View >>> Color >>> Bonds
¾ Click All (press OK).
¾ Select TRANSPARENT (press OK).
This concludes the Bond Selection Tutorial.

Substructure Selection Tutorial
10.5 Substructure Selection Tutorial

• Select from Chain on page 156
• Select via Defined Sets on page 158
• Select by Monomer on page 159
Before you begin: The functionality described in this tutorial requires the
Biopolymer license (“BioPolymer”).
Select from Chain
¾ Clear the SYBYL screen of all molecules and background images.
¾ In the textport, type: take $TA_DEMO/tut_big.spl
SYBYL loads crambin.
¾ Biopolymer >>> Composition>>> Excise Monomer
SYBYL opens the Sequence Expression dialog.
Unlike the Atom and Bond Expression dialogs, the Sequence Expression dialog
has only one option in the upper left: Monomer.
¾ Select the six residues from ILE33 through ALA38.
Use the scroll bar below the field showing the chain residue list to move to
ILE33. Highlight ILE33 through ALA38 in the chain list. (Note: As long as any
portion of a residue’s name in the list is highlighted, it is considered to be
selected.)

Tip: If you highlight the wrong residues, click Clear and try again.
The monomer sequences in the selected molecule area are listed. All atoms in
the 6 selected residues are highlighted in the display area.
¾ Click Clear.

Select via Defined Sets
¾ In the Sequence Expression dialog, click Sets to open the Sets dialog.
Defined sets (in the macromol dictionary) are listed. Selection based on
available conformational states, as defined in the dictionary, can also be made
in this dialog.
¾ Select HYDROPHOBIC from the Sets list (press OK).
All atoms in residues considered to be hydrophobic are highlighted with the

green selection marker.
Note that the equation in the Sequence Expression field is:
M2({HYDROPHOBIC})
¾ Click Clear.

Select by Monomer
¾ In the Sequence Expression dialog, click Monomer Types to open the

Residue Types dialog.
The Residue Types dialog lists all possible monomer types available in the
dictionary. Highlighting one or more of the types and clicking OK selects all
residues in the molecule of the specified type(s).
¾ In the Residue Types dialog, select ALA in the list. (press OK).
All of the alanine residues are highlighted with the green selection marker.
¾ In the Sequence Expression dialog, click Cancel.
This concludes the Substructure Selection Tutorial.

Chapter 11. Get Information on SYBYL Objects
Chapter 11.
Get Information on SYBYL Objects
• Report Information on an Individual Atom, Bond, or Substructure on

page 162
• List Coordinates, Distances, or Angles (Same Molecule Area) on page
163
• List Information on One or More SYBYL Objects on page 164
• Print Information on One or More SYBYL Objects on page 165

Report Information on an Individual Atom, Bond, or Substructure
11.1 Report Information on an Individual Atom,

Bond, or Substructure
Menubar: Options >>> Info
Command INFORM object_type object_sel
Line: • object_type—ATOMS, BONDS, SUBSTRUCTURES.
• object_sel—ID for individual object. Prompting continues
until you enter the end-loop character (|).
To label an atom according to the Tailor variable GRAPHICS MOUSE_LABEL,

Ctrl-right-click that atom. Use this feature for instant information about an
atom, bond or substructure.
• Mouse Label Options in Toolbox Icons (Graphics Attributes section) of
the Graphics Manual.

List Coordinates, Distances, or Angles (Same Molecule Area)
11.2 List Coordinates, Distances, or Angles (Same

Molecule Area)
Menubar: Analyze >>> Measure >>> Topography
List Bond Angles TOPOGRAPHY ANGLES atom_expr
via Command • atom_expr—Expression indicating angle(s). All
Line: angles having the center atom in this atom
expression are listed
List Bond Lengths TOPOGRAPHY BOND_LENGTH atom_expr
via Command • atom_expr—Expression indicating bond(s). All
Line: bonds having either their origin or their target in
this expression are listed.
List Coordinates TOPOGRAPHY COORDINATES atom_expr
via Command • atom_expr—Expression indicating atoms whose
Line: coordinates are to be listed.
Coordinates listed by this command are affected by
rotations and translations applied to molecule on the
terminal. To list coordinates in memory, use the LIST
ATOMS command. Alternatively, cancel rotation/transla-
tion matrix using the reset feature on your terminal, or
FREEZE coordinates before issuing the TOPOGRAPHY
command.
List Non-bonded TOPOGRAPHY NON_BONDED_LENGTH atom_expr1
Distance via Com- atom_expr2
mand Line: Distances between every atom in atom_expr1 and every
atom in atom_expr2 are listed.
List Torsion TOPOGRAPHY TORSION_ANGLE bond_expr
Angles via Com- • bond_expr—Expression indicating torsion(s). All
mand Line: torsion angles having the center bond in this bond
expression are listed.
• Record Output from a Single Command on page 219.
• Intra-/Intermolecular Measurements on page 128.
• BIOPOLYMER MEASURE to conveniently measure omega and zeta angles.
• BIOPOLYMER CHECK_GEOMETRY to report deviations from standard
geometry.

List Coordinates, Distances, or Angles (Same Molecule Area)
11.2.1 List Information on One or More SYBYL Objects
Menubar: Options >>> List

Command LIST object_type object_expr [mode]
Line: • object_type—AGGREGATES, ATOMS, BACKGROUNDS,
BONDS, BUILT_IN_SETS, CENTER_OF_MASS, CENTROID,
CONSTRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE,
SUBSTRUCTURES, TABLE, TAILOR, UNITY_FEATURE,
VIOLATIONS.
• object_expr—Particular set of objects of object_type to
list.
• mode—BRIEF (one line summary for each object or FULL
(all available information for each object) for most
objects. ALL, TYPE, or NAME for UNITY features. (In
picking mode, NAME allows picking on the screen of a
particular feature.)
In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (i.e., a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (i.e., a ring which spans substructure boundaries). Substructures cannot
participate in internal rings but they can be members of external rings.
For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.
• Record Output from a Single Command on page 219to copy the listing
into a file.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of atom listings.

Print Information on One or More SYBYL Objects
11.3 Print Information on One or More SYBYL

Objects
PRINT object_type object_expr [mode]
object_type Type of object to include in the output:

AGGREGATES, ATOMS, BACKGROUNDS, BONDS,
BUILT_IN_SETS, CENTER_OF_MASS, CENTROID, CON-
STRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE,
SUBSTRUCTURES, TABLE, TAILOR, VIOLATIONS.
object_expr Objects to include in the output.
mode Listing mode to use (BRIEF or FULL). This argument does not
apply to all objects.
Use the full generality of the object expression syntax to determine which
objects to include. The PRINT command writes out the file SYBYLPRINT.LIS and
submits it to lpr for printing.
In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (that is, a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (a ring which spans substructure boundaries). Substructures cannot partic-
ipate in internal rings but they can be members of external rings.
For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of the listings.

Chapter 12. Clear and Reset the SYBYL Display
Chapter 12.
Clear and Reset the SYBYL Display
Delete Molecules
¾ Build/Edit >>> Zap (Delete) Molecule. If there is more than one

molecule on the screen, click All, then OK in the Molecule Expression
dialog.
Menubar: Build/Edit >>> Zap (Delete) Molecule

Command Line: ZAP area_expr
ZAP deletes molecules and their associated data structures from program
memory. It clears the molecule area. All associated display structures (e.g., dots,
ribbons, …) are removed from the graphics screen as well.
Delete Backgrounds
¾ View >>> Delete All Backgrounds.
The system removes any displayed backgrounds.
Delete Annotations
¾ View >>> Annotation.
The system opens the Annotation Palette.
¾ On the Annotation Palette, click Select All.
¾ On the Annotation Palette, click Delete (press Close).
The system removes any displayed annotations and closes the Annotation
Palette.
Reset Scaling, Translation, and Rotation
¾ Click the icon and click Everything (press Q).
The system returns to the original scale, translation, and rotation settings.

Undo Last Operation
Each work area has a one level stack associated with it. Prior to any operation
performed on a molecule, the current state is saved on this stack. If an error
occurs in the performance of the operation specified by the command, the
system uses this stacked copy to return the molecule data to a valid state.
Similarly, if you choose to reverse the action of a command, this stacked data is
available to return to the previous state.
• Restore Contents of Molecule Area to Previous State on page 168
• Force Saving of Molecule Area(s) Contents to the Save/Restore Stack on
page 169
Notes:
1. The “current state” saved to the stack includes the coordinates, atom types,
bond types, etc.
2. UNDO does not reverse the effect of labels or colors.
3. If you want to reverse the effect of the LABEL command, use UNLABEL.
4. You can not reverse the effect of the COLOR command (in the Graphics
manual). If you have a color scheme you wish to save, you need to save the
molecule with that color scheme.
Restore Contents of Molecule Area to Previous State
Menubar: Build/Edit >>> Undo

Command Line: RECOVER mol_area
UNDO
Restores contents of all molecule areas (RESTORE M*).
If the AUTOSAVE is OFF, RECOVER copies molecule structures on the stack to

and restores them to the molecule area, the stacked copy is retained. However,
the UNDO command does not do anything. If the AUTOSAVE mode is ON, the
copy is restored and the stack is popped. (See SET AUTOSAVE in the Graphics
Manual).
LIST MOLECULE * BRIEF is used, identifies molecules that currently have

recovery stack contents by an asterisks “*” in the left column.
MONITOR pairs are not saved and, therefore, are lost if RECOVER is executed.
This is because MONITOR pairs may involve more than one molecule area.

Force Saving of Molecule Area(s) Contents to the Save/Restore Stack
SAVE mol_area
Only useful when AUTOSAVE mode is disabled. If AUTOSAVE mode is in effect,

any changes to molecule data structures cause an automatic save of the
molecule data structure before any operation is done.
After a SAVE operation is performed, any RECOVER command causes contents of

this stack to be restored to the molecule area. Similarly, if a catastrophic error
occurs in the program’s operation, a recovery initiated from within the program
causes this saved molecule to be restored.
See SET AUTOSAVE for information on automatic saving of molecules on the

recovery stack and for an explanation of the operation (in the Graphics Manual).

Chapter 13.
Use Molecule Databases
• Database Tutorial on page 174

• Open/Close Databases on page 181
• Obtain Information on Databases on page 187
• Retrieve Molecules on page 188
• Managing Database Content on page 192
• Save Database Molecules to MOL2 or MOL Files on page 196
• Connect to External Relational Databases on page 197
• DATABASE Command List on page 205
Database Formats
There are currently two different formats for molecule databases:

• mol2dbms—A directory of MOL2 files, containing individual
molecules, and several other utility ASCII files. Often referred to as a
MOL2 database. The directory name identifies the database. This format
was introduced in SYBYL 6.1.
• mdbms—A single file, binary format, introduced in SYBYL 5.x.
Note: To explore chemical and biological databases use UNITY, our search and
analysis system. See the UNITY Manual.
Because MOL2 databases are composed of only ASCII files, they are more
portable across different machine platforms than binary databases (e.g., MOL2
databases are portable across platforms, whereas binary databases are not).
MOL2 databases are less susceptible to corruption than binary databases and are
more recoverable in case of corruption, since molecules can be held in separate
files. However, manipulating files within a MOL2 database via the system shell
while the database is open can generate error messages. Closing the database
(and any tables using the database) and reopening it usually eliminates such
errors.
You can create a MOL2 database using the DATABASE CREATE and DATABASE
XCREATE commands, or from the system shell using existing MOL2 files
created by other parts of SYBYL. For example, see the Database Tutorial on
page 174. Also see the TAILOR SET DATABASE command for information
about the MULTIMOL2 variable and how it affects MOL2 databases created from
the system shell.

Chapter 13. Use Molecule Databases
Database Qualifiers
A database qualifier is added to a query expression to explicitly specify the

database to which the expression applies. It consists of a database name (or
alias) placed before the query expression, separated from the query by the “!”
character. A query expression without a database qualifier automatically applies
to the default user database.
SYBYL first checks the names of open databases (which can be seen using the
ALLOPEN command). If the database qualifier matches a name of an open
database, that database is selected for the operation. If no open database name
matches, then the SYBYL checks the alias of any open database. If there is a
match, that database is selected for the operation. If no aliases of open databases
match, then the qualifier is considered to be invalid. (The same process applies
to the open database arguments of the ALIAS, DEFAULT, XADD, XCLOSE, and
XSTATUS subcommands.)
Note: Double quotes must be used when spaces occur in a database qualifier.
Also, if the special character “!” occurs in a molecule name, the molecule name
should be enclosed in double quotes.
Examples
Retrieve tryptophan from the default database and place it in M1. (No database
qualifier is needed.)
DATABASE GET (tryptophan) m1
Retrieve all molecules whose names begin with t (or T) from the database /usr/
me/mydb.mdb. For multiple matches, select one.
DATABASE GET /usr/me/mydb.mdb!(t*) m1
Retrieve the molecule named botulin from the database whose alias is toxins
and place it in M3. (A database such as /usr/me/project_xyz/toxins.mdb is
automatically assigned the alias toxins when opened.)
DATABASE GET toxins!botulin m3
See the OPEN and ALIAS subcommands for additional information about
database aliases.

System Shell Utilities
Since system shell commands like rm and cp behave differently when operating
on regular files versus directories (without additional flags), the following
system shell scripts are provided in $TA_BIN.
• db_rm removes molecular databases of either format:
db_rm db1 ... dbN
• db_cp copies a molecular database of either format:
db_cp source_db target_db
The format of target_db is the same as that of source_db. target_db is

overwritten if it already exists.
LQSample and NCI Databases Distributed with SYBYL
Databases called LQSample and nci_2000 are distributed with SYBYL. These
databases are located in $TA_ROOT/data/tdb_databases and are used in
numerous tutorials. They have the Tripos database format. (See the UNITY
Manual for a description of Tripos Databases.)
• LQSample—41393 registered compounds. These compounds are a small
sample from an older version of the LeadQuest library and are no longer
sold. The LeadQuest library contains drug-like compounds with prede-
termined characteristics, guaranteed purity and identity, and of known
synthetic feasibility. To see the current LeadQuest library:
http://www.tripos.com/leadquest
• nci_2000—250251 registered compounds. These compounds were
screened by the National Cancer Institute in 2000. They are not commer-
cially available compounds, but the CAS number is included with the
structure. For a newer listing see:
http://dtp.nci.nih.gov/docs/3d_database/Structural_information/
structural_data.html

Database Tutorial
13.1 Database Tutorial

This tutorial describes some of the capabilities developed for the manipulation
of molecule databases. This tutorial demonstrates:
• Adding new molecules to a database.
• Defining sets of molecules in the database. Note: Definition of database
sets is only possible via the DATABASE command.
• Defining relations on these sets.
• Several access methods for looking at the contents of a database.
Set Up
2. Copy a file from the demo directory to your working directory. When you type
this command in the textport, be careful to include the space and period at the
end of the line.
¾ dcl cp -r $TA_DEMO/aa.mdb .
Open the Database
1. Open the database of amino acids and examine its contents.

¾ File >>> Database >>> Open
¾ Select aa.mdb (press Open).
¾ Select UPDATE (press OK).
The textport reports that the database is open and in UPDATE mode.
Databases can be opened in UPDATE or READONLY mode. If opened in

READONLY mode, any number of users may simultaneously access the
database. On the other hand, no changes can be made to a database unless it is
opened in UPDATE mode.

Database Tutorial
2. Display a list of the molecules in the amino acid database.
¾ File >>> Database >>> List
¾ Select MOLECULE (press OK).
¾ Accept * as the Object Name (press OK).
SYBYL displays the names in the textport.
Define (Static) Sets of Molecules
1. Enter the DATABASE mode.
¾ In the textport, type: MODE DATABASE
Note: The prompt in the textport changes to Database command>.
Tip: Use the MODE command for complex commands which have many options.
It allows you to establish the upper level command and only enter options until
you exit this mode. When you are in this mode, any command not available as
an option can be invoked by preceding it with the word COMMAND.
2. Organize the polar amino acids, according to their charge, into sets named
basic, acidic, and polar_neutral. Include a comment string describing the set.
¾ Type the following.

Important: Do not introduce spaces in the list of amino acids for the
Query Expressions.
Database command> DEFINE SET basic
Query Expression<*> lysine,arginine,histidine
Comment String<> Amino acids with positively charged R
groups
Database command> DEFINE SET acidic
Query Expression<*> *acid
Comment String<> Amino acids with negatively charged R
groups
Database command> DEFINE SET polar_neutral
Query Expression<*>
glycine,serine,threonine,cysteine,tyrosine,aspar-
agine,glutamine
Comment String<> Polar amino acids with uncharged R groups

Database Tutorial
Database sets are user-defined groups of molecules which have some shared
property (or properties). These properties are distinguished from the ones which
Tripos defines (molecule types,…) and database classes. The group membership
of database sets is static.
3. Examine the contents of the newly created sets.
¾ SHOW SET *
The definitions of all sets in the current database are shown in the textport.
There is no limit on the number of sets.
Define (Dynamic) Classes of Molecules
1. Define two database classes by specifying rules that identify groups of

molecules as hydrophilic or hydrophobic.
¾ Type the following:

Database command> DEFINE CLASS hydrophilic
Query Expression<*> basic+acidic+polar_neutral
Comment String<> Polar amino acids
Database command> DEFINE CLASS hydrophobic
Query Expression<*> ~hydrophilic
Comment String<> Nonpolar amino acids
Important: Database classes are defined by a formula, such as

(basic+acidic+polar_neutral), which is stored as the definition of the group.
Whenever the membership is to be evaluated, it reflects the contents of the
database at that time—not at the moment when the definition was made. In this
way they become dynamic, adapting their contents to the database as it changes.
2. Examine the contents of the classes.

¾ Type: SHOW CLASS *
The definition and contents of all classes in the database are displayed. Notice
how HYDROPHOBIC contains everything that is not HYDROPHILIC (or more
precisely, “not in the property group hydrophilic”).

Database Tutorial
Build a New Molecule
Add hydroxyproline to the database.
1. Retrieve proline from the database to use as a template.

¾ File >>> Database >>> Get Molecule
¾ Select PROLINE (press OK).
2. Label the atoms.
¾ View >>> Label >>> Atom Name
¾ Press All (press OK).
3. Add the hydroxyl group.

¾ Build/Edit >>> Add >>> Group
¾ Select OH (press OK).
¾ Select REPLACE (press OK).
¾ Select H6 on the proline structure (or in the selection dialog, select

H6 (press OK).
Add the New Molecule to the Database
Give the molecule its proper name and add it to the database. Molecule names
may be any arbitrary string.
1. Name the new molecule

¾ Build/Edit >>> Name Molecule
¾ In the Name Molecule dialog, for Molecule name, enter hydrox-

yproline (press OK).
2. Add hydroxyproline to the database.
¾ File >>> Database >>> Put Molecule
¾ In the Option dialog, select KEEP (press OK).

The textport reports that hydroxyproline is added to the database.

Database Tutorial
Redefine a Set and its Effect on the Class
1. Since hydroxyproline is an uncharged polar molecule, add it to the

POLAR_NEUTRAL set.
¾ Type the following:
Database command> DEFINE SET polar_neutral
Query Expression<*> polar_neutral+hydroxyproline
¾ Press Return when prompted for a comment string.
Sets may be redefined at any time, even in terms of their own current contents,
so that it is easy to add a new member.
2. Re-examine the classes.

¾ Type: SHOW CLASS *
Notice that hydroxyproline has been automatically added to the definition of

HYDROPHILIC. Since the class “hydrophilic” was defined in terms of the
groups “acidic”, “polar_neutral”, and “basic”, hydroxyproline automatically
becomes a member of “hydrophilic”.
Search the Database
The next few sections present different ways of accessing database molecules.
The simplest way to retrieve is by molecule name. If you do not know the name,
either at all or exactly, use a wildcard to search the database (by name) for any
matching string. The wildcard (*) alone selects all of the molecules.
¾ Set the Screen mode to Quartered.
¾ Type: SEARCH NAME *

The textport displays Select Command<SELECT>.
¾ Press the Enter key.
The textport displays Query Expression<*>
1. Select leucine from the database.
¾ Type: leucine
The textport displays Selected Molecule: LEUCINE
¾ In the molecule area dialog, select M2 (press OK).
Use the SELECT command with either the molecule’s full or partial name (with
wildcards).

Database Tutorial
2. Retrieve histidine from the hydrophilic class.
The DATABASE command can use property group definitions as a basis for
generating selection menus. The Standard Fragment Library is organized using
just this feature.
¾ Type: SEARCH MENU Hydrophilic NAME

The following appears in the textport:
Hydrophilic
1. basic
2. acidic
3. polar_neutral
Menu items are selected by number. You may move down a level, back up a
level, or go to the top.
¾ Enter 1.
Basic
1. ARGININE
2. HISTIDINE
3. LYSINE
¾ Enter 2.
¾ Select M3 as the molecule area (press OK).
3. Use an expression to retrieve glutamic acid after first restricting your search to
molecules that are both hydrophilic and acidic.
¾ Type: GET (hydrophilic&acidic)
¾ At the Selection Command<SELECT>, press the Enter key.
¾ At Query Expression<*>, type: glu*
¾ Select M4 as the molecule area (press OK).
You can use any combination of union, intersection, difference, and negation of
property groups and name specifications (with or without wildcards) to select
molecules for retrieval. These facilities, coupled with the ability to organize
molecules into groupings meaningful to you, allow arbitrarily complex struc-
tures to be manipulated with ease.

Database Tutorial
Close the Database
1. Exit the DATABASE command mode.
¾ Type: ENDMODE
2. Close the database.
¾ File >>> Database >>> Close

Open/Close Databases
13.2 Open/Close Databases

The Database Selection dialog and the DATABASE OPEN command are used to
open a molecule database so that its contents may be examined or modified.
SYBYL attempts to assign an alias to the newly opened database using the base
name of the full database name. For example, if the full database name is /usr/
me/mydb.mdb, SYBYL attempts to assign it the alias “mydb”. This makes
using database qualifiers easier. See the ALIAS subcommand for more infor-
mation about database aliases.
• Open Database via the Menubar on page 182
• Open Database via Command Line on page 184
• Open a New, Empty Database on page 184
• Copy Database Contents to New Database on page 185
• Define Alias for Database via Command Line on page 185
• Specify a Default Database on page 185
• Close Database via the Command Line on page 186
Notes:
• The database that is opened becomes the default user database.
• If the database is already open, the access mode of the open database is
changed to the newly specified mode.
• Any number of users may have the same database open READONLY.
However, if one user has a database open in APPEND or UPDATE
mode, nobody else has any access to it until the database is closed. If
one user has a database open in READONLY mode, nobody else is
allowed to open it in APPEND or UPDATE mode.
• MOL2 files written via the DATABASE command(s) have at least 6 digits
of precision. If the tailor variable MOL COORD_PLACES is set to < 6
(such as the default of 4), it is set to 6 during the operation of the
DATABASE command and reset when complete. If the value is > 6, the
tailor’s value is used throughout.
To unlock a database that was not properly closed because of a system crash,
enter the following in a textport:
$TA_BIN/<your_platform>/dbunlock
UIMS2 Variable:
• DATABASE OPEN assigns a value to the UIMS2 variable
DATABASE_NAME.

• TAILOR SET DATABASE to alter characteristics of the database opening.
13.2.1 Open Database via the Menubar

File >>> Database >>> Open

Directory Current directory. Relative file or directory specifica-

tions entered in Database Name field are evaluated rel-
ative to this directory. This field is for display only and
cannot be edited. To change the directory of interest, use
the Sub-Directories list or the Search Directory but-
ton.
Sub-Directories Click [Parent] to go up one level in the directory tree.
Pick sub-directory containing the database to open.
Note: The number of items visible in the list can be
extended using the Tailor variable DIALOG
NUM_SUBDIR_VISIBLE.)
Other Directo- Lists your current working directory and others speci-
ries fied as follows.
Notes:
• To provide easy access to other directories from this
dialog, add the following line to the .sybylrc file in
your home directory:
setvar OTHER_DIRECTORIES "<space-
separated directory list>"
• The number of items visible in the list can be
extended using the Tailor variable
TAILOR!DIALOG!NUM_OTHERDIR_VISIBLE.
Directories Database directories available in the selected directory.
Clicking once on a item in this list highlights it and
places it in the Database Name field, for possible edit-
ing. Clicking twice on a item opens it.
Database Name Shows full path of database selected in the list. Alter-
nately, enter the full path of the database directly in this
field.

13.2.2 Open Database via Command Line
User Database: DATABASE OPEN filename access_mode

• filename—Database to open (default extension is
.mdb).
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.
System Data- DATABASE SYSTEM system_db access_mode
base: • system_db—Tripos-supplied database that becomes a
“user” database: FRAGMENT_LIBRARY or
GROUP_LIBRARY. (When opened, it becomes the default
database.)
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.
Using APPEND or UPDATE prevents others from accessing
the system database, either directly or through FRAGMENT or
ADD GROUP commands, until database is closed.
Note: Care should be exercised when modifying the Tripos-
supplied databases, since much of the program’s operation
depends on their contents.
13.2.3 Open a New, Empty Database
Menubar: File >>> Database >>> New

Command Line: DATABASE CREATE filename
filename—Name for database file. Default extension .mdb
is provided automatically.
or: DATABASE XCREATE dbtype filename
• dbtype—Database format: MDBMS or MOL2DBMS.
• filename—Name for database file. Default extension
.mdb is provided automatically.
The database that is created becomes the default user database. It is automati-
cally opened in UPDATE mode; there is no need to open the database after
creation. If a file already exists with the given file name, you have a choice of
replacing the old one or issuing the command again to give another file name.
Replacing the old file creates a new file with that same name and deletes the
contents of the old file.
UIMS2 variable:
• The DATABASE CREATE and DATABASE XCREATE commands assign a
value to the UIMS2 variable DATABASE_NAME.

13.2.4 Copy Database Contents to New Database

DATABASE TO_MOL2DB source destination
source File specification for the source database.

destination File specification for new database, i.e., the MOL2 data-
base. If file exists, you can replace the old one or issue the
command again to give another file name. Replacing old
file creates a new file with that same name and contents of
old file are deleted.
13.2.5 Define Alias for Database via Command Line

DATABASE ALIAS db_name alias
db_name Name or alias of an open user database.

alias New alias.
A database can only have one alias. If the specified database already has an
alias, the old alias is overwritten. A user assigned alias is lost when a user
database is closed.
Aliases are useful in conjunction with database qualifiers. An alias can be used
in a qualifier instead of the full database name, thus decreasing typing effort.
13.2.6 Specify a Default Database
Menubar: File >>> Database >>> Default

Command Line: DATABASE DEFAULT db_name
Database operations are applied to the default database if no database is

explicitly specified in a command.
UIMS2 Variable:
• DATABASE DEFAULT assigns a value to the UIMS2 variable
DATABASE_NAME.

13.2.7 Close Database via the Command Line
Menubar: File >>> Database >>> Close

Command Line: DATABASE CLOSE
or: DATABASE XCLOSE db_name
If the default database is closed and other databases are open, one is arbitrarily
selected as the new default user database.

Obtain Information on Databases
13.3 Obtain Information on Databases

• List All Open Databases on page 187
• Show Status for Database on page 187
• List Contents of Open Database on page 187
• List Molecule and Group Information for Open Database on page 187
13.3.1 List All Open Databases

DATABASE ALLOPEN
Full database names are listed along with aliases given in parentheses. The
default user database is denoted.
13.3.2 Show Status for Database
Default Database: DATABASE STATUS

Any Open Database: DATABASE XSTATUS db_name
Lists contents, including the database filename, alias, format, access mode and
the number of molecules, sets, and classes currently defined.
13.3.3 List Contents of Open Database
Menubar: File >>> Database >>> List

Command Line: DATABASE DIRECTORY item_type name_expr
• item_type—ANY, CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to list (may
include database qualifier, otherwise default database is
assumed).
13.3.4 List Molecule and Group Information for Open Database

DATABASE SHOW item_type name_expr [listing_mode]
item_type ANY, CLASS, MOLECULE, SET.

name_expr Expression specifying names of items to list (may include
database qualifier, otherwise default database is assumed).
listing_mode • BRIEF—Abridged information about selected items,
one-item-per-line.
• FULL—Detailed listing for each item (for ANY or
MOLECULE only).

Retrieve Molecules
13.4 Retrieve Molecules

• A Note on Query Expressions on page 188
• Retrieve a Molecule on page 190
• Search for Molecule(s) to Retrieve on page 191
• Create/Modify a Table of Data on page 191
A Note on Query Expressions
Database query expressions retrieve information about molecules in a database.

The molecules can be retrieved, placed into a group, or simply examined by
name. Molecules can be identified by whole or partial names, by membership in
defined groups, or by a combination of these.
The simplest form of a query expression is a molecule name, which specifies a

single molecule. When specifying a name to retrieve a molecule from the
database, names containing blanks and special characters, such as hyphens or
parentheses must be enclosed in double quotes. Names beginning with letters
and followed by nothing but letters, digits, or underscores may be used without
quotes. This is necessary to distinguish characters in names from operators in
database query expressions.
The next level of complexity in query expressions allows wildcards in molecule

names (but not group names). Finally, operations on groups provide a powerful
technique to designate molecules. They can consist of the logical operators
union, intersection, difference, and negation and the elements to which they are
applied.
The Venn diagrams below illustrate the logical operators. A, B, and C are
general object sets. Shaded areas represent the selected set D which results from
the indicated operations. The outer circle represents the total set from which the
subsets are chosen.
Union Intersection Difference Negation

In either set In both sets In first set and Do not have speci-
not in second fied property
D=A+B or D=A&B D=A-B D=~A
D=A,B

Retrieve Molecules
In database query expressions, operators are evaluated from left to right, with
operations of highest precedence evaluated first. The order of operator prece-
dence is (from highest to lowest):
Negation ~ highest
Intersection &
Union, Difference +– lowest
Parentheses group the elements of the expression for evaluation in a specified

order.
Examples
Retrieve tryptophan from current database and place it in M1.
DATABASE GET (tryptophan) m1
Retrieve all molecules whose names begin with t (or T) from current database.
For multiple matches, you are asked to select one.
DATABASE GET (t*) m1
Retrieve all molecules whose names begin with h (or H) and are members of the
group substrate from current database. For multiple matches, you are asked to
select one molecules.
DATABASE GET (substrate & h*) m1
Retrieve all molecules whose names begin with 1,4,5 T and are members of the
group reaction1 or reaction2 (or both). Use parentheses to ensure the union
operation takes place before the intersection.
DATABASE GET (“1,4,5 T*” & (reaction1 + reaction2))
Double quotes around the (partial) molecule name are required since it contains
special characters.

Retrieve Molecules
13.4.1 Retrieve a Molecule
Menubar: File >>> Database >>> Get Molecule

Command Line: DATABASE GET expression [{selection_query}]
[mol_area]
• expression—Database query expression specifying
molecule(s) to retrieve (may include database qualifier,
otherwise default database is assumed).
• selection_query—
ASSIGN—Similar to DATABASE DEFINE SET. Use
SELECT and UNSELECT to specify molecules to assign.
QUIT—Exit DATABASE GET without loading any
molecules.
RETRIEVE—Retrieve multiple molecules from open
database. To retrieve all molecules in a selection, enter
molecule area for first molecule. Other molecules are
placed in alphabetical order in consecutive work areas.
Previous contents of molecule areas are overwritten.
SELECT—Choose subset of currently selected
molecules. Selection can be a multi-step process.
UNSELECT—Return to set of molecules obtained by last
SELECT command. Can be used as many times as
SELECT.
• mol_area—Molecule area where first (or single)
retrieved molecule is placed (skipped if no molecule
present).
This command behaves differently depending on whether the expression maps

to a single molecule, no molecule, or multiple molecules.
• Single molecule, you are prompted for the molecule area to hold the
molecule.
• No molecules, a message indicates that molecule could not be found.
• Multiple molecules are listed on the terminal and you have access to
additional commands to narrow the selection. Retrieved molecules are
placed in consecutive molecule areas, starting with the one specified
when you entered the command.
• A Note on Query Expressions on page 188.

Retrieve Molecules
13.4.2 Search for Molecule(s) to Retrieve

DATABASE SEARCH search_mode name_expr [action]
search_mode How to search the database:

• NAME—Search by molecule name.
• MENU—Search using menus. The menus provide a
hierarchical structure within databases. The FRAGMENT
command, for example, uses a menu structure to
control searching of the fragment database. Menus are
formed by evaluating molecule groups (sets and
classes). A class which is the union of several groups
appears on a menu listing the component groups. A
group consisting of molecules appears as a menu of
molecule names. Selections continue recursively until
the final molecule is chosen.
name_expr Initial query of the molecule/group name (may include
database qualifier, otherwise default database is assumed).
action Varies depending on the search_mode.
This command is useful for browsing through an unfamiliar database, as well as

for setting up groups which are otherwise difficult to define.
13.4.3 Create/Modify a Table of Data

The table of data must pertain to the series of molecules from an open user
database. Data can be entered explicitly or calculated from the molecules.
Menubar: File >>> Molecular Spreadsheet

Command Line: DATABASE TABLE
• The Molecular Spreadsheet Manual for a complete description.

Managing Database Content
13.5 Managing Database Content

• Add Molecule(s) on page 192
• Delete Molecule(s) on page 193
• Organize Molecules into Groups (Sets and Classes) on page 193
13.5.1 Add Molecule(s)

Notes:
• The molecule being added must have a name. (See MODIFY MOLECULE
NAME to give the molecule a name, or Formats for Specifying Objects on
page 228 for syntax of molecule names.)
• The database must be open in UPDATE mode, or APPEND mode is
sufficient if the molecule does not already exist in the database
Menubar: File >>> Database >>> Put Molecule

Add to Default DATABASE ADD area_expr [disposition]
Database via Com- • area_expr—Expression defining molecules to add to
mand Line: default user database (either a single molecule area
or a comma-separated list of areas).
• disposition—KEEP or REPLACE original molecule.
Add to Database DATABASE XADD db_name area_expr [disposi-
via Command tion]
Line: • db_name—Name or alias of open user database.
• area_expr—Expression defining molecules to add
(either a single molecule area or a comma-separated
list of areas).
Name Molecule DATABASE SAVE_AS mol_area new_name [dispo-
and Add to Data- sition]
base via Com- • mol_area—Molecule area containing molecule to
mand Line: save.
• new_name—Name for molecule (may include
database qualifier, otherwise default user database is
assumed).

13.5.2 Delete Molecule(s)
Menubar: File >>> Database >>> Delete Molecule

Command Line: DATABASE DELETE item_type name_expr NO | YES
• item_type—CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to delete
(may include database qualifier, otherwise default user
database is assumed).
Deletion of groups from a database has no effect on the molecules which were
inside those groups. Molecules themselves must be explicitly deleted.
The database must be open in UPDATE mode for this command to operate
successfully.
13.5.3 Organize Molecules into Groups (Sets and Classes)

• Grouping Mechanisms on page 193
• Define/Modify Definitions of Groups on page 194
• Rename Group or Molecule on page 194
• Reorganize and Compress Database Contents on page 195
Grouping Mechanisms
Molecules in a database can be organized into groups by the user, providing a

convenient method for representing relationships between molecules. It is
important to recognize the distinction between the sets described below and the
sets of atoms, bonds, or substructures. Here the term “set” is used to refer to a
collection of molecules, not to a particular molecule’s constituents.
Database Sets—A named, static collection of molecules explicitly created
by the user. Examples might be groups called “current_project,”
“substrates,” or “minimized.” Members of a set may be specified by a
database query expression which is evaluated at that time to determine the
members of the set. To update the contents of a set, simply give it a new
definition which incorporates its own value. For example, the following
removes hydroxyproline from the set HYDROPHOBIC.
DATABASE DEFINE SET hydrophobic (hydrophobic-hydrox-
yproline)
Database Classes—Molecules matching a specified database query
expression. Once defined, the class is reevaluated each time it is referenced,
to reflect the current database contents.

Define/Modify Definitions of Groups
DATABASE DEFINE CLASS | SET name expr comment
name Name of the class or set.

expr Database query expression (may include database qualifier, other-
wise default database is assumed).
comment Short descriptive string explaining significance of class/set.
Note:
• Database must be open in UPDATE mode for this command to operate
successfully, or APPEND mode is sufficient if the molecule group does
not already exist in the database.
• Each time a defined class’ name appears in a database query expression,
it is reevaluated and its members determined for the database.
• If a molecule, defined as a member of a set, is deleted, that molecule is
automatically removed from the set.
• The Database Tutorial on page 174 for an example.
Rename Group or Molecule
Menubar: File >>> Database >>> Rename Molecule

Command Line: DATABASE RENAME item old_name new_name
• item—CLASS, MOLECULE, SET.
• old_name—Current name of group or molecule.
• new_name—New name for group or molecule.
Notes:
• If new_name for a molecule already exists in the database, you are asked
whether or not the new molecule should replace the current one.
• If new_name for a group already exists in the database, the operation
fails.
• Database must be open in UPDATE mode for this command to operate
successfully.
• Both names may contain a database qualifier. However, the operation
fails if the qualifiers do not refer to the same database.

Reorganize and Compress Database Contents
DATABASE REORGANIZE filename
filename Name of the database file (default extension is .mdb).
Reorganizing and compressing the contents of a molecule database allows

unused space to be reclaimed.
mol2dbms:
• MOL2 files containing more than one molecule are broken into multiple
MOL2 files, one molecule per MOL2 file. This “flattens” the database.
• MOL2 files are renamed so file name matches (or nearly matches) name
of molecule in file.
• Reorganization can decrease access time, but has little effect on database
size, since MOL2 databases rarely accrue unused space.
• Reorganizing a MOL2 database is useful only when the database was
created by the user directly from the system shell. This is because MOL2
databases, created and accessed only via the DATABASE command, have
neither multi-mol2 files nor misnamed MOL2 files.
• Whenever SYBYL writes MOL2 files via the DATABASE command(s),
they are written with at least 6 digits of precision. If the value of the
tailor variable MOL COORD_PLACES is less than 6 (such as the default of
4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If, however, the values higher than 6, the tailor’s
value is used throughout.
• Warning: The DATABASE REORGANIZE command creates a new MOL2
database with a temporary name. This name is generated in the directory
set by the environment variable TMPDIR. If the variable is not set, the
new database is created in the working directory. If this variable is
defined in your environment, that is where the new database ends up,
and hence appears to be lost.
mdbms:
• A consistency check ensures the database contents match the index
structure. This is the only accepted method of recovery for a corrupted
database (as indicated by the error message RECORD_KEY_ERROR).
• Database must not be open by any user when the REORGANIZE command
is given. The reorganized database overwrites the old file.
• Highly active databases should be periodically reorganized to recover
unused space. Compressing the files can have a significant impact on
access time.

Save Database Molecules to MOL2 or MOL Files
13.6 Save Database Molecules to MOL2 or MOL

Files
Menubar: File >>> Database >>> Write MOL2 File
File >>> Database >>> Write MOL File
Command DATABASE WRITE_FILE2|WRITE_FILE expression
Line: selection_query [filename]
• expression—Molecule(s) to write out to file(s) (may
include database qualifier, otherwise default database is
assumed). Multiple molecules are listed in textport.
• selection_query:
SELECT expr—Available if multiple molecules are
specified. Choose a subset of molecules. Expression
provided here is limited to currently specified molecules,
even though other database molecules might match.
Selection continues until either OUTPUT or QUIT is chosen.
UNSELECT—Available if multiple molecules are specified.
Return to set of molecules obtained by last SELECT
command. UNSELECT can be entered as many times as
SELECT was used to narrow the selection.
OUTPUT—Write selected set of molecules to file.
QUIT—Exit command without writing the file.
• filename—File to hold molecules (default extension is
.mol2). This argument is skipped if QUIT is entered.
WRITE_FILE2 creates MOL2 files, WRITE_FILE creates MOL
files.
The MOL MULT_OUT command (with the variable defined by TAILOR SET MOL
FILE_FORMAT set to MOL) has the same purpose.
Note: MOL2 files written via the DATABASE command(s) have at least 6 digits
of precision. If the tailor variable MOL COORD_PLACES is set to < 6 (such as the
default of 4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If the value is > 6, the tailor’s value is used throughout.

Connect to External Relational Databases
13.7 Connect to External Relational Databases

The RDBMS command is used to define information needed to connect SYBYL’s
RDBMS subsystem to external relational database engines and execute queries
against the connected relational database instances.
Manage Queries Manage Connections

• Define a Query • Define a Reference
• Evaluate a Query (Database Connection)
• Save a Query • Save a Reference
• Delete a Query • Delete a Reference
• List Query Information • List Reference Information
Once connections to external databases and queries have been defined, use the
RDBMS Search menubar option to execute queries against external databases,
creating a MSS from the results. Additional columns can then be added to this
MSS using AutoFill and then selecting the RDBMS column type. You may
make use of a suite of SPL expression generators named %RDBMS_*() to build
custom scripts for accessing external databases using the information defined
via the RDBMS command.
Note: You may have multiple RDBMS instances, but only one active query per
instance.
Environment Variables:
The following environment variables affect the behavior of RDBMS and must
be set prior to starting SYBYL.
• TA_RDBMS_READ_TIMEOUT controls how long SYBYL waits for a
RDBMS query to respond. Complex queries or queries to remote
databases can take long to report back to SYBYL. Increasing this
variable forces SYBYL to wait longer. The time-out value is specified in
milliseconds and is an integer value. Default is 500 milliseconds.
• TA_RDBMS_REFS indicates location of rdbms_ref.col (defines connec-
tions).
• TA_RDBMS_QUERIES indicates location of rdbms_queries.col (defines
queries).
Both rdbms_ref.col and rdbms_queries.col are found in $TA_ROOT/

rdbms/tables. You may supersede these definitions by placing a personal
copy of these files in your home directory. This behavior is defined in
$TA_ROOT/tables/rdbms_init.col. Modification of rdbms_init.col affects
the operation of all users.

• TAILOR SET TABLE to alter the treatment of nulls in RDBMS vector
and integer arrays.
• The UNITY Manual.
13.7.1 Define a Query

RDBMS QUERY DEFINE alias ref_name query_string
query_attrib
alias Unique name given to a query definition.

ref_name Name of RDBMS REFERENCE to associate with query.
query_string A free formatted string defining a query against an external
relational database. String may consist of several separate lines
and must be terminated with a line consisting of a single period
(“.”).
query_attrib A list of attribute name/value(s) ending with DONE:
• QUERY_TYPE—Type of query being entered.
RDBMS_SPECIFIC—An explicit query native to external
relational database being queried. This is default type.
(Note: An SQL query must be RDBMS_SPECIFIC.)
RDBMS_UNITY—Database engine independent query
(created only for Tripos internal use).
• REGISTRATION_VARIABLE—Name of variable in query
string to associate with a structure’s registration ID.
Default is REGID. Do not include special delimiter, “:”, in
this name.
• STRUCTURE_DB—Associate UNITY structure database
with this query via a path.
Each time this command is invoked, a new RDBMS query is added to your
SYBYL session. Each query is referenced by a unique alias name. Use of an
already existing alias name results in the previous query being replaced by the
new definition.
Once an RDBMS query is defined, it is accessed via other RDBMS commands,

expression generators and the UNITY >>> RDBMS Search menu item.
When creating an MSS via RDBMS Search, “STRUCTURE_DB path” defined

in a query supersedes structure database paths defined in the associated
RDBMS reference.

Example:
RDBMS QUERY DEFINE row_names oracle_sgi
select distinct(name) from sample_data
.
STRUCTURE_DB /usr4/krypton/3DB/Databases/sample \
DONE
RDBMS QUERY DEFINE logp_sample oracle_sgi

select logp from sample_data where NAME=:REGID
.
DONE
RDBMS QUERY DEFINE sigma_sample oracle_sgi

select sigma from sample_data where NAME=:REGID
.
DONE
RDBMS QUERY DEFINE bioact_sample oracle_sgi

select bioactivity from sample_data where NAME=:REGID
.
DONE
13.7.2 Delete a Query

RDBMS QUERY DELETE alias
alias Name associated with query to delete.
Queries deleted with this command are removed from SYBYL session only.
Example:
RDBMS QUERY DELETE sigma_sample
13.7.3 Evaluate a Query

RDBMS QUERY EVALUATE alias_name eval_attrib DO_EVAL
alias Name associated with the query to evaluate.

eval_attrib List of attribute/value(s) which affect how records
returned from the evaluation are reported.
• DO_EVAL—Perform the evaluation.
• OUTPUT_FILENAME filename—Save reported
records to specified file. If you enter STDOUT or
STDERR as the filename, records are written to the
standard I/O output channel (typically your display,
unless redirected).
Writes returned records to a specified file. Each field in a returned record is

separated by double quotes (“ ”).

Examples:
RDBMS QUERY EVAL row_names output_file regids DO_EVAL
sh cat regids
The following information is displayed in the textport:

1,2,3,4-tetrahydroisoquinoline
1,2,3,4-tetrahydronaphthalene
1,2,3,4-tetrahydroquinoline
1,2,4-trioxolane
1,2,5-oxadiazole
1,2-benzisothiazole
1,3,4-thiazoline
1,3,4-thiodiazole
1,3,5(10)-gonatriene
1,3,5-cycloheptatriene
1,3-cycloheptadiene
1,3-cyclohexadiene
.
.
13.7.4 List Query Information

RDBMS QUERY LIST ALL|SPECIFIC_QUERY
ALL List all queries.

SPECIFIC_QUERY List only the named query.
Examples:
RDBMS QUERY LIST ALL

Registered RDBMS Query Aliases
==============================
Alias: bioact_sample
Database: oracle_sgi
Query Type: DB_SPECIFIC
REGID Symbol: REGID
Structure DB: (null)
Query: select bioactivity from sample_data where NAME=:
REGID
Alias: logp_sample


REGID Symbol: REGID
Structure DB: (null)
Query: select logp from sample_data where NAME=:REGID
Alias: row_names
REGID Symbol: REGID
Structure DB: /usr4/krypton/3DB/Databases/sample
Query: select distinct(name) from sample_data
13.7.5 Save a Query

RDBMS QUERY SAVE filename
filename Name of file to hold query definitions.
All defined queries are saved in a collect file for later use. If file exists, the new
definitions are appended to the file.
13.7.6 Define a Reference (Database Connection)

Each use of the RDBMS REFERENCE DEFINE command creates an entry in the
RDBMS reference list of the SYBYL session. Definitions referencing previ-
ously used reference names replace original definitions. Information contained
in the reference is used by other RDBMS commands and expression generators.
(Note: To access an external database using the current machine username and
password, specify RDBMS_ACCESS_INFO NONE NONE.)
RDBMS REFERENCE DEFINE alias instance_name db_type

db_host ref_attrib
alias Name to identify this reference within other RDBMS com-

mands.
instance_name Name of external database instance to connect.
db_type Type of relational database connected (ORACLE, INGRES,
RDB).
db_host Name of machine on which connected relational database
engine resides.
ref_attrib A list of attribute name/value(s) ending with DONE:

MACHINE_ACCESS_INFO username password

• username options=
CURRENT_USERID—Request username of account
currently running SYBYL.
EXPLICIT_USERID—Specify a username to use.
PROMPT_FOR_USERID—Prompt for a username.
NONE—No username is presented.
• password options=
EXPLICIT_PASSWORD—Specify password to use.
PROMPT_FOR_PASSWORD—Prompt for password.
ENCRYPTED_PASSWORD—User makes use of an explicit
password which is encrypted. Must be used initially in
interactive mode to enter password. RDBMS SAVE writes
encrypted password in rdbms_refs.col which is
decrypted when file is taken.
NONE—No password is presented.
RDBMS_ACCESS_INFO username password
Request username and password to gain access to external
database instance when reference is opened. Username and
password options are the same as for
MACHINE_ACCESS_INFO.
RDBMS_REGID_COLUMN
Request name of column in database instance containing
registration identifiers.
RDBMS_STRUCTURE_DB
Request default path to UNITY structure database contain-
ing structures corresponding to registration IDs found in
database.
RDBMS_TABLE name
RDBMS_STRUCTURE_DB|RDBMS_STRUCTURE_COL
Defines information specific to a database table.
• name—Name of a database table.
• RDBMS_STRUCTURE_DB path—Use specified UNITY
structure database, associated with the table denoted by
name above.
• RDBMS_STRUCTURE_COL column—Use specified
database column in custom scripts to obtain structure
information corresponding to registration IDs obtained
from the database.

Example:
RDBMS REFERENCE DEFINE oracle_sgi oracle oracle polaris \
MACHINE_ACCESS_INFO CURRENT_USERID PROMPT_FOR_PASSWORD \
RDBMS_ACCESS_INFO EXPLICIT_USERID unity PROMPT_FOR_PASSWORD \
RDBMS_REGID_COLUMN NAME \
RDBMS_TABLE sample_data RDBMS_STRUCTURE_DB \
/usr4/krypton/3DB/Databases/sample \
RDBMS_TABLE cas30k_data RDBMS_STRUCTURE_DB \
/usr4/krypton/3DB/Databases/cas30k \
DONE
RDBMS REFERENCE DEFINE oracle_ibm SID oracle eagle \
MACHINE_ACCESS_INFO CURRENT_USERID PROMPT_FOR_PASSWORD \
RDBMS_ACCESS_INFO EXPLICIT_USERID unity PROMPT_FOR_PASSWORD \
RDBMS_REGID NAME \
DONE
13.7.7 Delete a Reference

RDBMS REFERENCE DELETE name
name Name of a previously defined reference.
Deletion of a reference affects current session only. The rdbms_refs.col file is

not affected unless RDBMS REFERENCE SAVE is used.
Example:
RDBMS REFERENCE DELETE oracle_ibm
13.7.8 List Reference Information

RDBMS REFERENCE LIST ALL|SPECIFIC_REF
ALL List all references.

SPECIFIC_RE List only the named reference.
F

Example:
RDBMS REFERENCE LIST ALL

Registered RDBMS References
==============================
RDB alias: oracle_sgi
Name: oracle
Engine: oracle
Host: polaris
Default Struct DB: (null)
Struct DB for cas30k_data: \
/usr4/krypton/3DB/Databases/cas30k
Struct DB for sample_data: \
/usr4/krypton/3DB/Databases/sample
13.7.9 Save a Reference

RDBMS REFERENCE SAVE filename
filename Path to file where RDBMS references are to be written.
All currently defined RDBMS references are written to a collect file for later
use. If specified file exists, RDBMS references are appended to file.
Example:
RDBMS REFERENCE SAVE rdbms_refs.col
sh cat rdbms_refs.col

RDBMS REFERENCE DEFINE oracle_sgi oracle oracle polaris \
MACHINE_ACCESS_INFO EXPLICIT_USERID mandl \
PROMPT_FOR_PASSWORD RDBMS_ACCESS_INFO EXPLICIT_USERID \
unity PROMPT_FOR_PASSWORD RDBMS_REGID_COLUMN NAME \
DONE

DATABASE Command List
13.8 DATABASE Command List

The DATABASE command provides functionality to manipulate molecule
databases, whether they have been supplied by Tripos or defined by the user.
DATABASE functions can be accessed in two ways:

• Precede each subcommand with the word DATABASE.
• Type MODE DATABASE to enter the DATABASE mode. To exit this mode,
type either the end-loop character (|) or ENDMODE. Selecting another
menu category also exits the DATABASE mode. When in DATABASE
mode, other SYBYL commands can be accessed by preceding them with
COMMAND.
Below is a list of the subcommands:
ADD ALIAS ALLOPEN

CLOSE COMMAND CREATE
DEFAULT DEFINE DELETE
DIRECTORY ENDMODE GET
OPEN RENAME REORGANIZE
SAVE_AS SEARCH SHOW
STATUS SYSTEM TABLE
TO_MOL2DB WRITE_FILE WRITE_FILE2
XADD XCLOSE XCREATE
XSTATUS

Chapter 14. Manage SYBYL Sessions
Chapter 14.
Manage SYBYL Sessions
• Save a Session on page 208

• Restore a Saved Session on page 215
• Delete a Saved Session on page 216
• Record and Play SYBYL Sessions on page 217

Save a Session
14.1 Save a Session

A SYBYL session, in its current state, can be saved in a specified directory.
This allows you to return to SYBYL at a later date and continue your work from
the point where you saved the session (see Restore a Saved Session on page
215). The default is to save the session in the current working directory and the
default name for the directory is the current date and time
(dd_mmm_yyyy_hh_mm). To change the default from the current working
directory to a different location, use the environmental variable
$SAVE_SESSION_DIR (must be set prior to starting SYBYL).
Save the Session
Menubar: File >>> Session >>> Save

Command Line: SESSION SAVE dir_name
Save the Session and Exit SYBYL
Menubar: File >>> Session >>> Save and Exit

Command Line: SESSION SQUIT dir_name
What is Saved?
• Tailors and parameter files (.tpd)
• Scaling
• Global/display area transformations
• Screen mode (full, half, etc.)
• View mode (mono, orthographic, relaxed, and crossed stereo) but not
SIAW
• Graphics data specific to the terminal type:
• CPK variables, colors, fonts, lighting, Z-clipping mid/width, depth
cue scale, line widths, dot types, Z-clip state, stereo separation and
opsis, per pixel lighting state (SGI only), anti-aliased backgrounds
state (OGLX only), clean translucency state (OGLX only), multisam-
pling (SGI only).
• All molecules
• Object transformation, visibility state, the Z clip status of the
molecule, the label color, the ColorByType state, the display mode
state, and the current label type are all retained.

Save a Session
• For each molecule, a .mol2 file is written to the saved session’s

directory. When a molecule is saved, the displayed molecule’s state
is changed to indicate that the molecule is no longer modified.
• Data necessary to restore dynamic Hbonds, distance and bump
monitoring.
• Data necessary to preserve the rotatable bond angles (where twist freeze
has not been applied).
• 10 types of backgrounds — The molecule association, object transfor-
mation, visibility state, and the Z clip status of the background are all
retained. See Details About Saved Backgrounds on page 210 for more
information. (Note: If a background is not supported for saving, a
message is produced in the textport.)
• Rulers
• MOLCAD surfaces
• Mixed rendering of atoms
• Mixed rendering of proteins
• Biopolymer ribbon
• Hbond
• VOLUME/MVOLUME
• Potential
• Dots
• QSAR contours
• Table types
• Based on molecule databases (including analyses).
• Hitlists
• MDL SD/RD
• Dynamics
• Search — .ang files are not cross platform compatible
• Nonstructural/generic
• Import
The default molecule area and correct default table are restored. If the
row labels are 2D structures when saved, then restoring also shows these
labels.
Supporting files for CoMFA, EVA, and CoMSIA are saved.
• Databases — The default database and the access mode.

Save a Session
What is Not Saved?

• Backgrounds not supported:
• Generalized Surfaces
• GenDensity
• GenPotential
• GenOrbital
• Isosurfaces
• Contour display created surfaces-CoMFA region
• MOPAC
• AMPAC
• Force Field constraint
• Old annotate
• grlist
• Table graphs
• Table types not supported:
• NMR-based tables
• UNITY database backed tables
• BIO_LOOP tables
• Protein tables
• New annotations
Details About Saved Backgrounds

• MOLCAD Surfaces on page 211
• Mixed Rendering of Atoms on page 211
• Mixed Rendering of Proteins on page 211
• Biopolymer Ribbon on page 212
• Hbond on page 212
• VOLUME/MVOLUME on page 212
• Potential on page 213
• Dots on page 213
• QSAR Contours on page 214

Save a Session
MOLCAD Surfaces
• The surface style (lines, dots, etc.) and the current coloring property are
retained.
• If the color of a MOLCAD surface is changed with the BACKGROUND
COLOR command, the color will not be restored correctly.
Mixed Rendering of Atoms

• The values of the following settings, at the time of the session saving,
are retained: opaque/transparency, coloring, atom and bond quality,
scaling method for ball and stick rendering, bond radius, and quality for
spacefill, ball and stick, stick, and capped stick rendering.
• The setting for TAILOR!RENDER!SURFACE_TYPE at the time of creation
is retained.
• These backgrounds can only be created with TERM OGLX and can only
be restored with TERM OGLX.
Mixed Rendering of Proteins

• The opaque/transparency at the time of the session saving is retained.
• Settings for TAILOR!RENDER!SURFACE_TYPE,
TAILOR!RENDER!HELIX_DISPLAY, and
TAILOR!RENDER!SEC_STR_SRC, at the time of creation, are retained.
• The values for the following TAILOR!RENDER options are taken from
the tailor.save file at the time of the session saving:
• ARROW_SCALE
• HELIX_COLOR
• HELIX_CYL_RADIUS
• NARROW_RES
• NSEGMENTS
• OTHER_COLOR
• RIBBON_HEIGHT
• RIBBON_WIDTH
• SHEET_COLOR
• TUBE_DIAMETER
• TUBE_MAX_DIAMETER
• TUBE_MIN_DIAMETER
• If the coloring is by table column, it will not be retained.

Save a Session
• These backgrounds can only be created with TERM OGLX and can only
be restored with TERM OGLX.
Biopolymer Ribbon
• The number of strands and color are retained.
• The value for TAILOR!RIBBON!RIBBON_WIDTH is taken from the
tailor.save file at the time of the session saving.
Hbond
• The atom set and color are retained.
• The values for the following TAILOR!HBOND options are taken from the
tailor.save file at the time of the session saving:
• ANGLE
• MAX_DISTANCE
• MIN_DISTANCE
• TICK_DENSITY
• The .dsp file is not saved, as the background will be recreated upon
restoration of the session.
• These backgrounds are only available with TERM OGLX or X.
VOLUME/MVOLUME
• The volume color and surface type used at creation are retained using the
TAILOR!CONTOUR!DISPLAY_AS setting.
• The values for the following TAILOR!VOLUME options are taken from
the tailor.save file at the time of the session saving:
• GRID_SPACING
• CONTOUR_PLANES
• MAP_RANGE (not used with MVOLUME)
• The .dsp and .cnt files are not saved, as the background will be
recreated upon restoration of the session.
• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
types can be restored without needing to prompt the user.
• Volumes created with TAILOR!VOLUME!MAP_RANGE=FIXED_RANGE are
not restorable.
• These backgrounds are not restorable with TERM NO.
• Only surfaces created with TAILOR!CONTOUR!DISPLAY_AS=OLD are
restorable in TERM X.

Save a Session
Potential
• The surface type used at creation is retained using the
• The values for the following TAILOR!POTENTIAL options are taken
from the tailor.save file at the time of the session saving:
• CONTOUR_LEVEL_1
• CONTOUR_LEVEL_2
• CONTOUR_LEVEL_3
• CONTOUR_COLOR_1
• CONTOUR_COLOR_2
• CONTOUR_COLOR_3
• CONTOUR_PLANES
• CUTOFF_RADIUS
• DIELECTRIC_CONSTANT
• DIELECTRIC_FUNCTION
• EDGE_EXTEND
• GRID_SPACING
• NUMBER_LEVELS (always forced to 3 for potentials)
• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
• These backgrounds are not restorable with TERM NO.
• Only surfaces created with TAILOR!CONTOUR!DISPLAY_AS=OLD are
restorable in TERM X.
Dots
• The coloring method used at creation is retained.
• The values for the following TAILOR!DOTS options are taken from the
tailor.save file at the time of the session saving:
• ADD_CONSTANT
• CUTOFF_RADIUS
• DENSITY
• DIELECTRIC_CONSTANT

Save a Session
• DIELECTRIC_FUNCTION
• INTERSECTION_HANDLING
• POTENTIAL_COLOR_METHOD
• POTENTIAL_DISTANCE
• SCALE_CONSTANT
• The .dot file is not saved, as the background will be recreated upon
restoration of the session.
• The filename originally used to create the .dot file is not retained. A
default name is used to guarantee that more than one of these surface
QSAR Contours
• The graph field file must be saved during the contour creation. This file
is saved if the contour was created from the QSAR GRAPH FIELD
command. If the View CoMFA dialog was used, the Save to File(s)
check box must be on.
• The surface type used at creation is retained using the
• All TAILOR!TABLE and TAILOR!GRAPH values are taken from the
tailor.save file at the time of the session saving.

Restore a Saved Session
14.2 Restore a Saved Session

Previously saved SYBYL sessions can be restored using either of the following.
Menubar: File >>> Session >>> Restore

Command Line: SESSION RESTORE dir_name
During restoration:
• The program checks to see if the saved session is being restored on a
different platform, terminal type, or SYBYL version and notifies you in
such cases.
• Many aspects of a saved session can be restored correctly on a different
terminal type. However, a message is displayed if you are trying to
restore something that is not supported on that type.
• Prompts are also presented regarding the deletion of any currently
displayed molecules, backgrounds, and tables before continuing.
• The program checks for files in your currently working directory that
have the same name as files that are being restored and issues a warning
about overwriting them.

Delete a Saved Session
14.3 Delete a Saved Session

Saved SYBYL sessions can be deleted using either of the following.
Menubar: File >>> Session >>> Delete

Command Line: SESSION DELETE dir_name

Record and Play SYBYL Sessions
14.4 Record and Play SYBYL Sessions

SYBYL has two powerful procedures for tracking commands and terminal
dialog. They are useful for documenting a session and when tracking potential
problems in the use of SYBYL. It is important to activate these options at the
beginning of your SYBYL session.
• Record Session Commands on page 218
• Record Output from a Single Command on page 219
• Record Terminal Dialog of Session on page 219
• Insert a Pause in a Recorded Session File on page 220
• Play Recorded Session on page 220
• Read Command Input From Text File on page 221
A collect/take file consists of a series of command lines where each command

must appear on a single logical line. Lines are terminated by an end-loop
character (|) unless the last character on the line is a back slash (\).
The following characters, when first on one line, have special meaning in a
collect file:
# ignore the line, typically used for comments,
% if current session is interactive ask user for confirmation before
continuing, typically used to pause during playback.

14.4.1 Record Session Commands

When enabled, all commands and arguments are captured into a file which can
be replayed to reproduce a session. The file closes automatically at the end of
the SYBYL session.
Menubar: File >>> Log Commands

Command Line: COLLECT action [filename]
• action:
APPEND—Reopen existing file and continue journaling.
COMMAND—Force collection of next command even if
collection was suspended.
FILTER—ON/OFF; whether to collect all SPL
constructs.
FORCE_RESUME—Resume journaling even if multiple
SUSPEND commands were made.
ON—Enable journaling of command input in file.
OFF—Stop journaling of commands and close file.
RESUME—Cancel last SUSPEND.
SUSPEND—Temporarily suspend journaling without
closing file.
• filename—File to receive journaled commands. Default
extension is .col.
To store actions of menu picks in a collect file, first issue the command MENU
COLLECT ON.
Only one COLLECT file can be open at a given time.
UIMS2 Variable:
• UIMS2_COLLECT_FILE—Name of the current collect file.
• Record Terminal Dialog of Session on page 219
• Insert a Pause in a Recorded Session File on page 220

14.4.2 Record Output from a Single Command

The terminal output from a single command can be sent to a file. This is useful
for storing lengthy output of commands such as minimizers, LIST, TOPOG-
RAPHY, etc. The file can then be sent to a line printer.
CAPTURE filename command
filename File to receive output generated by specified com-

mand. No default file extension.
command A single SYBYL command with all its arguments.
14.4.3 Record Terminal Dialog of Session

When enabled, the complete terminal dialogue is recorded in a file. Program
prompts, user responses, commands, and program output are recorded in this
file. It can be used to document sessions with the program as an adjunct to a
laboratory notebook. The file closes automatically at the end of the SYBYL
session.
Menubar: File >>> Log Session

Command Line: PHOTO status [filename]
• status:
ON—Record terminal dialog to specified file. Infor-
mation is first stored in a buffer. By default, buffer is
automatically flushed to the file as soon as it is full.
OFF—Terminate recording.
FLUSH—Write all currently buffered PHOTO infor-
mation immediately to file. Future I/O flushing is not
affected by this command.
LINEBUFFER—Line buffer pending and all future
PHOTO I/O, data is flushed continuously to file. LINEB-
UFFER is off initially. If you turn PHOTO OFF then back
ON, you must explicitly turn on LINEBUFFER again.
• filename—File to receive the terminal dialog. There is
no default extension.
UIMS2 Variable:
• UIMS2_PHOTO_FILE—Name of the current photo file.

• Record Output from a Single Command on page 219
• Play Recorded Session on page 220
14.4.4 Insert a Pause in a Recorded Session File

PAUSE delta_time
delta_time Number of seconds to pause program execution.
By inserting this command into the recorded session file, you can halt program
execution for a specified number of seconds or indefinitely, if delta_time is set
to zero. In this way, you can give the user ample time to read the comments.
PAUSE is used in preparation of demonstration scripts. Note: These scripts
cannot be played back in menu mode.
As an alternative to PAUSE, inserting the WAIT command suspends execution

until either C (continue), G (go), or Q (quit) is entered. Enter either command at
the keyboard during the recording session or edit the file afterwards.
• Record Session Commands to prepare a script.
• Play Recorded Session to play back a prepared script.
14.4.5 Play Recorded Session

A recorded session can be used to repeat a series of commands on several
different molecules, to replay a demonstration script, or to recover one’s
position lost as a result of system failure.
Menubar: File >>> Take Commands

Command Line: TAKE filename
When an incomplete command line is encountered in the file, interactive

prompting takes place to finish the command before proceeding to the next
command line.

Play a SYBYL 5.1 Recorded Session
TAKE51 filename
This command reads commands from a SYBYL 5.1 collect file. Text in the file
is executed as if it was manually entered through the keyboard. It is no longer
possible to create a SYBYL 5.1 collect file. However, the TAKE51 command
has been provided for reading old style collect files.
14.4.6 Read Command Input From Text File

TTY filename
Input is read from the specified file (file extension must be included) until an
end-of-file condition is encountered. The text in the file is executed as if it was
manually entered by the keyboard. This is convenient when generating
command procedures without the use of the COLLECT command. (The tutorial
files (.demo) have this format.)
Warning:
TTY does not understand command context as does the TAKE command. Thus
any mistakes in the TTY file are faithfully executed.

Chapter 15.
Objects and Expressions
• Definitions of SYBYL Objects on page 224

• Formats for Specifying Objects on page 228
• Atom Specification on page 229
• Bond Specification on page 230
• Substructure Specification on page 232
• Set Specification on page 232
• Molecule Specification on page 233
• Molecule Area Specification on page 233
• Monomer Sequence Specification on page 233
• Conformational Specifications on page 235
• Create Expressions on page 237

Chapter 15. Objects and Expressions
Definitions of SYBYL Objects
15.1 Definitions of SYBYL Objects

Atoms—The fundamental building blocks of molecules. You may name them
arbitrarily and specify their type. Parameters for over 30 different atom types
are provided in SYBYL. An extended list of more than 103 atom types is
available in the file $TA_DEMO/metals.tpd. You can easily expand this
number by adding new types of your own. Atoms can exist as bonded entities or
singly.
Bonds—Connection between atoms to form molecules. Bond types (single,

double, triple, amide, or aromatic) are determined by the types of atoms they
join. Bond types determined automatically by the program can be overridden to
accommodate exceptional circumstances in a particular molecule.
Features—Features are molecular characteristics. They can be based on atoms,

other features, or contain other information.
• Center of mass, centroid, extension point, line, normal, plane, and
various UNITY features
• Force field angle, distance, range, periodic boundary conditions and
torsional constraints
• Sets, including aggregates
• Search anchor atom, rotatable bonds, ring closure and distance
constraints
• Crysin unit cell parameters and space group
• Associated data file locations
• Associated dictionaries
• Alternate atom types
Molecule Areas—Work spaces which hold structures being manipulated. Areas

are designated by the letter M followed by an integer. Any number of molecule
areas can be defined at any time, since SYBYL can handle an unlimited number
of molecules simultaneously. They may be assigned in arbitrary order, and will
hold any named entity supplied either from an external file, through
construction internally, or from a database. A molecule area may contain a
single atom, multiple fragments, water molecules, ions, or other components,
and structures with unfilled valences.
Rings—SYBYL detects the formation and records the presence of rings at all
times in all molecules. Rings have wide-ranging implications for conforma-
tional manipulations as well as modification of internal parameters, such as
bond lengths and angles, and they play an important role in identifying similar-
ities among molecules.

• Internal ring—A ring completely contained within a substructure.

Atoms and bonds in an internal ring are distinguished by the character *
next to their name in the atom or bond list.
• External ring—A ring which spans substructure boundaries. Typically
occur in polymers which are cross-linked (e.g., a peptide structure which
has one or more disulfide bridges). Atoms and bonds in an external ring
are distinguished by the character @.
The figure below illustrates both internal and external rings. The boxes
delineate substructure (monomer) boundaries in this peptide fragment. The
phenyl group in the phenylalanine monomer is an internal ring since it occurs
completely within the confines of a substructure. The heavy, dark bonds
indicate a ring formed by the cross-linking of the peptide by a disulfide bridge
between two cysteine monomers. It is termed an external ring because it crosses
substructure boundaries.
Sets—Named collections of objects substructures, atoms or bonds used for

identifying and naming important groups of atoms, bonds, or substructures in a
molecule. A set can be used as a shorthand notation for groups of atoms, bonds,
or substructures which are referenced often.
• Static sets—Membership is identified at the time of definition. Once
specified, this membership does not change unless one of the elements
(atoms, bonds, substructures) is deleted from the molecule. For example,
identify the amino acids in the active site of an enzyme and name them
for quick access.
• Dynamic sets—Membership is defined in terms of a rule and evaluated
at the time of reference. For example, the environment around a
particular atom in a molecule can be defined as a set using a sphere of
specified radius. As the molecule’s conformation is manipulated, the
membership in the set may change. When you reference this set’s name,
the contents of the volume are identified by evaluating the rule at that

time. The built-in sets in SYBYL are dynamic sets: Aromatic, H-bonds,
Backbone, Sidechain, Rings, and Bumps.
See Sets in SYBYL on page 241 for more details.
Substructures—Group of atoms in which it is possible to reach any atom from

any other atom along a bonded pathway. No atom in a molecule can belong to
more than one substructure. A substructure may be a single atom, molecule
fragments, functional groups, or monomers in a polymer. They are included in
the molecular description to help subdivide problems into manageable sizes and
easily reference pieces of the molecule.
Substructures are created and managed by SYBYL without intervention. For

example, when constructing a biopolymer from monomers defined in a
dictionary or reading one in from a standard biopolymer structural file such as
the Protein Data Bank, each monomer (residue) is always a substructure. An
example of the substructure assignment for a short peptide sequence is shown
below (substructure boundaries marked by parentheses).
In the case of non-polymers, the only control you have over the creation and
designation of substructures is in the order you construct the molecules or in
fragments chosen from the standard fragment library. All fragments in the
fragment library are designated as substructures. There is no unique assignment
of substructures to molecules. One person might assign them differently from
another. For example, the figure below shows two copies of a single molecule
which have been partitioned differently into substructures. Neither one is neces-
sarily a better choice than the other; they are merely different.


Formats for Specifying Objects
15.2 Formats for Specifying Objects

There are a number of general naming conventions and special symbols used to
denote the various objects in SYBYL.
Molecules Names can be arbitrarily long and complex, containing any

characters (alphanumeric, underscore,...). Enclose name in
double quotes (“ ”) if it starts with a numeric character, has
special characters, or a space.
Atoms, Sub- No limit on the number of characters in a name. Tripos rec-
structures, ommends 7 characters for atoms and substructures, and 31
Sets, Features for sets and features. Names must start with an alphabetic
character, but are case insensitive (characters are held inter-
nally in uppercase). Names may contain digits, underscores
(_), and apostrophes (') in any position after the first.
• CA CA12—Valid atom names
• 1C C(1)—Invalid atom names
Note: Only set names are required to be unique.
Chains Names are restricted to 4 characters and must start with an
alphanumeric character. If the name begins with an alpha-
betic character, the following characters can be A-Z, 0-9, _, $
or '. If the name begins with a numeric character, the follow-
ing characters must also be numeric. They may contain
underscores in any position after the first position and before
the last position.
* Match any number of characters of any type.
@ Match a single character of any type.
In addition to the conventions listed in the table above, there are also object-
specific protocols. These are discussed in the following sections:
• Atom Specification on page 229
• Bond Specification on page 230
• Substructure Specification on page 232
• Set Specification on page 232
• Molecule Specification on page 233
• Molecule Area Specification on page 233
• Monomer Sequence Specification on page 233
• Conformational Specifications on page 235

15.2.1 Atom Specification

When requested to supply an atom or group of atoms, several methods are
available:
Specify by: Note and Examples

ID Number Avoid using IDs, as they change if molecule is modified.
Name • HIS1.CA—CA atom in residue HIS1.
• HIS1.*—All atoms in substructure HIS1.*.
• *.CA—All atoms named CA in all substructures.
• *—All atoms in default molecule area.
• A*.C1—All atoms named C1 in substructures whose name
begins with A.
Type • <N.2>—All sp2 nitrogens.
• <O.*>—All oxygens (equivalent to O).
• <C*>—All carbons, plus any atom type beginning with a C
(e.g., calcium, chlorine, etc.).
Case insensitive. Modifier identifies different forms of same
element (not necessarily hybridization states).
See the Force Field Manual for list of predefined SYBYL atom
types.
Molecule • M1—All atoms in molecule area 1.
Area
Substructure • {PHENYL}—All atoms in substructure(s) named
and Set PHENYL.
• {5}—All atoms in substructure with group ID 5.
• {HELIX}—All atoms in set named HELIX.
• {HYDROPHOBIC}—All atoms in set named HYDRO-
PHOBIC.
• {HIS*}—All atoms in all histidine residues (same as
{HIS*}).
• {SPHERE(PHE20.CA, 10.5)}—All atoms in 10.5 Å sphere
around the α-carbon of residue PHE-20.
Substructures are searched first for name matches, then, if
none match, all forms of both local and global sets are
searched. Only sets with atoms as objects are valid.
Note: For macromolecules, a number in braces indicates
sequence number, which may differ from substructure ID.
Connected • C1:C10—All atoms on all paths from C1 to C10, inclusive.
Path • 5:8—All atoms on all paths from atom 5 to atom 8,
inclusive.
If rings are in path, all paths through rings are searched.
Note: Connected paths where end point atoms are members of
rings are ambiguous and may not produce desired selections.

Substructure • {PHE10:HIS25}—All atoms in all monomers of a

Path biopolymer chain from PHE10 to HIS25, inclusive.
• {1:10}—All atoms in all monomers of a chain from residue
1 to 10, inclusive.
Braces ({}) identify all atoms in substructures on the path, not
just atoms in bonded pathway.
Only monomers on direct backbone path between first and sec-
ond monomer are identified, even in presence of rings.
Note: Sets are not defined in terms of connectivity, only the
substructure name list is searched for matches to determine the
origin and targets of the scan.
Chain • A/HIS1.CA—CA atom in residue HIS1 of chain A.
Note: Only one chain specification per expression. Chain spec-
ification cannot be combined with single or range ID numbers
because IDs constitute unique identifiers.
See also the Atom Expression dialog to make your selection with the mouse.
15.2.2 Bond Specification

Several mechanisms exist for selection of bonds in a molecule:
ID Number Avoid, since IDs change if molecule is modified.

Name • CA—All bonds connected to the CA atom(s).
• O*—All bonds to atoms whose name starts with an O.
Name one or both endpoint atoms.
Type • <2>—All double bonds.
• <AR>—All aromatic bonds.
SYBYL bond types: single <1>, double <2>, triple <3>, aro-
matic <AR>, and amide <AM>.
Molecule • M1—All bonds in molecule area 1.
Area
Substructure • {MONTYPE(TYR)}—All bonds in substructure(s)/
and Set monomer(s) of type tyrosine.
• {5}—All bonds in substructure with group ID 5.
Substructures are searched first for name matches, then, if
none match, all forms of both local and global sets, are
searched. Only sets with bonds as objects are valid.

Substructure • {PHE10:HIS25}—All bonds in all monomers of a

Path biopolymer chain from PHE10 to HIS25, inclusive.
• {1:10}—All bonds in all monomers of a chain from residue
number 1 to residue 10, inclusive.
Braces ({}) identify all atoms in substructures on the path, not
just atoms in bonded pathway.
Only monomers on direct backbone path between first and sec-
ond monomer are identified, even in presence of rings.
Note: Sets are not defined in terms of connectivity, only the
substructure name list is searched for matches to determine the
origin and targets of the scan.
Chain • A/HIS1.CA—Bonds involving CA atom in residue HIS1 of
chain A.
Specific • C1=C10—Bond between atoms C1 and C10.
Bond • HIS1.CA=HIS1.CB—Bond between alpha (CA) and beta
(CB) carbons in residue HIS1 (Note: In this case, endpoint
atoms must be unique. This technique can only be used to
designate one unique bond.)
• 3=7—Bond between atoms whose IDs are 3 and 7.
Note: Atoms must be bonded directly to one another.
See also the Bond Expression dialog to make your selection with the mouse.

15.2.3 Substructure Specification

Substructure specification can be accomplished using several mechanisms
discussed in the following table.
Note: Enclosing a substructure’s name or ID in braces ({}) is only required

when specifying the name of a set to select the substructures of interest. This
forces both the substructure name list and set name list to be searched for
matches with the input name. Otherwise, only the substructure name list is
searched.
ID Number • For macromolecules—ID refers to monomer sequence (e.g.

15 in ALA15);
• For small molecules—ID refers to substructure ID.
A hash or pound sign (#) preceding a number is interpreted as
a substructure ID, even for macromolecules.
Name • {RING*} or RING*—All substructures whose name starts
with RING.
Name must start with an alphabetic character. Digits, under-
scores, or apostrophes may follow.
Substructure {PHE10:HIS25}
Path • In macromolecule, all monomers along direct backbone
path from PHE10 to HIS25.
• In small molecule or sequence numbers, all substructures
on all paths from PHE10 to HIS25.
Chain • A/ALA15—Substructure with name of ALA15 in chain A.
Set Name • {MONTYPE(ALA)}—All substructures that are monomers
of type alanine. MONTYPE is a built-in set.
Only sets with substructures as objects are valid and appear on
menu.
15.2.4 Set Specification

Braces ({}) are not necessary for set designation, but are accepted for consis-
tency (e.g., RING_A {HELIX_*})

15.2.5 Molecule Specification

A molecule’s full name, or a fraction thereof, and the wild character (*) can be
used. Enclose names that start with a numeric character, contain special
characters, or a space, in double quotes.
”alpha_chymotryp“
”active isome #3“
”5HT“
15.2.6 Molecule Area Specification

The default molecule area is the one in which you are normally performing all
operations. To perform operations on another molecule without changing the
default area (e.g., to measure intermolecular distances), specify the molecule
area before the expression, which is enclosed in parentheses:
M2(C3)
This example specifies all atoms named C3 in molecule area M2.
The molecule area name (M#) associated with a molecule remains the same
during a session.
15.2.7 Monomer Sequence Specification

Monomer sequence specifications can be divided into two categories, generic
and specific (see also the Sequence Expression dialog to make your selection
with the mouse).
Generic Monomer Sequences
A generic monomer sequence is a list of monomer names connected by an equal

sign (=). Monomer names may be given as the normal monomer name (1 to 4
characters long), or as the one character code, as defined in the macromol
dictionary.
gly=ala=phe
e=p=f
The sequence may contain numerical repeat counts to indicate repetition of a

sequence (the sequence to be repeated must be enclosed in parentheses).
2(arg)=val=phe=3(ser=cys)
is equivalent to:
arg=arg=val=phe=ser=cys=ser=cys=ser=cys
and also equivalent to:
arg=arg=val=3(ser=cys)

Specific Monomer Sequences
A specific monomer sequence is a sequence in the default molecule area. The

following forms are allowed:
mon=mon=mon= Connected linear sequence of monomers. * in

place of a monomer matches any monomer.
mon:mon:mon: Guided range of monomers. All monomers on a
direct path along the backbone of the biopolymer
between adjacent monomers are selected.
* The entire biopolymer.
molecule area(sequence) Sequence in stated molecule area.
“mon” may be:

• General monomer name matching any monomer of that type (e.g. phe)
• Specific monomer name detected by the presence of digits and matching
only a monomer with that exact name (e.g. phe27)
• Sequence number matching any monomer with that sequence number as
part of its name (e.g. 18)
• The < or > character matching the beginning and ending monomers of a
chain, respectively.
Note that monomer names, as defined in the dictionary, may not contain digits,
and each monomer in a molecule should contain a sequence number in its name
(usually indicating its position in the chain).
Sequence specifications can be combined by separating them with commas. To

specify a sequence on a particular chain of the biopolymer, prefix the specifi-
cation with the chain name followed by a slash (e.g. A/*). To specify a
sequence in a molecule area other than the default area, enclose the entire speci-
fication in parentheses, and prefix it with the molecule area (e.g. M3(glu3)).

As an example, consider the nucleic acid fragment:

a1=c2=g3=g4=u5=a6=c7=a8=g9
Entering this: Selects this:

g3:a6 g3=g4=u5=a6
a=c a1=c2, a6=c7
6:8 a6=c7=a8
* a1=c2=g3=g4=u5=a6=c7=a8=g9
c=*=g c2=g3=g4, c7=a8=g9
u,a1=c2 u5, a1=c2
7:> c7=a8=g9
A number refers to the monomer with that sequence number as part of its name
(e.g. 8 in GLY8). As a special case, to identify the monomer by its substructure
ID number, precede the ID number with a hash or pound sign (#). This is partic-
ularly useful when dealing with unresolved ends of protein chains.
15.2.8 Conformational Specifications

This type of data specification dictates the conformation of all or part of a
biopolymer. Conformational state names, or conformational angle names with
the angle value (in degrees) are both acceptable. Conformational states and
angles are defined in the dictionary. (Note: Only the minimum number of initial
characters of the name required to distinguish it from other conformational
states or angle names needs to be typed.)
Separate multiple specifications with commas. The formats for conformational

specifications are as follows:
• statename—Assigns angle values as defined in the given state.
• angle1=xxx,angle2=yyy—Alters the present angles to the specified
values.
Examples:
alpha_helix
alph
phi=-58.0,psi=-47.0
staggered,beta=120

The valid state names are given in the following table.
alpha_helix none three/10_helix

aturn pi_helix trans
beta_sheet random trans6
b_like random_12 turnI
c5 random_13 turnII
c7ax random_14 turnIII
c7eq random_16 turnVIa
cis ribbon_2_7 turnVIb
invaturn

Create Expressions
15.3 Create Expressions

Objects (atoms, bonds, etc.) can be combined, using standard operations, to
yield complex expressions.
When SYBYL prompts you for an object (atom, bond, etc.), you can use any of
the methods described in the previous section, which yields exactly one object
when interpreted. When you are prompted for an object expression, you may
enter a group of objects. Object expressions allow you to combine various
objects to produce a resultant set, which is the exact portion of the molecule that
you want to manipulate.
15.3.1 Logical Operators

Expressions can consist of the logical operators union, intersection, difference,
and negation (represented by the symbols + or comma, &, - and ~, respectively)
and the elements to which they are applied.
In the discussions which follow, an abstract definition of a logical operation is

given using A, B, and C as general object sets and D as the general resultant set.
The general form of the allowable expression is very similar to the algebraic
form of mathematical equations. Parentheses group the elements of the
expression for evaluation in a specified order.
The Venn diagrams below illustrate the logical operators. Shaded areas
represent the selected set D which results from the indicated operations. The
outer circle represents the total set from which the subsets are chosen.
Union Intersection Difference Negation

In either set In both sets In first set and Do not have speci-
not in second fied property
D=A+B or D=A&B D=A-B D=~A
D=A,B
Note: Since SYBYL uses spaces as delimitors between commands and

arguments, spaces are not allowed in expressions.

Create Expressions
Examples
Union
Locate all carbons and oxygens in a molecule and color them green.
COLOR ATOM <C>+<O> GREEN
Color all alpha carbons, other carbons, nitrogens, and oxygens red (these atoms
make up a peptide backbone).
COLOR ATOM CA,C,N,O RED
Intersection
Identify atoms in the active site of an enzyme and also in a helical secondary
structure:
LIST ATOMS {HELIX*}&{ACTIVE_SITE} BRIEF
This presumes that the sets {HELIX} and {ACTIVE_SITE} have been defined
previously.
Locate all carbons which have a partial charge between 0.0 and 0.10 in a
particular molecule and color them red.
COLOR ATOM <C>&{CHARGE(0.0,0.1)} RED
This example makes use of one of the built-in sets: {CHARGE}.
Difference
Color all atoms not in the backbone of a biopolymer yellow:
COLOR ATOM *-{BACKBONE} YELLOW
The asterisk selects all atoms and then the backbone atoms are subtracted.
{BACKBONE} is a built-in set defined for all polymers.
List all carbons not sp3 hybridized:

LIST ATOMS <C>-<C.3> BRIEF
Negation
Select sidechain atoms for a biopolymer, exclude backbone atoms:
COLOR ATOM ~{BACKBONE} YELLOW
This is functionally identical to the color command shown as the difference

operator example.

Create Expressions
15.3.2 Parentheses and Grouping of Operations

When grouping operations into more complex expressions, keep in mind that
intersection has a higher precedence than union, just as multiplication has
precedence over addition in algebra. Parentheses are used to force evaluation of
the expression in a particular order by grouping objects and operators.
Examples
Display only heteroatoms in a molecule, combine a union operation with a

negation operation:
DISPLAY ~(<C>,<H>)
Locate all carbons and oxygens which are in hydrophobic residues of a protein:
DISPLAY (<C>+<O>)&{HYDROPHOBIC}
The set {HYDROPHOBIC} must have been defined previously.

Chapter 16.
Sets in SYBYL
• Global Sets on page 243

• Local Sets on page 247
• Dynamic Sets on page 249
• Built-in Sets on page 251
• Static Sets on page 256
• Working with Sets on page 258
Some sets are closely associated with the particular molecules for which they
are defined (local sets), while others may be applied in a blanket fashion to any
molecule (global sets). Once applied to a particular molecule, the definitions of
all sets are stored in and retrieved from the database along with all other
molecular data.
When you reference a set name in the context of a command, the members of
the defined set are automatically identified as the object of the action. If the
request is for atoms or bonds, the specified substructures are expanded to their
respective atom or bond constituents automatically.
The diagram below shows sets used in SYBYL and their interrelationships.
• Global Sets on page 243—Set whose definition is applicable on a

system-wide basis, i.e., it may be applied to any molecule.
• Local Sets on page 247—Created for specification of objects in a
particular molecule. Membership is associated only with that molecule.
• Dynamic Sets on page 249—Uses a rule to define membership.
Membership is determined when it is referenced, by interpreting the
expression in the context of the current molecular description. Both local
and global sets can exhibit dynamic properties.

Chapter 16. Sets in SYBYL
• Built-in Sets on page 251—Always a dynamic global set and based on

properties or geometrical relationships which are subject to change. Can
be applied to atoms, bonds, or substructures.
• Static Sets on page 256—Membership is identified at the time of set
definition.
• Aggregates—Local sets, always static, and user-defined. If defined by a
dynamic rule, it is immediately evaluated and membership becomes
static. Aggregates are recognized by the minimizer as groups of atoms
and bonds whose relative geometry is not to be optimized. (See the
discussion of Aggregates in the Force Field Manual for additional infor-
mation.)
• User-Defined Sets—Either dynamic (local or global) or static sets
created by the user. Global sets defined by the user are always dynamic
and are used exactly as those carried in the macromol dictionary. In
some cases, a set can be defined equally well as static or dynamic,
depending upon whether membership is likely to change during the
course of the project. For example:
• Alpha_helical region of a peptide.
• Chair and boat conformations of six-membered rings in a polycyclic
structure.
• Charge range for atoms carrying an electrostatic charge between the
values of 0.1 and 0.5 esu.

Global Sets
16.1 Global Sets

Global sets are dynamic sets not directly associated with any specific molecule.
They may be defined at any time and can be applied to any molecule. They are
always of the dynamic type. By their very nature they cannot include specific
objects. Once applied to a particular molecule, they are copied to that
molecule’s set list and remain associated with it, unless explicitly deleted. For
example, the definition of POSITIVELY_CHARGED.
Global sets which are built into the program are typically defined in the
macromol dictionary. (See Global Sets in the macromol Dictionary on page
245.) When the dictionary is opened, sets are available for use automatically.
• Define a Global Set on page 243
• Modify a Global Set on page 244
• Remove a Global Set on page 244
• Global Sets in the macromol Dictionary on page 245
16.1.1 Define a Global Set

DEFINE GLOBAL_SET object_type object_expr name comment
object_type Class of object to be members of set: ATOM, BOND or SUB-

STRUCTURE.
object_expr Set of objects of indicated class (evaluated only when set is
referenced).
name Name for set. Must be unique. First character must be alpha-
betic and a maximum of 30 additional characters must be
alphanumeric or underscores (_).
comment Arbitrary string associated with set.

Global Sets
16.1.2 Modify a Global Set
Menubar: Build/Edit >>> Modify >>> Set

Create/Modify MODIFY GLOBAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
quotes when entering spaces or special characters.
Change Defini- MODIFY GLOBAL_SET DEFINITION set_expr
tion via Com- {object_exp}
mand Line: • set_expr—Expression indicating set to modify.
• object_expr—Rule for determining membership of the
dynamic set.
Global sets must be dynamic, hence the definition must be
in terms of a general expression rather than specific mem-
bers. The class of objects selected by a global set cannot
be altered by this procedure, only the definition.
Note: If a global definition is modified, it is modified in all instances associated

with the molecules in memory. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, modification of the global set of the same name
does not affect the local copy.
16.1.3 Remove a Global Set

REMOVE GLOBAL_SET set_expr
set_expr Expression indicating set to remove, may include the wild-

card character (*). For example, to remove both g1 and g2,
enter g* or the expression g1,g2.
Note: If a global definition is deleted, its copies associated with the molecules
in the work areas are also deleted. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, deletion of the global set of the same name does not
affect the local copy.

Global Sets
16.1.4 Global Sets in the macromol Dictionary

Although you can define a new global set as it becomes necessary, several
global sets are already associated with the macromol dictionary and automati-
cally become available for use when the dictionary is opened.
The table below provides a complete listing of global sets currently available in
the macromol dictionary, accompanied by objects to which they apply and a
defining expression explaining how the various sets were created.
Name Objects Defining Expression
ACIDIC Substs {MONTYPE(asp,glu,tyr)}

BASIC Substs {MONTYPE(his,arg,lys)}
BLOCK Substs {MON-
TYPE(ace,nme,pyr,amd,for,nmt,nmm,cme,mes
,ees,boc)}
BULKY Substs {MONPROP(MOL_WT,140,9999)}
CALPHA Atoms CA
CAP Substs {MONTYPE(amn,cxl,ami,cxc)} for proteins
{MONTYPE(hb,he)} for DNA and RNA
DISULFIDE Bonds sg-cb-hg-lpg1-lpg2,sd-cg-hd-1pd1-1pd2
DNA Substs {MONTYPE(dA,dG,dC,dT)}
HYDROPHOBIC Substs {MONTYPE(gly,ala,ile,leu,met,phe,pro,
trp,val)}
MOD_AA Substs {MONTYPE(abu,aib,arz,asz,bal,cym,cyx,glz,
hcx,hcy,hid,hie,hip, hpr,hse,hyp,lyz,nle,nva,
orn,orz,phg,pse,psm,psz,ptm,pty,ptz)}
NEUTRAL Substs {MONTYPE(tyr,his,asn,cys,gln,ser,thr)} +
{HYDROPHOBIC}
POLAR Substs {MONTYPE(asp,glu,tyr,asn,gln,thr,ser,cys,
his,lys,arg)}
PURINE Substs {MONTYPE(dG,dA,rG,rA)}
PYRIMIDINE Substs {MONTYPE(dC,dT)} for DNA
{MONTYPE(rC,rU)} for RNA
RNA Substs {MONTYPE(rA,rG,rC,rU)}

Global Sets
Name Objects Defining Expression
STD_AA Substs {MONTYP(ala,arg,asp,asn,cys,glu,gln,gly,his,

ile,leu,lys,met,phe,pro,ser,thr,trp,tyr,val)}
SUGAR Substs {MONTYPE(glb,mab,maa,gaa,gab,frb,fra,dra,
drb,rba,rbb)}

Local Sets
16.2 Local Sets

Membership is associated only with that molecule. Local sets may be defined
by any user at any time. An example is the definition of ACTIVE_SITE.
• Modify a Local Set on page 247
• Remove a Local Set on page 248
16.2.1 Modify a Local Set
Menubar: Build/Edit >>> Modify >>> Set

Create/Modify MODIFY LOCAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
quotes when entering spaces or special characters.
Change Defini- MODIFY LOCAL_SET DEFINITION set_expr
tion via Com- {object_expr [merge]}
mand Line: • set_expr—Expression indicating set to modify.
• object_expr—Membership (for a static set) or rule for
determining membership (for a dynamic set).
• merge—NO/YES, for static sets only, whether to add to
or replace current definition.
For dynamic sets, there is no merge option; they are com-
pletely redefined by this command.
Change Name via MODIFY LOCAL_SET NAME set_expr {name}
Command Line: • set_expr—Expression indicating set to modify.
• name—Name for set.
First character of set name must be alphabetic and may be
followed by up to 30 additional characters, including
alphabetic, numeric, and the underscore (_). Names must
be unique among all other (GLOBAL or LOCAL) sets and
also among substructures.
Note: Aggregates are local sets and their description can be changed using this
command.

Local Sets
16.2.2 Remove a Local Set

When an atom or a bond involved in a static local set is removed from the
molecule, the set membership is automatically updated.
Menubar: Build/Edit >>> Delete >>> Set

Command REMOVE LOCAL_SET set_expr
Line: • set_expr—Expression indicating set to remove, may
include wildcard character (*). For example, to remove
both s1 and s2, enter s* or the expression s1,s2.

Dynamic Sets
16.3 Dynamic Sets

• Define a Dynamic Set on page 249
• Dynamic Set Example on page 249
• Manage Dynamic Hydrogen Bonds on page 250
A dynamic set is a group of objects whose membership is evaluated dynami-

cally (only when the set name is used in a command or is referenced by an
application routine). A standard object expression is analyzed at the time of
reference to determine the current set of objects meeting the requirements of the
expression. The expression must be valid for the type of object the set is to
contain.
Because objects are not permanently assigned to a set of this type, dynamic sets
are most often used to monitor properties of molecules which are subject to
change, such as conformation, charge, strain energy among many others.
16.3.1 Define a Dynamic Set
Menubar: Build/Edit >>> Define >>> Dynamic Set

Command DEFINE DYNAMIC_SET object_type object_expr
Line: name comment
• object_type—Class of object to be members of the set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class, to
include in set (evaluated only when set is referenced).
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 more characters (alpha-
numeric or underscores (_)).
• comment—Comment string.
16.3.2 Dynamic Set Example

To define all substructures (monomers) within 10 Å of atom C1 in residue A17
as members of the set called ACTIVE_SITE:
DEFINE DYNAMIC_SET SUBSTRUCTURE {SPHERE(A17.C1,10)} \
active_site “10Å radius around A17”
If the atoms are manipulated (e.g., conformations are modified), membership in
this set can change.
To color the atoms that are members of the dynamic set ACTIVE_SITE:
COLOR ATOM {active-site} MAGENTA

Dynamic Sets
The membership is evaluated at the time of reference according to the definition

rule. Substructures belonging to the set are expanded into their constituent
atoms for the execution of the command.
16.3.3 Manage Dynamic Hydrogen Bonds

Color H-Bonds
Dynamic H-bonds, since they are created via AUTOMONITOR, are treated as
monitor lines. The color of the line changes with the distance between the
atoms: red if less than a minimum value; yellow if within a certain range, and
no line is drawn if farther apart than a maximum distance. The minimum and
maximum values are specified by the tailor variables HBONDS MIN_DISTANCE
and HBONDS MAX_DISTANCE, respectively.
Delete H-Bonds
To delete dynamic H-bonds, you must turn automonitoring off by selecting
VIEW >>> AUTOMONITOR >>> AUTOMONITOR >>> ALL_OFF.
Resize H-Bonds
Dynamic H-bonds (created using VIEW >>> DISPLAY H-BONDS >>>
DYNAMIC (or the AUTOMONITOR HBOND command) cannot be resized.

Built-in Sets
16.4 Built-in Sets

The membership of a built-in set is subject to change through the use of SYBYL
and must be determined at the time it is referenced. Built-in sets may not be
created, removed, or altered by the user.
Built-in sets differ from the general dynamic set types:

• Evaluation rules are built into the program.
• May require one or more arguments to direct their evaluation. Required
arguments are specified in parentheses after set name, separated with
commas. For example, {SPHERE(C2,5)} specifies all atoms within 5 Å
of atom C2.
Note: Atomic weights correlate with the latest accepted figures from IUPAC
and NIST. The average difference is 0.01% of the old values. In the cases of
unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem., Vol.75, No.8, pp 1107-1122, 2003.
• National Institutes of Standards and Technology (NIST)
• SYBYL Atom Types in the Tripos Force Field manual.
The table below contains a complete listing of built-in sets currently available in
SYBYL, the forms in which they are invoked (commands and arguments
required, if any), explanations, and examples.
AROMATIC {AROMATIC(atom_expression)}
• Atoms Atoms in the same aromatic system as the specified
atom(s).
LIST ATOM {AROMATIC(9)} BRIEF
BACKBONE {BACKBONE}
• Atom Set Atoms belonging to the backbone as defined in the macro-
mol dictionary.
COLOR ATOM {BACKBONE} RED
• Bonds {BACKBONE}
Bonds belonging to the backbone as defined in the macro-
mol dictionary.
SCAN {BACKBONE}

Built-in Sets
BUMPS {BUMPS(atom1,atom2)}
• Atoms Atoms in one group having van der Waals contacts with
atoms of the other group. van der Waals parameters stored
in the file $TA_ASCTABLES/ATOM_DEF are used.
Use TAILOR SET GENERAL
BUMPS_CONTACT_DISTANCE to define the cutoff dis-
tance. Negative values allow overlap of van der Waals
spheres, positive values prohibit it. Default is -0.16 Å.
COLOR ATOM {BUMPS(atom1,atom2)} MAGENTA
CHARGE {CHARGE(minimum,maximum)}
• Atoms Atoms having a residual charge in the specified range.
COLOR ATOM {CHARGE(-.05,-.01)} BLUE
CHIRAL {CHIRAL(atom_expression,RS)}
• Atoms Atoms of the specified chirality or pro-chirality. Specify
the atoms to search as an expression. Chirality is indicated
by the second argument as: R, S, RS, PRO_R, PRO_S, or
PRO_RS. If RS or PRO_RS is entered, all centers are
included in the set. The default is to search all atoms (*)
for all chiral centers (RS).
COLOR ATOM {CHIRAL(CA,S)} YELLOW
FINDCONF {FINDCONF(state1+state2+,sequence)}
• Substructures Monomers having the specified conformational state(s) as
defined in the macromol dictionary. Entering a sequence
limits the search to the specified regions of the biopolymer
(“*” searches whole biopolymer). Separate conformational
states by plus signs.
LABEL SUBSTRUCTURE {FINDCONF(ALPHA_HELIX,*)}
HBOND {HBOND(atom_expression,type)}
• Atoms Atoms of the specified type participating in hydrogen
bonds. Valid types include: ALL, DONOR, ACCEPTOR, or
HYDROGEN. Definitions for the donor and acceptor atoms
are in the parameter table $TA_ASCTABLES/ATOM_DEF
as H_ACCEPTOR and H_DONOR fields.
LIST ATOM {HBOND(1+2+3+4+5+6,donor)} BRIEF

Built-in Sets
MONPROP {MONPROP(keyword,minimum,maximum)}
• Substructures Monomers having the specified property as identified by a
keyword and (optional) minimum and maximum values.
Enter only the keyword to select all monomers having that
keyword. Enter the keyword and a minimum to select
monomers with the keyword whose value matches the
minimum. The keyword may be any arbitrary string. Val-
ues may be real, integer, or string. Properties are stored in
the macromol dictionary (molecular weight is stored as
MOL_WT).
LABEL SUBSTRUCTURE {MONPROP(MOL_WT,150,200)}
MONTYPE {MONTYPE(type1,type2,...)}
• Substructures Monomers of the specified type(s). Types are defined in
the macromol dictionary. As many types as desired may
be specified as arguments. An asterisk (*) specifies all
substructures that are monomers.
LABEL SUBSTRUCTURE {MONTYPE(A,T)}
POSSIBLE_HBON {POSSIBLE_HBOND(atom_expression,type)}
D Atoms of the specified type which can potentially partici-
• Atoms pate in hydrogen bonds. Valid types include:
• ALL
• DONOR—Potential H bond donor atom, attached to a
hydrogen or has at least one free valence.
• ACCEPTOR—Potential H bond acceptor.
• HYDROGEN—Hydrogen attached to an H bond donor.
LIST ATOM {POSSIBLE_HBOND(*,all)} BRIEF
RINGS {RINGS(atom_expression,type)}
• Atoms Specified atoms which are included in rings of the speci-
fied type. Types include:
• I—Internal rings (completely contained within a
substructure).
• E—External rings (crossing substructure boundaries).
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to {rings(*,EI)}.
COLOR ATOM {RINGS(*,E)} BLUE
• Bonds {RINGS(bond_expression,type)}
Specified bonds which are included in rings of the speci-
fied type. Types include:
• I—Internal rings (completely contained within a
substructure)
• E—External rings (crossing substructure boundaries)
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to {rings(*,EI)}.
COLOR BOND {RINGS(*,I)} RED

Built-in Sets
• Substructures {RINGS(substructure_expression,type)}
Substructures in the expression, which are included in
rings of the specified type.
COLOR SUBSTRUCTURE {RINGS(*,E)} YELLOW
SEQUENCE {SEQUENCE(sequence1,sequence2,)}
• Atoms Atoms in monomers of the specified sequence(s). Mono-
mers are defined in the macromol dictionary. See Mono-
mer Sequence Specification on page 233 for information
on how to select specific monomer sequences.
COLOR ATOM {SEQUENCE(GLY=PRO,GLY=GLY)} BLUE
COLOR ATOM {SEQUENCE(A/1:25)} RED
COLOR ATOM {SEQUENCE(<,>)} MAGENTA
• Bonds {SEQUENCE(sequence1,sequence2,)}
Bonds in monomers of the specified sequence(s). Mono-
mers are defined in the macromol dictionary.
SCAN {SEQUENCE(GLY=PRO)}
• Substructures {SEQUENCE(sequence1,sequence2,)}
Monomers in the specified sequence(s). Monomers are
defined in the macromol dictionary.
LABEL SUBSTRUCTURE {SEQUENCE(A=T=C,T=*=U)}
SIDECHAIN {SIDECHAIN}
• Atoms Atoms belonging to sidechains as defined in the macromol
dictionary.
COLOR ATOM {SIDECHAIN} RED
• Bonds {SIDECHAIN}
Bonds belonging to sidechains as defined in the macromol
dictionary.
SCAN {SIDECHAIN}
SPHERE {SPHERE(atom_expression,radius)}
• Atoms Atoms falling within sphere(s) of the specified radius. The
expression defines the sphere center(s). When multiple
atoms are selected, the final set is the union of sets of
atoms within spheres of indicated radius about each cen-
ter. All spheres have the same radius.
COLOR ATOM {SPHERE(ALA23.CA,10)} MAGENTA
• Bonds {SPHERE(atom_expression,radius)}
Bonds falling within sphere(s) of the specified radius. The
expression defines the sphere center(s). When multiple
atoms are selected, the final set is the union of sets of
bonds within spheres of indicated radius about each cen-
ter. Note: Only bonds with both endpoint atoms in the
sphere are accepted. All spheres have the same radius.
SCAN {SPHERE(N15,8)}

Built-in Sets
• Substructures {SPHERE(atom_expression,radius)}
Substructures falling within sphere(s) of the specified
radius. The expression defines the sphere center(s). When
multiple atoms are selected, the final set is the union of
sets of substructures within spheres of indicated radius
about each center. Note: Substructure is accepted, even if
only one of its atoms falls within the sphere. All spheres
have the same radius.
LABEL SUBSTRUCTURE {SPHERE(G16,12)}
SUBST_SPHERE {SUBST_SPHERE(atom_expression,radius)}
Atoms, bonds, or substructures falling within sphere(s) of
the specified radius. The expression defines the sphere
center(s). When multiple atoms are selected, the final
SUBST_SPHERE set is the union of sets of substructures
included in spheres of indicated radius about each center.
Note: Substructure is accepted, even if only one of its
atoms falls within the sphere (identical to sphere for sub-
structures).
TO_ATOMS {TO_ATOMS(atom_expression)}
• Bonds Bonds with one or both atoms in the specified expression.
SCAN {TO_ATOMS(CA)} CYAN

Static Sets
16.5 Static Sets

• Define a Static Set on page 256
• Manage Static Hydrogen Bonds on page 257
Membership of a static set is determined by a standard object expression

analyzed at the time of definition. Once specified, this membership does not
change unless one of the elements is deleted from the molecule. In this case, it
is automatically removed from the set as well and the membership is redefined.
With the exception of set members deleted from the molecule, every time you
reference a static set, the same elements are selected. Only local sets can have
static properties.
The latitude with which you can define members of a static set provides great
flexibility in the manipulation of molecular data. For example, static sets can
define:
• Active site portion of an enzyme (select atoms or monomers involved)
• Diene and dienophile portions of a molecule designed to undergo an
intramolecular cyclo-addition reaction
• Glycone and aglycone portions of a nucleoside
• Acyclic precursor region of what becomes part of a larger structure upon
cyclization
In addition, in SYBYL’s Biopolymer and COMPOSER programs, static sets are

automatically generated when molecules are read in from Protein Data Bank
files.
16.5.1 Define a Static Set
Menubar: Build/Edit >>> Define >>> Static Set

Command Line: DEFINE STATIC_SET object_type object_expr
name comment
• object_type—Class of object to be members of set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class,
to include in set. object_expr is not retained with set
definition.
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 additional characters
(alphanumeric or underscores (_)). Default is the
current name plus and underscore and number.
• comment—Comment string. If you modify the set, the
default comment is the current comment plus _new.

Static Sets
16.5.2 Manage Static Hydrogen Bonds

Color H-Bonds
The color of static H-bonds is specified at the time of creation. To recolor them:
¾ Select View >>> Backgrounds >>> Color.
¾ Specify the appropriate background (normally named Hbonds).
¾ Select the new color.

Note: Every time you select View >>> Display H-BONDS >>> STATIC a
new background containing H-bonds is created and colored as specified.
Delete H-Bonds
Static H-bonds are treated as backgrounds and can be deleted in the same way
as any background.
Resize H-Bonds
Static H-bonds (created using VIEW >>> Display H-Bonds >>> Static or the
HBONDS command) can be resized:
¾ Select Options >>> Tailor
¾ Select Graphics.
¾ Change BKG_LINEWIDTH to a larger number.
¾ Press Apply button and the bonds are resized (press Close).

Working with Sets
16.6 Working with Sets

When you modify, list, or remove sets, SYBYL displays a Set selection dialog,
if an expression is not specified on the command line. Click the molecule in the
list and use the selection tools to specify the desired sets to modify, list, or
remove. Highlighting a set in the list also highlights the atoms in that set in the
SYBYL window.
The example below shows the Set selection dialog for List Local Sets.
Select a molecule: Select the molecule area and molecule from the list.
Select all sets: Click Select All
Invert selection: Click Invert
Remove selection: Click Clear

Chapter 17.
Libraries of Chemical Groups and Fragments
SYBYL provides functional groups and fragments that allow you to easily build
most molecules. In some instances, however, you may need to have
additional fragments included in the standard library. These operations
can be accomplished once you know a little about the SYBYL file structure.
In this section, you will find:

• Group Library Structure and Contents on page 260
• Fragment Library Structure and Contents on page 261
• Using the Fragment Library (Refer to the FRAGMENT command)

Chapter 17. Libraries of Chemical Groups and Fragments
Group Library Structure and Contents
17.1 Group Library Structure and Contents

As supplied by Tripos, the group library contains a variety of small functional
groups frequently used in the construction of molecules. Each functional group
is represented as a distinct molecule within a SYBYL database:
ALLYL AMIDE BENZYL

CN CO CO2
CO2MINUS CS CYCLOHEXYL
EPOXY ETHYL ISOPROPYL
N-AMIDE N-BUTYL N-N
N-PROPYL N3 N=N
NH2 NO NO2
OCO OH ONO
OO PHENYL SEC-BUTYL
SH SO SO2
SO2N SO2O T-BUTYL
VINYL
For convenience, the molecules in the library are given these same names.
Each group has a unique attachment point, internally equal to the root atom of
the root substructure of the molecule. Externally, a convention has been estab-
lished which identifies the attachment point as the first atom in the molecule
name (except for Phenyl). The internal convention must be observed for all
user-added groups in order for commands like ADD GROUP to function properly.

Fragment Library Structure and Contents
17.2 Fragment Library Structure and Contents

As supplied by Tripos, the fragment library contains approximately 200 small
molecules (fragments) which can be used to build organic molecules with good
initial geometries. Each fragment is the result of averaged crystallographic
observations (i.e., averaged geometries from the Cambridge data file).
The library is organized in a hierarchical fashion, using both “sets” and

“classes”. If you are unfamiliar with this terminology, read about database
grouping mechanisms in Organize Molecules into Groups (Sets and Classes) on
page 193.
The basic idea is that each molecule in the fragment library is a member of one
(or more) static database sets. These sets form the lowest level of the hierarchy,
and group together those molecules which are very closely related in structure
and/or function. At higher levels of the hierarchy, those molecules related in a
more general sense appear in the same group. This produces a structure which
looks like an inverted tree, with general categories at the top diverging into
more and more specific categories until, at the bottom, a single molecule is left.
For example, one of the high-level categories is “Cyclic Systems”—clearly a

very general grouping. From this category you may descend to heterocyclic
systems with two rings, then to those with one heteroatom, then to 56 ring
systems. At this point you reach the lowest level categories, those consisting of
static sets of actual molecules where, in this case, you would find indole or
benzofuran.

The lowest level groups—those which contain the actual molecules—are static
sets, while all higher level categories are dynamic classes, defined as the union
of those groups directly under them. Thus the “56 Systems” are contained in a
static set, such as FIVESIX, but the group which corresponds to “1 Heteroatom”
in the above diagram is a dynamic class defined as the union of FIVESIX and
SIXSIX (FIVESIX+SIXSIX). Similarly, “Heterocyclic 2 Rings” is a dynamic
class defined as the union of “1 Heteroatom”, “2 Heteroatoms” and “>2
Heteroatoms”.
Tripos’ standard fragment library contains about 200 molecules partitioned into
44 static sets, and categorized into a hierarchy comprised of 17 dynamic classes.
Below is the full listing of sets and classes provided by Tripos to organize the
fragment library. In the listing, the dynamic classes are represented in italic
script, all others are static sets.

A: Acyclic Functions
• AA: Carbon Only
• AB: Function N
• AC: Function O
• AD: Function S
• AE: Function NO
• AF: Function SO
• AG: Function PO
• AH: Other
B: Cyclic Functions
• BA: Homocyclic, 1 Ring
BAA: Saturated
BAB: Unsaturated, 1 Double Bond
BAC: Unsaturated, 2 Double Bonds
BAD: Unsaturated, >2 Double Bonds
BAE: Aromatic
• BB: Homocyclic, 2 Rings
BBA: Saturated
BBB: Unsaturated
• BC: Homocyclic, 3 Rings
• BD: Homocyclic, 4 Rings
BDA: Steroids
BDB: Other
• BE: Heterocyclic, 1 Ring
BEA: 1 Heteroatom
• BEAA: 5 Membered Ring, Saturated
• BEAB: 5 Membered Ring, Unsaturated
• BEAC: 6 Membered Ring, Saturated
• BEAD: 6 Membered Ring, Unsaturated
• BEAE: Other
BEB: 2 Heteroatoms
• BEBA: 5 Membered Ring, Saturated
• BEBB: 5 Membered Ring, Unsaturated
• BEBC: 6 Membered Ring, Saturated
• BEBD: 6 Membered Ring, Unsaturated
BEC: >2 Heteroatoms
• BF: Heterocyclic, 2 Rings

BFA: 1 Heteroatom
• BFAA: 56 Systems
• BFAB: 66 Systems
BFB: 2 Heteroatoms
• BFBA: 56 Systems
• BFBB: 66 Systems
BFC: >2 Heteroatoms
• BG: Heterocyclic, 3 Rings
BGA: 1 Heteroatom
• BGAA: 656 Systems
• BGAB: 666 Systems
• BGAC: 676 Systems
BGB: 2 Heteroatoms
• BGBA: 666 Systems
• BGBB: 676 Systems
BGC: >2 Heteroatoms
C: Amino Acids
D: Nucleic Acids
• DA: Bases
• DB: Ribose Monophosphate
E: Biologically Important Molecules
• EA: Vitamins
• EB: Sugars
• EC: Lipids

SYBYL Basics Index
A Attach
chain 95, 104
Abort
Attributes
a command 31 remove
Access help 28 from atom 101
Acidic global se 245 from bond 103
from stereo atom 108
Add
atom 94
from stereo bond 108
bond 101 Automatic command execution 34
chain 95 Average molecule 113
features and constraints 122
group 104
hydrogens 96 B
rawatom 95 Backbone
ADD_PSEUDOATOMS 96 built-in set 251
Aggregate Basic global set 245
sets 242 Basics
ALLMOLS 32 introduction 9
Alternate atom types 98 Bibliography
Amide bond 230 chirality assignment 106
SHAKE algorithm 113
Amino acid
global sets 245 BIOPOLYMER
sets 245
Angle
between planes 129 Block
measure 128 global set 245
modify 103 Bond
Aromatic bond 230 add 101
angle list 163
Aromatic built-in set 251 attributes 106
Atom definition of types 137
add 94 expression rules 230
chirality attribute 106 length
expression rules 229 list 163
modify 97 naming conventions 230
naming conventions 229 remove 103
rawatom 95 selecting 133
remove 100 stereo attributes 106
renumbering 121 SYBYL object definition 224
selecting 133 type
SYBYL object definition 224 modify 102
Atom expression select by 140
dialog 135 Bond expression
Atom types dialog 135
alternate set 98 Boolean operators
modify 98 select using 141
select by 140 Building
Atomic coordinate small molecule 87
topography 163 Built-in sets 251
SYBYL 7.3 SYBYL Basics Index-265

Bulky global set 245 Connectivity
Bumps quick bonds 101
built-in set 252 Continuous Drawing Mode
Cancel point of attachment 88
C Conventions (see Names)

Coordinates
C-alpha carbon global set 245
list 163
Cambridge MODIFY 97
read/write CSSR files 54
Copy 61
Cap global set245 molecule area contents 61
CAPTURE 219 Creating
Center of mass 115 small molecules 87
Centroid 116 Customize
start up 34
CGQ prompt 41
Chain
of atoms 95 D
Change DATABASE 205
molecule name 109, 194 Database
substructure name 105 add molecules 192
Charge classes 193
built-in set 252 close 186
modify 97 copy contents to new database 185
CHIRAL 106 copy database directories 173
create empty database 184
Chiral built-in set 252 create table 191
Chirality DATABASE command list 205
atom attribute 106 define alias 185
check 75 define class or set 194
invert 107 example 175
select by 141 delete 193
Class deleting database directories 173
define in a database 193 get a molecule 190
grouping mechanisms 193
Clear the screen 167 list
Close SYBYL 27 contents of open database 187
Collect commands into a file 218 molecule and group information 187
open databases 187
Color open 184
dynamic hydrogen bonds 250 rename 194
static hydrogen bonds 257 reorganize contents 195
Command mode 30 save as 192
default values 31 save to MOL2 or MOL file 196
special characters 31 search 191
Commands example 178
basics list 7 sets 193
show status 187
Conformation specify default database 185
naming conventions 235 tutorial 174
SCAN 113 unlocking 181
valid state names 236
dbtranslate Unix utility
Index-266 SYBYL Basics SYBYL 7.3

see UNITY manuals 245
Disulfide global set
use in MACCS conversion 53 DNA global set 245
dbunlock Unix utility 181 Double bond 230
DCL 42 Dummy atom 115, 116, 119, 120
Default molecule area 60 Dynamic set 249
Defining (see also Local sets)
center of mass 116 SYBYL object definition 225
centroid 116
dynamic set 249
extension point 117 E
global set 243 Edit
line 118 text files 55
normal 119
plane 120
End SYBYL 27
static set 256 Environment variable
UNITY features 122 SAVE_SESSION_DIR 208
TA_HIDE_UNLICENSED_PRODS 36
Deleting
all atom attributes 101 Evaluating
all bond attributes 103 center of mass 116
atom 100 centroid 116
bond 103 extension point 117
center of mass 116 line 118
centroid 117 normal 119
dynamic hydrogen bonds 250 plane 120
extension point 117 Exit
global set 244 SYBYL 27
line 118
Extension point 117
local set 248
molecule in a database 193 External ring
non query atoms 122 SYBYL object definition 225
normal 119 Extract structures
plane 120 from molecule area 61
static hydrogen bonds 257
stereo atom attributes 108
stereo bond attributes 108 F
substructure 106 Features
SYBYL session 216 center of mass 115
UNITY feature 123 centroid 116
Difference extension point 117
operator line 118
in a database 188 normal 119
in object expressions 237 plane 120
Dipole moment 131 SYBYL object definition 224
UNITY 122
Directory
list database contents 187 File formats
.demo file 221
Display area 58
diagram 59 File selection dialog 46
Distance Files
measure 128 edit 55
modify 102 reading/writing
CSSR 54

SD file 53 color, delete, resize 250
SLN 52 static
Files created color, delete, resize 257
CAPTURE 219 Hydrogens
COLLECT 218 add 96
DATABASE 184 Hydrophobic
WRITE_FILE2 196 global set 245
FILES
CSSR 54
MOL2 and MOL 48 I
SD files 52, 53
Information
Fill valences 96 report on atom, bond, or substructure 162
Findconf built-in set 252 Interacting
FRAGMENT 85 with SYBYL 11
Fragment Internal ring
library 261 SYBYL object definition 225
access from sketcher 91 Intersection operator
structure and contents 261 in a database 188
Freeze in object expressions 237
coordinates before merging 62 Invert chirality 107
Fuse ring 110
tutorial 78
J
Join
G groups or molecules 112
Geometry Journal
measure 127 COLLECT command 218
modify 103 PHOTO command 219
Global
dictionary set 245
set 243
K
Grid Kollman atom types 98
SKETCH 92 display 99
Group library 260

add 104 L
SKETCH 92
Libraries 259
structure and contents 260
License requirements
SYBYL basics 9
H Line 118
Hardcopy 165 List
Hbond built-in set 252 object information 164
Height measurement 128 Load molecule 15, 45
Help 28 commands 50
special characters 31 fragment library 16
Hide menu options 36 Local set 247
Hydrogen bonds Log out of SYBYL 27

dynamic Logical operators in object expressions

difference 237 local set 247
grouping 239 molecule 109
intersection 237 substructure 105
negation 237 torsion 103
union 237 UNITY feature 123
Lone pair MOL 50
MODIFY 97 write multiple files 196
LQSample database 173 MOL2 50
Molecular Spreadsheet
M MACCS file conversion 53
Molecule
MACCS
build 69
convert to molecular spreadsheet 53 defining features 115
convert to UNITY hitlist 53
deleting in a database 193
read into SYBYL 52
evaluating features 115
write from SYBYL 52
expression rules 233
Manage extracting atoms 61
SYBYL session 207 modify 69, 109
MARK_RS isomerism 106 naming conventions 233
reading files 45, 46
MARK_ZE isomerism 106
save 48
Markush 124 save as 21
Measure save in a database 192
angle 128 selecting 133
distance 128 split 100
height 128 type 110
plane angle 129 writing files 45, 46
torsion 128 Molecule area
UNITY features 130 default 60
Menubar 36 naming conventions 233
command 30 rules 58
shortcuts 38 SYBYL object definition 224
Merge 62 Molecule expression
atoms 62 dialog 135
exceptions 62 Monomer
merging features 62 select by type 140
non-unique atom 62, 64 sequence expression rules 233
non-unique atoms example 65 sequence naming conventions 233
set 64
Monprop built-in set 253
source area 62
structures 62 Montype built-in set 253
target area 62 MREAD 50
unique atom 62
MODE 32 N
Modified amino acid global set 245
Name
Modify atom 229
angle 103 modify 97
atom 97 bond 230
bond 102 chain 234
distance 102 conformation specification 235
global set 244

general conventions 228 Printing 165
local set 247 PRO RS isomerism 106
molecule area 233
molecules 233 Purine global set 245
monomer sequence 233 Pyrimidine global set 245
generic 233
specific 234
set 232 Q
substructure 232 Query expressions 188
NCI_2000 database 173 QUICKBOND command 101
Negation operator Quit 27
in a database 188
in object expressions 237
Neutral global set 245
R
Non-bonded Radius
list 163 select within 141
Normal 119 Rawatom, adding 95

Notebook RDBMS 197
COLLECT command 218 46
Read file dialog
PHOTO command 219 Read molecule 45
commands 50
O fragment library 16
Read/save database molecules 196
Object
definitions 224 Recording
picking mode 33 COLLECT command 218
PHOTO command 219
Open molecule file 45
Recover contents of molecule area 168
Operator
difference 188, 237 References
grouping 239 chirality assignment 106
intersection 188, 237 SHAKE algorithm 113
negation 188, 237 Reflect atoms 108
precedence 189
Remove
union 188, 237
all atom attribute 101
all bond attribute 103
P atom 100
bond 103
Pause 220 center of mass 116
Pen up 88 centroid 117
PHOTO 217, 219 extension point 117
global set 244
Plane 120 line 118
measure angle 129 local set 248
reflect through 108 non query atoms 122
Play back session normal 119
COLLECT and TAKE files 217 plane 120
command file 220 stereo atom attribute 108
Polar stereo bond attribute 108
global set 245 substructure 106
UNITY feature 123
Possible_hbond built-in set 253

RENUMBER 121 Select objects 133
Replace chain 95, 104 by chirality 141
by combining sets 141
Reset the screen 167 by conformational state 139
Residues by sets 139
select by conformational state 139 by substructure 140
Resize by type 140
dynamic hydrogen bonds 250 how tos 138
static hydrogen bonds 257 using Boolean operators 141
within a radius 141
Restore
SYBYL session 215 Sequence
built-in set 254
Restore from stack
undo 168 Sequence expression
dialog 135
Retrieve molecules 190
SESSION 207
Ring
built-in set 253 Session 207
fusion 110 delete 216
list 164 restore 215
ring fusion tutorial 78 save 208
SYBYL object definition 224 SET
RNA global set 245 PICKING 30
Root atom 110 Sets 241
aggregates 242
Rotation built-in 251
modify center 109 database 193
of molecules 67 Delete 152
RS isomerism 106 dynamic 249
for biopolymers 245
global 243
S list 151
Save as local 247
molecules 48 modify 151
naming conventions 232
SAVE_SESSION_DIR 208 select by 139
Saving static 256
in the memory stack 169 SYBYL object definition 225
molecule in a file 45 user-defined 242
formats 49 working with 258
molecules 48
SHAKED command 112
in a database 192
select molecule(s) 49 Shortcuts
sketch 76 keyboard 44
SYBYL session 208 textport 43
Scanning Sidechain
torsions 113 254
built-in set
Scrolling text region 41 Single bond 230
SD file Sketcher 87
read/write files 53 add Z coordinate 91
branching 89
Search
change atom types 89
database 191 check chirality 75

draw a ring 90 T
draw multiple bonds 90
menu items 91 TABLE
move an atom 91 DATABASE 191
save 76 TAKE 220
techniques 88
TAKE51 221
tutorial 70
Terminate SYBYL 27
SLN
read/write file 52 Textport commands 30
SLN typer 98 Textport window
SYBYL 41
Small molecule building (see SKETCH) 87
Time
SMILES
performance of command 33
to MOL conversion 52
TMPDIR environment variable 195
SPAWN command 42
To_atoms built-in set 255
Sphere built-in set 254
Toolbox icons
Sphere selection 141
overview 39
Spiro fusion 111
Topography 163
Split molecule 100
Torsion
Standard amino acids list angle 163
global set 246 measure 128
Starting modify 103
SYBYL 12, 26, 35 Translation
Static set 256 of molecules 67
define 256 Triple bond 230
manage hydrogen bonds 257
Tripos Bookshelf
SYBYL object definition 225
help 28
Store molecules 192
TTY command 221
Subst_sphere built-in set 255 Tutorials
Substructure atom selection 143
expression rules 232 bond selection 153
modify 105 building a small molecule 70
naming conventions 232 file format 221
remove 106 interacting with SYBYL 11
root 105 ring fusion 78
select by 140 sketching a small molecule 70
selecting 133 small molecule sketching 70
SYBYL object definition 226 substructure selection 156
type 106
Substructure expression
dialog 135
U
Sugar global set 246 Undo last action 168
SYBYL Union
5.1 COLLECT/TAKE files 221 operator
in a database 188
SYBYL/TRIAD in object expression 237
See the TRIAD Manuals
UNITY
defining features 122
MACCS file conversion to hitlist 53

modify feature 123
remove
features and constraints 123
non query atoms 122
Unix utilities
dbtranslate
see UNITY manuals
use in MACCS conversion 53
dbunlock 181
User-defined sets 242
Z
ZAP 167
ZE isomerism 106

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Basics Manual

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SYBYL 7.3 SYBYL Basics TOC-3

TOC-4 SYBYL Basics SYBYL 7.3

SYBYL 7.3 SYBYL Basics TOC-5

TOC-6 SYBYL Basics SYBYL 7.3

SYBYL 7.3 SYBYL Basics TOC-7

TOC-8 SYBYL Basics SYBYL 7.3

Introduction to SYBYL Basics

SYBYL uses computer analysis to assist in the description and prediction of

When combined with SYBYL applications, SYBYL Base provides a completely

License Requirements for SYBYL Basics

The Substructure Selection tutorial requires the Biopolymer license

SYBYL 7.3 SYBYL Basics 9

Quick Introduction to SYBYL Tutorial

Run this tutorial to learn some basics operations in SYBYL:

A Matter of Time: this tutorial requires about 20 minutes of personal time.

SYBYL 7.3 SYBYL Basics 11

2.1 Start the SYBYL Program

2. In a system shell, type:

Tripos suggests starting SYBYL from an xterm shell.

3. Start the SYBYL program.

¾ Enter SYBYL’s program name at the system prompt.

12 SYBYL Basics SYBYL 7.3

4. Explore the parts of the interface.

SYBYL 7.3 SYBYL Basics 13

Note: The menubar and command line are available simultaneously.

14 SYBYL Basics SYBYL 7.3

2.2 Load Molecules

Load a Molecule via the Menubar

1. Load methotrexate (mtx.mol2).

¾ File >>> Read

SYBYL opens the Read File dialog.

¾ In File to read text box, type:

A molecule area is a region of memory that holds a particular molecule. The

2. Remove the molecule.

¾ Build/Edit >>> Zap (Delete) Molecule

The system removes the molecule.

SYBYL 7.3 SYBYL Basics 15

Load a Molecule via the Textport

¾ In the textport at the SYBYL prompt, type the following script:

2. Change the characteristics of your loaded molecule.

¾ Click the icon.

Load Molecules from the Fragment Library

¾ In the Option dialog, click 1,3-DIOXANE.

SYBYL places 1,3-DIOXANE in the Selection field of the dialog.

SYBYL opens the Molecule Area dialog.

2. Choose a molecule area for 1,3-dioxane.

¾ In the Molecule Area dialog, select M2: <empty>.

16 SYBYL Basics SYBYL 7.3

SYBYL now displays both 1,3-dioxane and dicloxacillin.

¾ Build/Edit >>> Get Fragment

¾ In the Option dialog, click 1,2,4-TRIOXOLANE.

SYBYL opens the Molecule Area dialog.

4. Choose a molecule area for 1,2,4-trioxolane.

¾ In the Molecule Area dialog, select M3: <empty>.

SYBYL now displays 1,3-dioxane, dicloxacillin, and 1,2,4-trioxolane. It is very

For more details, see Load Fragments on page 85.

SYBYL 7.3 SYBYL Basics 17

2.3 Change the Display

1. Toggle the display for each molecule off and on.

¾ Click the icon.

2. Change the display so you can see each molecule separately.