Basics

SYBYL® Basics Manual
SYBYL® 7.0
Fall 2004
Tripos Inc. Phone: +1.314.647.1099

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SYBYL Basics Table of Contents
Chapter 1.
Introduction to SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Chapter 2.
The Very Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.1 Start SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 How to Get Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.3 Work with Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.4 Undo Last Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.5 Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 3.
Sketch and Modify Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.1 Small Molecule Sketching Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2 Access the Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.3 Modify Molecules Outside of Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.4 Create/Modify Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Chapter 4.
SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.1 Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.2 Identify Atoms, Bonds, etc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.3 Create Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.4 Sets of Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Chapter 5.
Selection of Atoms/Bonds/Sequences . . . . . . . . . . . . . . . . . . . . . . . 109
5.1 Selection via the Expression Dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.2 Atom Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
5.3 Bond Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
5.4 Substructure Selection Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Chapter 6.
Molecule Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
6.1 Database Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
6.2 Open/Close Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
6.3 Obtain Information on Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
6.4 Retrieve Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
6.5 Managing Database Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.6 Save Database Molecules to MOL2 or MOL Files . . . . . . . . . . . . . . . . 153
6.7 Connect to External Relational Databases . . . . . . . . . . . . . . . . . . . . . . . 154
6.8 DATABASE Command List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
SYBYL 7.0 (Fall 2004) SYBYL Basics TOC-3

Chapter 7.
Expert’s Corner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .165
7.1 Manage Input/Output Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
7.2 Record and Play SYBYL Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
7.3 Modes for SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
7.4 Command Modes and Execution Options . . . . . . . . . . . . . . . . . . . . . . . 178
7.5 Execute Operating System Commands from Within SYBYL . . . . . . . . 181
7.6 Markush Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
7.7 Textport Output Presentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
7.8 Keyboard Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
7.9 Control Characters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
7.10 Menubar Shortcuts and Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
7.11 Libraries of Chemical Groups and Fragments . . . . . . . . . . . . . . . . . . . 187
7.12 Edit Text Files with the Text Editor . . . . . . . . . . . . . . . . . . . . . . . . . . 192
TOC-4 SYBYL Basics SYBYL 7.0 (Fall 2004)

Chapter 1.
Introduction to SYBYL
SYBYL is a state-of-the-art program in molecular modeling which uses

computer analysis to assist in the description and prediction of molecular
behavior. Although molecular modeling with computers is no longer new, the
facility with which SYBYL can be used as a research tool and its ability to
enhance productivity makes this particular program unique. SYBYL is easy to
learn and has an extensive help facility (HTML) for users at all levels of profi-
ciency.
Required License for SYBYL Basics

Functionality in the SYBYL Basics manual requires a SYBYL Base license
(“SybylBasic”).
SYBYL 7.0 (Fall 2004) SYBYL Basics 5

This page intentionally blank.
Chapter 2.
The Very Basics
• Start SYBYL on page 8

• Menubar on page 9
• Toolbox Icons on page 9
• Textport Window on page 9
• Default Molecule (Work) Area on page 10
• How to Get Help on page 11
• Work with Molecules on page 13
• Load Molecules from the Fragment Database on page 13
• Read/Write Files of Molecules on page 16
• Obtain Information on SYBYL Objects on page 20
• Copy/Paste/Merge on page 23
• Rotate the Molecules on page 25
• Measure Intra- and Intermolecular Distances/Angles on page 26
• Calculate Molecule’s Dipole Moment on page 28
• Clear the Screen on page 29
• Undo Last Operation on page 30
• Exit SYBYL on page 32

Chapter 2. The Very Basics
Start SYBYL
2.1 Start SYBYL

1. Log into the computer in the normal manner.
2. Start the SYBYL program.
¾ Enter SYBYL’s program name at the system prompt.

Note: SYBYL’s program name 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.
The computer responds by typing the identifying line for the SYBYL
program, indicating its version number and release date:
SYBYL’s graphical interface is displayed:
8 SYBYL Basics SYBYL 7.0 (Fall 2004)

Start SYBYL
Menubar
SYBYL’s menubar is similar to that of a PC application’s menubar. The

presence of an active (black font) SYBYL menubar indicates that the program is
waiting for your menu selection.
A menu item can be a simple command or a check box; it can also lead to a
submenu or a dialog. Additional categories may be available if you have
licensed special modules.
By default, all options are shown in the menus. Any options for which you do
not have a license are greyed out (these most likely will occur in the Tools
menu). The environment variable TA_HIDE_UNLICENSED_PRODS controls
whether or not the unlicensed options appear in the menus. To hide unlicensed
options, type the following before starting SYBYL:
setenv TA_HIDE_UNLICENSED_PRODS TRUE
Toolbox Icons
The SYBYL tools used to interact with the graphics are represented by icons
along the left edge of the SYBYL screen.
Descriptions of the individual icons can be found in the Toolbox Icons section
of the Graphics Manual. To activate an icon, place the pointer on it and press
the left mouse button. In cases where a dialog is displayed, you can close the
dialog by pressing the Q button.
Textport Window
The textport window enables you to enter any command, including HELP.
Review the Tripos Bookshelf for a complete listing of all SYBYL commands
available. After entering a command, the prompt is again printed on the
terminal.
Note: When running SYBYL, both menu selections and command line entry
are available simultaneously.

Start SYBYL
Default Molecule (Work) Area
The default molecule area (or work area) is the area targeted by operations. In
many cases, the default molecule area of M1 works just fine. Once in a while,
however, a number of operations may need to be performed on a structure in a
different area (e.g., M3). You could specify M3 for each operation. It may be
much easier, though, to change the default area, while working on that structure,
to M3.
Menubar: Options >>> Set >>> Default Molecule

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

How to Get Help
2.2 How to Get Help

The Tripos Bookshelf is SYBYL’s online help tool. This interactive documen-
tation enables you to view Tripos documentation online. It is context sensitive
and is a valuable tool to help you learn more about SYBYL. The Tripos
Bookshelf contains:
Index Citations
Connection to the Tripos web site Articles
Full color pictures Work flow charts
FAQs PDF library
Search functionality
Menubar: The Help menu is on the far right side of the menubar.
• Help >>> On Help—Activate Tripos Bookshelf and
provide information about SYBYL’s help system.
• Help >>> Start Bookshelf—Display Tripos Bookshelf’s
main page. From here you can view documentation
regarding every module of SYBYL.
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.
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.
To 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.

How to Get Help
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 legal
value.

Work with Molecules
2.3 Work with Molecules

There are several ways to display a molecule in SYBYL, three of which are:
• Load Molecules from the Fragment Database on page 13
• Read/Write Files of Molecules on page 16
• Obtain Information on SYBYL Objects on page 20
• Copy/Paste/Merge on page 23
• Draw the structure via the sketcher (see Access the Sketcher on page 41)
• Rotate the Molecules on page 25
• Measure Intra- and Intermolecular Distances/Angles on page 26
• Clear the Screen on page 29
2.3.1 Load Molecules from the Fragment Database
Menubar: Build/Edit >>> Get 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).

Work with Molecules
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.
Additional Information:
• Libraries of Chemical Groups and Fragments on page 187.
Example
1. Load 1,3-DIOXANE into SYBYL.
¾ Build/Edit >>> Get Fragment
¾ Select 1,3-DIOXANE.
¾ Press OK.
The molecule loads into SYBYL’s display area 1, also known as D1. Its
default location is in molecule area 1, also known as M1.
A molecule area is a region of memory that holds a particular molecule.

Molecule areas do not have a defined number (the number depends on the
computer’s memory). You can place hundreds (if not thousands) of molecule
areas in a display area on a standard workstation.
A display area is where your molecule is going to be displayed on the screen.

SYBYL has four unique display areas: D1, D2, D3, and D4.
Note that molecule areas have rules:

Work with Molecules
• M1 is always in display area D1.

If additional molecule areas are used, they simply recycle through the display
areas:
The figure below demonstrates this pattern:
2. Change the characteristics of your loaded molecule.
¾ Press .
The Display Options dialog is displayed. This dialog enables you to modify
the various look of your display area and molecules.
¾ In the Display Options dialog, select Sticks.
The lines making up your molecule become thicker and the color codes are
more defined. From now on, if you load any molecule in SYBYL, it will
load in Sticks mode.
¾ Press Q to close the Display Options dialog.
3. Load another molecule into SYBYL.
¾ Select 1,2,4-Trioxolane.
¾ Press OK.

Work with Molecules
M1 is already being used by 1,3-dioxane. However, the other molecule

areas (M2 - M10) are currently empty. You must choose which molecule
area should house the newly loaded molecule.
¾ In the Molecule Area dialog, select M2:<empty>.
¾ Press OK.
You have now placed two molecules within SYBYL (1,3-Dioxane and
1,2,4-Trioxolane). The two molecules reside in two unique molecule areas
(M1 and M2).
2.3.2 Read/Write Files of Molecules

• Read in Structure from File via the Menubar on page 17
• Write out Structure from File via the Menubar on page 18
• Read/Write MOL/MOL2 Files via Command Line on page 18
Additional information on using different input formats in SYBYL is available

in Manage Input/Output Formats on page 166.

Work with Molecules
Read in Structure from File via the Menubar
¾ To open a file for reading, select File >>> Read.
The Read File dialog uses the filename as the default for the molecule name
when reading a single file. If any form of molecule name is present in the input
file, that name is used instead.
Directory Current directory.

Sub-Directories Click on one of the sub-directories to select a file from
it. Click on [Parent] to go up one level in the directory
tree, then select a directory from among those appear-
ing in the presented menu. This new directory then
becomes the current directory and its descendants may
be selected.
Other Directo- Lists your home directory and the SYBYL default
ries directory if it is different from your home directory.
Note: You can customize the set of directories listed
here by adding two lines to the file the environment
variable (logical) TA_USER_STRT points to. The vari-
able can also be changed interactively as needed

Work with Molecules
Files Select a file from the list. Its name appears in the Files
to read field.
Files to read 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 Selecting a file type from this menu reduces the list of
files presented in the Files list.
Molecule Select a work area from the list. If a work area is
needed, SYBYL automatically selects the first available
one. If the file type selected does not require a work
area, this field is inactive.
A subset of this dialog, is accessed from several other dialogs.
Write out Structure from File via the Menubar

¾ Select File >>> Save As.
¾ Specify Format.
Multiple structures can be selected from the list and saved to a MOL file,
MOL2 file, SD File, or SLN file. Use the Select All, Invert, and Clear buttons
to manipulate the selections in the molecule list.
Read/Write MOL/MOL2 Files via Command Line
MOL2 direction [mol_area] [filename]

or
MOL direction [mol_area] [filename]

or
MREAD direction [mol_area] [filename]

Work with Molecules
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 it already exists, it is
overwritten.
The filename is used as the default for the molecule name when reading a single
file. If any form of molecule name is present in the input file, that name is used
instead.
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.)
• MOL2 files are used by SYBYL to store molecules resulting from many
batch minimizations (ANNEAL, MAXIMIN2, and MULTIFIT), LATTICE
generations, BIOPOLYMER CONSTRUCT_BACKBONE, and other computa-
tions.
• 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

Work with Molecules
bond information, rotatable bond definitions and plane equations. To

preserve the complete molecular description, use the MOL2 file format.
• When reading files in, if the file name supplied has no extension, the
system, by default, looks for a .mol2 file first, then a .mol file, and
lastly a file with no extension.
• The format of the file written out (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.
2.3.3 Obtain Information on SYBYL Objects

• Report Information on an Individual Atom, Bond, or Substructure on
page 21
• List Coordinates, Distances, or Angles (Same Molecule Area) on page
21
• List Information on One or More SYBYL Objects on page 22
• Print Information on One or More SYBYL Objects on page 23

Work with Molecules
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 (|).
<CTRL>+right-clicking on an atom also labels that atom according to the tailor

variable GRAPHICS MOUSE_LABEL. Using this feature, instant information
about an atom, etc. is always available.
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.

Work with Molecules
• Record Output from a Single Command on page 173.
• Measure Intra- and Intermolecular Distances/Angles on page 26.
• BIOPOLYMER MEASURE to conveniently measure omega and zeta angles.
• BIOPOLYMER CHECK_GEOMETRY to report deviations from standard
geometry.
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.
An asterisk (*) in the column after the ID of sets indicates that the set is defined
and managed by the system.
• Record Output from a Single Command on page 173 to copy the listing
into a file.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of atom listings.

Work with Molecules
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.
The full generality of the object expression syntax can be used to determine
which objects to include. The PRINT command writes out the file SYBYL-
PRINT.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.
An asterisk (*) in the column after the ID of sets indicates that the set is defined
and managed by the system.
• TAILOR SET GENERAL ATOM_IDENTIFIER to alter the characteristics
of the listings.
2.3.4 Copy/Paste/Merge
• Copy/Paste Contents between Molecule Area and Clipboard on page 24
• Copy Contents To Different Molecule Area on page 24
• Copy Atoms and Associated Data Structures To Different Molecule
Area on page 24
• Merge Copy of Atoms and Associated Data Structures Into Molecule
Area on page 24

Work with Molecules
Copy/Paste Contents between Molecule Area and Clipboard
Menubar: Build/Edit >>> Copy >>> to Clipboard

Command MOL2|MOL|MREAD XCOPY mol_area
Line: MOL2|MOL|MREAD XPASTE mol_area
Copy Contents To Different Molecule Area
Menubar: Build/Edit >>> Copy >>> Molecule Area

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 contents (properties, colors, and associated displays
(backgrounds)) of one work area into another. Origin molecule is unaltered.
Previous contents of 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 contents of target area. All local set definitions
associated with extracted atoms are copied to new area as well. Origin area is
left unchanged.
If atom_expr does not include a work area specifier, the default work area is
used.
If atomic charges are present before extraction, atoms in target molecule still
bear same charges. 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 Copy of Atoms and Associated Data Structures Into Molecule Area
Menubar: Build/Edit >>> Merge

Command Line: MERGE atom_expr target_area
If atom_expr does not include a work area specifier, the default work area is
used.

Work with Molecules
Any set definitions, with names and types identical to those present in the target
work area, are merged into the target area.
An atom with the same type and coordinates as an atom in the target area is
considered to be non-unique (identical). If coordinates are the same but atom
types are different, the atom is still considered to be unique and is merged into
the target area. A message states that atoms of different types have the same
coordinates.
Non-unique atoms may be merged into the target area when the target atom,
identical in coordinates and type to an atom in the origin area, does not have
enough unfilled valences to make bonds with the atoms being merged. The non-
unique atom is included in the merge so that these bonds are successfully added.
A message states that atoms have the same coordinates due to lack of free
valences in the target area atom.
If molecules have been rotated and/or translated, use FREEZE to transform the
coordinates before invoking MERGE.
If atomic charges were calculated for either molecule before the merge, atoms
in the target molecule will bear the same charges. They are marked “possibly
invalid” but can be used in SYBYL by setting the Charges option menu to
Use Current in the Energy dialog. Note that the MMFF94 force field always
recalculates its own set of charges.
• TAILOR SET MERGE to alter the characteristics of merging.
2.3.5 Rotate the Molecules

The Mouse Focus Option dialog, can be used to work with both display areas
and molecule areas.
1. Use the Mouse Focus Option dialog to differentiate between the two molecules
that were previously displayed:
The display area 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.
¾ Rotate the molecules by pressing the right mouse button and moving
your mouse in any direction.
Notice that both molecules move. This is because your current molecule
setting is on Global (global).

Work with Molecules
2. Move 1,3-DIOXANE to the upper right corner:
¾ Press the button.
¾ Select D1 in the Mouse Focus Options dialog.

By selecting D1, you are telling SYBYL to focus in on 1,3-DIOXANE.
¾ Press the middle mouse button and move 1,3-DIOXANE to the upper
right corner of SYBYL.
3. Move 1,2,4-TRIOXOLANE to the upper left corner:
¾ Unselect D1 and select D2 in the Mouse Focus Options dialog.

By deselecting D1 and selecting D2, you are telling SYBYL to focus in on
1,2,4-TRIOXOLANE.
¾ Press the middle mouse button and move 1,2,4-TRIOXOLANE to the

upper left corner of SYBYL.
Additional information regarding moving and rotating molecules can be found

in the Graphics Manual, within the Toolbox Icons section. Look for the
following topics:
• The Mouse Focus Options dialog.
• The physical dial box.
Note: You may also separate the molecules by separating the display areas.
This is accomplished in the Display Options dialog (Screen column).
2.3.6 Measure Intra- and Intermolecular Distances/Angles

• Intra-/Intermolecular Measurements on page 27
• Intramolecular Angle Between Planes on page 27
• Parameters of a UNITY Feature on page 28
• BIOPOLYMER MEASURE to measure omega and zeta angles.
• TAILOR SET GENERAL ANGLE_RANGE to specify how an angle range
should be displayed.

Work with Molecules
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.
UIMS Variable: measure_height
Torsion Angles
Menubar: Analyze >>> Measure >>> Torsion
Command Line: MEASURE TORSION {atom1 atom2 atom3 atom4}
UIMS Variable: measure_torsion
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.
UIMS Variable: measure_plane_angle

Work with Molecules
Parameters of a UNITY Feature
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
2.3.7 Calculate 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.

Work with Molecules
UIMS2 Variables:
The following variables are assigned values:
DIPOLE_X DIPOLE_Y DIPOLE_Z

DIPOLE_TOTAL DIPOLE_CHARGE
2.3.8 Clear the Screen
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.

Undo Last Operation
2.4 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 and a copy is
made. 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 30
• Force Saving of Molecule Area(s) Contents to the Save/Restore Stack on
page 30
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.

Undo Last Operation
• SET AUTOSAVE for information on automatic saving of molecules on the
recovery stack and for an explanation of the operation (in the Graphics
Manual).

Exit SYBYL
2.5 Exit SYBYL

To terminate 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 exits 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.

Chapter 3.
Sketch and Modify Molecules
• Sketch Molecules
• Small Molecule Sketching Tutorial on page 34
• Access the Sketcher on page 41
• Modify Molecules Outside of Sketcher on page 47
• Atoms on page 47
• Bonds on page 53
• Group on page 56
• Substructures on page 56
• Molecule’s Center of Rotation, Name, Type, etc. on page 58
• Combine Two Molecules From Different Molecule Areas on page 59
• Ring Fusion Tutorial on page 60
• Combine Two Molecules or Groups in Same Molecule Area on page
66
• Chirality on page 66
• Adjust Bond Lengths and Angles to Match Standards on page 69
• Scan Torsions to Remove van der Waals Contacts on page 69
• Create Molecule by Averaging Existing Molecules on page 70
• Create/Modify Features on page 71

Chapter 3. Sketch and Modify Molecules
Small Molecule Sketching Tutorial
3.1 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 34
• Set Up on page 35
• Enter the Sketching Mode on page 35
• Build Piperidine Ring in Chair Conformation on page 36
• Add a Chain on page 38
• Add a Group on page 39
• Check Chirality on page 39
• Clean Up on page 39
• Save the Sketched Molecule on page 40
3.1.1 Preface
In this tutorial, you will build and minimize Atropine by building the most
complex ring system first an 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
3.1.2 Set Up
1. Clear the SYBYL screen of all molecules and background images.
¾ Build/Edit >>> Zap (Delete) Molecule
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
2. Set your screen as follows (see the Graphics Manual if necessary).
¾ Use the Reset graphics tool to reset Everything.
¾ Set your display to Full screen mode with the Display Options
graphics tool.
3.1.3 Enter the Sketching Mode

1. Bring up 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).

Upon entering the sketching mode, 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 1.54Å. (This is the sp3 carbon to sp3 carbon bond length.) The
grid scales with the molecule to always show the correct bond length.
¾ Select Grid on the Sketch Molecule menu.

Later, if the grid gets in your way, you can easily toggle it off by selecting
Grid again in the Sketch Molecule menu.

3.1.4 Build Piperidine Ring in Chair Conformation

1. Build the ring as follows:
¾ Click on a point in space located in the middle of the screen.

A highlighted cross or small circle, representing an unconnected atom,
appears at the selected point. The highlight indicates that this atom is the
current atom of attachment and any subsequent point chosen is attached to
this atom.
¾ Pick a point above this atom and about one grid spacing to the right
(see atom 2 in the figure below).
A bond is drawn to the newly created second atom.
¾ Continue sketching the 6-membered ring by picking 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.
2. Change the type of atom 1 to a nitrogen.

¾ Select N from the atomic symbol menu.
¾ Pick atom 1 on the sketched molecule.

A label appears 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 below.

¾ Select Move on the Sketch Molecule menu.
¾ Select N in the ring and then pick a new screen location that is
somewhere above the ring.
¾ Select atom 4 and move it below the ring by the same amount.
Do not be concerned if the structure sketched is not a perfect chair. The ring is
optimized later.
4. Add the bridge across the ring.
¾ Select Draw on the Sketch Molecule menu to return to continuous

Draw mode.
¾ Pick atom 2 as the current attachment atom.
¾ Pick a point below this atom and then another point diagonal to the
new atom.
¾ Pick atom 6 to close the ring.
5. Clean up the ring system.

¾ Select Tailor on the Sketch Molecule menu.
¾ Select CLEAN_UP (press OK).
¾ Select 5_QUICK_MINIMIZE (press OK).

¾ Press End.
¾ Select Clean_up on the Sketch Molecule menu.
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 window.
3.1.5 Add a Chain

1. Center the molecule on the screen.
¾ Select Center on the Sketch Molecule menu.
¾ Rotate the molecule until its orientation is similar to that shown in the
figure below.
2. Add a carbon chain to the ring.
¾ Select atom 4 as the current atom of attachment.
¾ Sketch the sidechain by picking 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 there.
3. Draw a double bond for the carbonyl group.

¾ Select atom 10 as the new point of attachment and then pick a point
above the atom.
¾ Pick atom 10 again.
The double bond appears and continuous draw mode is deactivated since an
existing atom was chosen.

4. Add a carbon to the nitrogen.
¾ Pick atom 1 then a point to its left.
5. Sketch in 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.
3.1.6 Add a Group

1. Access a list of predefined chemical groups and add a phenyl ring to the
molecule.
¾ Select Group on the Sketch Molecule menu.
¾ Select PHENYL and pick atom 11.
2. Center the molecule again.
¾ Select Center on the Sketch Molecule menu.
3.1.7 Check Chirality

Make sure atom 11 has a chirality of S.
¾ Select Chiral on the Sketch Molecule menu 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.
3.1.8 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. (Note that 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 Select Tailor on the Sketch Molecule menu.
¾ Select CLEAN_UP (press OK).
¾ Select 4_SCAN (press OK).

¾ Press End.
¾ Select Clean_up on the Sketch Molecule menu.
2. Add the necessary hydrogens to all unfilled valences.
¾ Select Addh on the Sketch Molecule menu.

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

A final clean up is done automatically every time you exit the Sketch
Molecule menu.
3.1.9 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, type atropine as the File name.
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.
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 on your own using molecules from your own research.

Access the Sketcher
3.2 Access the Sketcher

Menubar: Build/Edit >>> Sketch Molecule
See Sketcher Menu Items on page 45.
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 rotation of the structure has
occurred. Any atoms added subsequent to a rotation assume the transformed Z-
coordinate of the atom to which it is bonded. Unconnected atoms are always 2-
dimensional since there is no reference point.
• CONCORD for fast conversion of 2D coordinates to 3D.
• 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.
MENU CLEAN_UP Ring is “cleaned up”.

Access the Sketcher
MENU ADDH Hydrogens are added to all unfilled

valences.
MENU EXIT SKETCH is exited.
3.2.1 Sketching Techniques

The following sections discuss some basic ideas and techniques which you
should become familiar with before using the Sketcher.
• Always Review the Sketched Model on page 42
• Atomic Symbols Only on page 43
• Atom Types on page 43
• Branching on page 43
• Edit Existing Molecules on page 43
• Label and Color on page 44
• Multiple Bonds on page 44
• Rings on page 44
• Z Coordinate on page 44
Always Review the Sketched Model
Although flexible enough to enable building any structure, the sketcher does
have enough chemical sense to warn you when something unnatural has been
done. For example, if the valence of an atom is about to be exceeded, a message
is issued to inform you of this aberration. It is then your decision to continue or
not.
A Note About Continuous Drawing Mode
Continuous drawing may be stopped (also referred to as “pen up movement”)

by doing one of the following:
• Click on the last atom drawn. This cancels the selection of a point of
attachment. The cursor can then be moved to another part of the
molecule without drawing a bond. Once you pick a new point of
attachment, continuous drawing mode is turned on again.
• Click on an existing atom. A bond is drawn from the current atom to this
existing atom and then the pen up movement is initiated.

Access the Sketcher
Atomic Symbols Only
Only atomic symbols are used to designate atom types in order to eliminate the
burden of having to decide the proper SYBYL atom type.
Atom Types
Atom types can be changed in two different ways:

1. To change the default atom type before adding the new atom to the model:
• Choose the Default_type option.
• Pick the desired atomic symbol from the menu.
Subsequent atoms have the new atom type until Default_type is
selected again. This technique is useful if you want to draw a chain of
atoms other than carbons.
2. To modify the type of an existing atom:
• Pick the new atom type from the atomic symbol menu.
• Pick the atom whose type you want to change.
The atom type is immediately updated. Whenever an atom type is
selected without first being preceded by a Default_type command,
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 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. The highlight is
removed and continuous draw mode is temporarily shut off. Choose a new point
of attachment. Once the new attachment point is selected, the continuous
drawing mode is automatically turned on and a new chain of atoms can be
added as described above.
If a point of attachment is chosen in error, picking that atom again initiates

another pen up movement. A new point of attachment can then be selected.
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

Access the Sketcher
the molecule maintains its current geometry. This option may be disabled by
setting TAILOR SET SKETCH AGGREGATES to OFF. In this case, the whole
molecule is considered in the cleanup phase.
Label and Color
Heteroatom labeling and molecule color, coded by atom type, are the defaults
used by the sketcher to make different atom types easily identified. Labeling
can be toggled off and a different coloring scheme can be chosen if you desire.
Multiple Bonds
Draw the single bond as outlined above.

• 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 shut 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, continuous draw mode is temporarily
shut off, allowing you to choose a new point of attachment. To add a bond to
the current atom, select that atom again.
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

Access the Sketcher
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.
3.2.2 Sketcher Menu Items
Draw Activate continuous drawing mode (default action, with

cursor defined as a carbon atom). To draw a chain of car-
bons pick a point on the screen where first atom is to be
located; a cross appears. Pick another point on the screen;
that point appears and a line (bond) between the two atoms
is automatically drawn. Repeat until desired chain length
has been obtained. Note that current atom of attachment is
always highlighted.
Move Prompts you for atom to move and its new location. The
atom and all bonds connected to it are then moved to new
location. This mode remains active until another option is
chosen. This capability is useful when building a particu-
lar conformer.
Remove_atom Delete atoms and any bonds connected to them from mole-
cule being sketched. This mode remains active until
another option is chosen.
Remove_bond Remove bond from drawn structure. You must select two
bonded atoms.
Fragment Access Standard Fragment Library. (Refer to Fragment
Library Structure and Contents on page 188 for more
information.)
Group Access Group Library. Groups have predefined attachment
points. This mode remains active until another option is
chosen. (Refer to Group Library Structure and Contents on
page 187 for more information.)
Zap Delete current sketch molecule.
Center Center molecule on screen.
Chiral Specify whether a chiral center is R or S.
Default_type Change default atom type used for drawing. Select new
atom type from atomic symbol table. Any atoms drawn
after this point have new type.

Access the Sketcher
Clean_up Adjust molecule geometry according to method specified

via the Tailor button or the TAILOR SET SKETCH
CLEAN_UP command. Also determine proper atom hybrid-
ization based upon bond type and atom type of connected
atoms. No matter what option is chosen for clean-up, the
atom and bond type conversion is always done.
Addh Add hydrogens to all unfilled valences.
Undo Undo last operation, restoring molecule to its previous
state.
Tailor Access Tailor variables for sketcher (AGGREGATES,
CLEAN_UP, COLOR_BY_TYPE, and LABEL).
Remove_h Remove all hydrogens in sketched molecule.
Modify_angle Modify bond angle of three connected atoms.
Modify_torsion Modify torsion angle of four connected atoms.
Grid Toggle 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 Perform clean up procedure and assign SYBYL atom
types (see description for Clean_Up).
Rotate_X85, Rotate current molecule in specified direction on a static
Rotate_Y85 device. Introduces depth (Z-coordinates) to the molecule.
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 Access the STATIC command. Available on static devices
only.
Reset Reset all rotations. Available on static devices only.
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 defi-
nition table are represented in this menu.

Modify Molecules Outside of Sketcher
3.3 Modify Molecules Outside of Sketcher

• Atoms on page 47
• Bonds on page 53
• Group on page 56
• Substructures on page 56
• Molecule’s Center of Rotation, Name, Type, etc. on page 58
• Combine Two Molecules From Different Molecule Areas on page 59
• Ring Fusion Tutorial on page 60
• Combine Two Molecules or Groups in Same Molecule Area on page 66
• Chirality on page 66
• Adjust Bond Lengths and Angles to Match Standards on page 69
• Scan Torsions to Remove van der Waals Contacts on page 69
• Create Molecule by Averaging Existing Molecules on page 70
3.3.1 Atoms
• Add Atom to Existing Structure on page 47
• Add Atom Without Attaching to Any Present Structure on page 48
• Add Chain of Atoms of Same Type on page 48
• Fill Empty Valences on page 48
• Add Pseudoatoms (Centroids) on page 49
• Modify an Atom on page 49
• Remove Atoms or Atom Attributes on page 53
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.)
Coordinates are automatically determined, 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 atom by specifying coordinates or 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.
Chains are attached to existing structure with ideal geometry. Coordinates of all
atoms are determined 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
license is available, it 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.
Bond lengths and angles are set 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 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. Types of
bonds associated with the atoms are modified to fit new
atom types.
Geometry around atoms or atom names are 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, the types of associated
bonds are modified to fit new atom types. For non-ring
atoms, bond lengths are also adjusted. Bond lengths and
types are taken from $TA_ASCTABLES/
BOND_LENGTHS and BOND_TYPES. If bond type is
ambiguous (i.e., more than one possible bond type to
connect the two atom types) or unknown, you are
prompted.
Atoms may be renamed 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 then 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 “BIOPOLY-
MER” license.
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>
You must use MODIFY ATOM OTHER_TYPES UNLABEL
to remove alternate type labels.
Kollman and AMBER atom types require a “BIOPOLY-
MER” license.
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. 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
All bonds involving that atom are removed and any features (normal, plane,
constraint) attached to that atom. Atoms and bonds are renumbered to reflect
removal of objects from the molecular description. If removed atom is a
member of a static set, set membership is updated. (REMOVE ATOM * is equiv-
alent to ZAP for the molecule.)
Alternatively, the Split functionality can be used to remove a portion of a

molecule by simply specifying two bonded atoms:
Menubar: Build/Edit >>> Other Tools >>> Split

Command Line: SPLIT origin_atom target_atom
The bond between the specified atoms is deleted along with all atoms on the
target side of that bond. Note: The Split functionality cannot be used if the
indicated bond is in a ring. The ring must first be broken 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
3.3.2 Bonds
• Add Bonds on page 53
• Modify a Bond on page 55
• Remove a Bond or Bond Attributes on page 55
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. A single
bond is added 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.
A bond is added 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 automatic determination of
bond type according to types of atoms at each
end of 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, coordinates of last specified item,
and all atoms attached to it, are altered. 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 removal of objects from the molecular
description.
Attributes can be removed from one or more bonds without deleting the bond
itself.

Command Line: REMOVE ALL_BOND_ATTRS expression
3.3.3 Group
A chemical group can be added to the molecular structure and 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 187).
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 187 for details.
3.3.4 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 exten-
sively in the manipulation of macromolecules where it
is synonymous with monomer. Generally you should
not alter the substructure types; they are managed 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.
3.3.5 Molecule’s Center of Rotation, Name, Type, etc.
Change Center of Build/Edit >>> Center

Rotation via Or View >>> Center of Rotation >>> Molecule
Menubar:
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 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.
3.3.6 Combine 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 (|).
The fused structure is placed in the molecule area of the first atom of each pair.
Coordinates of atoms used for the fusion are taken from the first molecule.
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.
• TAILOR SET FUSE to select default parameter set to alter character-
istics of the fusion.

3.3.7 Ring Fusion Tutorial

The following tutorial illustrates several examples of fusions:
• Fuse Two Planar Bonds on page 60
• Fuse Two Rings to Build a Spiro System on page 61
• Fuse Two Non Planar Bonds on page 61
• Fuse A Planar Bond With A Non Planar Bond on page 64
Set Up
2. Set the screen to quartered mode using the icon (press Q).
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 With M1:furan highlighted, press All and then OK.
¾ Select M2:pyridine, press All and then OK.

2. Fuse the two structures.
¾ Build/Edit >>> Other Tools >>> Fuse Rings
¾ Click on 6 in pyridine (M2), and then 2 in furan (M1) to form the first
pair.
¾ Click on 5 in pyridine, and then 3 in furan to form another pair.
¾ Press End Select.
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 on 4 in piperidine (M2), and then 4 in 4H-pyran (M1) to form the

first pair.
¾ Click on 12 in piperidine, and then 5 in 4H-pyran to form another pair.
Fuse Two Non Planar Bonds
In this example, tetrahydropyran (M1) is fused to piperidine. Several methods

are used:
• providing two pair of atoms (result in M2),
• providing three pair of atoms (result in M3),

• providing four pair of atoms (result in M4).
1. Use only two pair of atoms to fuse two non planar bonds. The ambiguity is
resolved 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 on 6 in piperidine (M2), and then 3 in tetrahydropyran (M1) to

form the first pair.
¾ Click on 5 in piperidine, and then 2 in tetrahydropyran to form another
pair.
2. Use three pair of atoms to fuse two non planar bonds. As in the previous
attempt, the ambiguity is resolved automatically by the program. The results are
displayed in M3.
¾ Options >>> Set >>> Default Molecule
¾ With M3:piperidine highlighted, press All and then OK.

¾ Click on 6 in piperidine (M3), and then 2 in tetrahydropyran (M1) to

pair.
¾ Click on 16 in piperidine, and then 1 in tetrahydropyran to form
another 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, press All and then 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, press All and then OK.
¾ Click on 6 in piperidine (M4), and then 2 in tetrahydropyran (in M1) to

pair.
another pair.
another pair.

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 on 5 in hexahydroazepine (M1), and then 1 in benzene (M2) to

¾ Click on 4 in hexahydroazepine, and then 2 in benzene to form
another pair.
another pair.
another pair.
Notice the poor quality of the geometry at the ring fusion and the fact that extra-
neous 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 on 1 in benzene (M2), and then 5 in hexahydroazepine (M3) to


¾ Click on 2 in benzene, and then 4 in hexahydroazepine to form

another pair.
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 ascertain 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 on 5 in tetrahydroazepine (M4), and then 1 in benzene (M3) to

¾ Click on 4 in tetrahydrazepine, and then 2 in benzene to form another
pair.
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.
Continue readingThis concludes the Ring Fusion Tutorial.

3.3.8 Combine 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 53 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.
3.3.9 Chirality
• Determine Chirality on page 67
• Invert Chirality on page 68
• Reflect Atoms Through a Plane on page 68

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.
RS isomerism of an atom is determined 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

and 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 including 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 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
3.3.10 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]
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
3.3.11 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.
3.3.12 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 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
3.4 Create/Modify Features

• Center of Mass on page 71
• Centroid on page 72
• Extension Point on page 73
• Line on page 74
• Normal on page 75
• Plane on page 76
• UNITY Query Features on page 76
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 22.
3.4.1 Center of Mass

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.
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.
3.4.2 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. (See TAILOR SET CENTROID to alter the charac-
teristics 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.

3.4.3 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 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.

3.4.4 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.

3.4.5 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. (See TAILOR SET NORMAL to alter the
characteristics of the normal.)
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.

3.4.6 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.
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.
3.4.7 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 • CONTAINING_VOLUME_CO
• CENTROID NSTRAINT
• DISTANCE_CONSTRAINT • DONOR_ATOM
• DONOR_SITE • EXCLUDED_VOLUME_CONS
• EXTENSION_POINT TRAINT
• HYDROPHOBIC • FRAGMENT
• LP_ANGLE_CONSTRAINT • LINE
• NEGATIVE_CENTER
• NORMAL_POINT • PARTIAL_MATCH_CONSTR
• PLANE AINT
• RECEPTOR_SITE • POSITIVE_N
• SPATIAL_LINE • SPATIAL_CAP
• SPATIAL_PLANE
• SPATIAL_POINT • 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}]
• 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.
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.

Chapter 4.
SYBYL Objects
This chapter defines some of the basic vocabulary and syntax you need when
working with SYBYL.
• Glossary on page 80
• Identify Atoms, Bonds, etc. on page 84
• General Naming Conventions on page 84
• Atom(s) Specification on page 85
• Bond(s) Specification on page 86
• Substructure(s) Specification on page 87
• Set(s) Specification on page 88
• Molecule(s) Specification on page 88
• Molecule Area(s) Specification on page 88
• Monomer Sequence(s) Specification on page 89
• Conformational Specifications on page 90
• Create Expressions on page 92
• Logical Operators on page 92
• Parentheses and Grouping of Operations on page 94
• Sets of Objects on page 95
• Global Sets on page 96
• Local Sets on page 99
• Dynamic Sets on page 100
• Built-in Sets on page 101
• Static Sets on page 106

Chapter 4. SYBYL Objects
Glossary
4.1 Glossary
Atoms—The fundamental building blocks of molecules. You may name them
arbitrarily and specify their type. Parameters for 32 different atom types are
provided in SYBYL. An extended list of 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 similarities
among molecules.

Glossary
• 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,
identifying 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

Glossary
time. The built-in sets in SYBYL are dynamic sets: Aromatic, H-bonds,
Backbone, Sidechain, Rings, and Bumps.
Read more about sets on page 95.
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.

Glossary

Identify Atoms, Bonds, etc.
4.2 Identify Atoms, Bonds, etc.

4.2.1 General Naming Conventions
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. (7 characters
structures, is recommended for atoms and substructures, and 31 for sets
Sets, Features and features). Names must start with an alphabetic character,
but are case insensitive (characters are held internally 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. They may contain underscores and
hyphens in any position after the first.
* 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(s) Specification on page 85
• Bond(s) Specification on page 86
• Substructure(s) Specification on page 87
• Molecule(s) Specification on page 88
• Molecule Area(s) Specification on page 88
• Conformational Specifications on page 90

4.2.2 Atom(s) 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.
4.2.3 Bond(s) 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.
4.2.4 Substructure(s) 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.
4.2.5 Set(s) Specification

Braces ({}) are not necessary for set designation, but are accepted for consis-
tency (e.g., RING_A {HELIX_*})
4.2.6 Molecule(s) 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”
4.2.7 Molecule Area(s) 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.

4.2.8 Monomer Sequence(s) 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.
4.2.9 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
4.3 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.
4.3.1 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
4.3.2 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.

Sets of Objects
4.4 Sets of Objects

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 96—Set whose definition is applicable on a system-

wide basis, i.e., it may be applied to any molecule.
• Local Sets on page 99—Created for specification of objects in a
particular molecule. Membership is associated only with that molecule.
• Dynamic Sets on page 100—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.
• Built-in Sets on page 101—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 106—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.)

Sets of Objects
• 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.
4.4.1 Global Sets

Global sets are simply 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 97.) When the dictionary is opened, sets are available for use automati-
cally.
• Define a Global Set on page 96
• Modify a Global Set on page 97
• Remove a Global Set on page 97
• Global Sets in the MACROMOL Dictionary on page 97
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.

Sets of Objects
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.
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 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
automatically become available for use when the dictionary is opened.

Sets of Objects
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)}
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)}

Sets of Objects
4.4.2 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 99
• Remove a Local Set on page 100
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.

Sets of Objects
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.
4.4.3 Dynamic Sets

• Define a Dynamic Set on page 100
• Dynamic Set Example on page 101
• Manage Dynamic Hydrogen Bonds on page 101
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.
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.

Sets of Objects
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
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.
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.
4.4.4 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

Sets of Objects
commas. For example, {SPHERE(C2,5)} specifies all atoms within 5 Å

of atom C2.
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 same aromatic system as specified atom(s).
LIST ATOM {AROMATIC(9)} BRIEF
BACKBONE {BACKBONE}
• Atom Set Atoms belonging to the backbone as defined in the MAC-
ROMOL dictionary.
COLOR ATOM {BACKBONE} RED
• Bonds {BACKBONE}
Bonds belonging to the backbone as defined in the MAC-
ROMOL dictionary.
SCAN {BACKBONE}
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 specified range.
COLOR ATOM {CHARGE(-.05,-.01)} BLUE
CHIRAL {CHIRAL(atom_expression,RS)}
• Atoms Atoms of specified chirality or pro-chirality. Specify
atoms to search as an expression. Chirality is indicated by
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. Default is to search all atoms (*) for all chiral centers
(RS).
COLOR ATOM {CHIRAL(CA,S)} YELLOW

Sets of Objects
FINDCONF {FINDCONF(state1+state2+,sequence)}
• Substructures Monomers having specified conformational state(s) as
defined in the MACROMOL dictionary. Entering a
sequence limits search to specified regions of the biopoly-
mer (“*” searches whole biopolymer). Separate conforma-
tional states by plus signs.
LABEL SUBSTRUCTURE {FINDCONF(ALPHA_HELIX,*)}
HBOND {HBOND(atom_expression,type)}
• Atoms Atoms of specified type participating in hydrogen bonds.
Valid types include: ALL, DONOR, ACCEPTOR, or HYDRO-
GEN. Definitions for 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
MONPROP {MONPROP(keyword,minimum,maximum)}
• Substructures Monomers having 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 keyword and minimum to select mono-
mers with the keyword whose value matches the mini-
mum. The keyword may be any arbitrary string. Values
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 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 specified type which can potentially participate
• Atoms 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

Sets of Objects
RINGS {RINGS(atom_expression,type)}
• Atoms Specified atoms which are included in rings of specified
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 specified
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
• Substructures {RINGS(substructure_expression,type)}
Substructures in the expression, which are included in
rings of specified type.
COLOR SUBSTRUCTURE {RINGS(*,E)} YELLOW
SEQUENCE {SEQUENCE(sequence1,sequence2,)}
• Atoms Atoms in monomers of specified sequence(s). Monomers
are defined in the MACROMOL dictionary. Read 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 specified sequence(s). Monomers
are defined in the MACROMOL dictionary.
SCAN {SEQUENCE(GLY=PRO)}
• Substructures {SEQUENCE(sequence1,sequence2,)}
Monomers in 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 MACRO-
MOL dictionary.
COLOR ATOM {SIDECHAIN} RED

Sets of Objects
• Bonds {SIDECHAIN}
Bonds belonging to sidechains as defined in the MACRO-
MOL dictionary.
SCAN {SIDECHAIN}
SPHERE {SPHERE(atom_expression,radius)}
• Atoms Atoms falling within sphere(s) of 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 same radius.
COLOR ATOM {SPHERE(ALA23.CA,10)} MAGENTA
• Bonds {SPHERE(atom_expression,radius)}
Bonds falling within sphere(s) of 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 same radius.
SCAN {SPHERE(N15,8)}
• Substructures {SPHERE(atom_expression,radius)}
Substructures falling within sphere(s) of specified radius.
The expression defines the sphere center(s). When multi-
ple 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 same
radius.
LABEL SUBSTRUCTURE {SPHERE(G16,12)}
SUBST_SPHERE {SUBST_SPHERE(atom_expression,radius)}
Atoms, bonds, or substructures falling within sphere(s) of
specified radius. The expression defines the sphere cen-
ter(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 specified expression.
SCAN {TO_ATOMS(CA)} CYAN

Sets of Objects
4.4.5 Static Sets

• Define a Static Set on page 106
• Manage Static Hydrogen Bonds on page 107
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.
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 (_)).
• comment—Comment string.

Sets of Objects
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).

Chapter 5.
Selection of Atoms/Bonds/Sequences
Selection of atoms, bonds, or sequences can be as simple as clicking on the

desired items in the SYBYL display area. However, selection may need to be
based on a particular type, a defined set, a detailed expression, or even on
Boolean operations.
• Selection via the Expression Dialogs on page 110
• What are Expressions? on page 110
• Atom, Bond, and Monomer Selection Mode on page 111
• Manage Selections on page 111
• Select Objects on page 112
• Atom Selection Tutorial on page 114
• Bond Selection Tutorial on page 123
• Substructure Selection Tutorial on page 126

Chapter 5. Selection of Atoms/Bonds/Sequences
Selection via the Expression Dialogs
5.1 Selection via the Expression Dialogs

The SYBYL dialogs used for selecting atoms, bonds, or sequences are designed
to allow as much flexibility as possible. They are activated by other dialogs
whenever an activity requires an atom, bond, or sequence expression as an
argument. For example, the menu item View >>> Color >>> Atoms (or the
command: COLOR ATOM) displays the Atom Expression dialog.
Option
Menu
• What are Expressions? on page 110

• Atom, Bond, and Monomer Selection Mode on page 111
• Manage Selections on page 111
• Select Objects on page 112
What are Expressions?
As selections are made by clicking on items 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 atoms, bonds, or sequences for action being
performed.
As the formula is created, corresponding ID numbers (or three letter codes, in

the case of residues) are echoed within the parentheses. 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 items, see SYBYL Objects on page 79.

Atom, Bond, and Monomer Selection Mode
The option menu in the upper left corner of the dialog can be thought of as the
selection mode. It indicates the type of object on which to base the expression
formula. For example, if Atoms is chosen, clicking on an atom highlights just
that atom and the formula will contain the atom ID. However, if Monomers is
chosen, clicking on an atom highlights the entire monomer to which the selected
atom belongs and the formula will contain the residue number.
Unlike the Atom and Bond Expression dialogs, the Sequence Expression dialog
only has one option available in the upper left menu: Monomer.
Manage Selections
Highlight selected Turn on the Highlight check box. (The

objects check box is on by default.)
Find number of The Selected information box at the top of
selected objects the dialog shows how many objects are
selected in the currently active molecule
area.
Change the active mol- The Molecules field (above the Expres-
ecule area sion field) lists molecule area and name of
all currently displayed molecules. The high-
lighted molecule, is active.
Remove any selection Press Clear.
Undo last action Press Undo. Useful when experimenting
with selections.
Invert selection Press Invert.
Add to current selec- Select Union from the option menu, next to
tion Highlight. Make additional atom selec-
tions. Press OK. Highlighted atoms are those
in either of the two groups of selected atoms.
Subtract from current Select Difference from the option menu.
selection Make additional atom selections. Press OK.
Atoms remaining highlighted are those
found in the first group of selected atoms,
but not the second.
Find atoms common to Select Intersection from the option menu.
two selections. Make additional atom selections. Press OK.
Atoms remaining highlighted are those
found in both groups of selected atoms.

Select Objects
To select: In the Expression Dialog:

Individual objects Left click on desired atom, atoms that form the
bond, or an atom in desired residue. (For bond
expressions, all bonds connected to the atom(s)
picked are selected.)
Everything Press All. An asterisk (*) between the parenthe-
ses in the formula means all.
By type Press Atom (Bond* or Monomer) Types. In
the Types dialog, select from the list of available
types. (For atom types, turn on a check box to
select a chemical element – all atom types
involving this element are highlighted in the list.
When bonds are being selected based on atom
types, all bonds connected to specified atoms are
highlighted.) Press OK.
By substructure Press Substructure. In the Substructures dia-
log, select from the lists of available residues,
waters and other substructures. Use the corre-
sponding All, Invert, and Clear buttons to
manipulate the items selected in a list. To apply
selection to more than one chain in the protein,
press Apply Selection to All Chains. Press
OK. (Note: In the expression field of the Selec-
tion dialog, set names are always surrounded by
braces.)
By predefined set Press Sets. In the Sets dialog, select from the
Sets list. Different sets are available for proteins
than for small molecules. When the option menu
is Monomers, a list of conformational states, as
defined in the MACROMOL dictionary, is also
available for selection. Press OK. (See Global
Sets on page 96.)
By built-in set Press Sets. In the Sets dialog, select from the
Built in Sets list. Press OK. (See Built-in Sets on
page 101.) Only available when the option menu
is Atoms or Bonds.
By chirality Press Sets. In the Sets dialog, turn on check
box(es) for the desired type(s) of chirality to
select. Press OK. Only available when the option
menu is Atoms.

By distance from a Click on one or more atoms to be the sphere’s

point center point. Press Sets. In the Sets dialog, turn
on the Sphere check box and enter the radius
(Å). Press OK. Only available when the option
menu is Atoms or Monomers.
By highlighting Only available when the option menu is Mono-
residues in chain mers. In the field under the All button, highlight
(in proteins) the desired residues.
*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
• Global Sets in the MACROMOL Dictionary

Atom Selection Tutorial
5.2 Atom Selection Tutorial

• Simple Atom Selection on page 114
• Atom Expression Field on page 115
• Select By Atom Types on page 116
• Select via Predefined Sets on page 117
• Select by Substructure on page 118
• Select by Monomer on page 119
• Select via Predefined Sets for Proteins on page 120
Setup
Clear the SYBYL screen of all molecules and background images.
¾ Type: take $TA_DEMO/tut.spl to load a dicloxacillin molecule.
Simple Atom Selection
¾ View >>> Color >>> Atoms
Atom
Option
Button
The option button in the upper left corner is set to Atoms, by default. This
button enables you to select various portions of a molecule (atoms or
monomers).

¾ Click on any five atoms with the left mouse button.

Since the Highlight toggle button is on (the default), selected atoms are
highlighted in green.
¾ In the Atom Expression dialog, press All to select all atoms in the
current work area.
The Selected Atoms information box at the top of the Atom Expression
dialog shows that 49 atoms are currently selected.
¾ Press Clear.
The 49 atoms are no longer selected (the Selected Atoms information box
now reports 0).
¾ Select any three atoms.
¾ Press Undo to unselect the last item you selected.

The Undo button enables you to “take back” the last operation. This is very
useful when experimenting with selections.
¾ Press Invert to deselect atoms that were selected and select all
others.
You now have 47 atoms selected, as shown in the Selected Atoms field.
¾ Press Clear.
Atom Expression Field
For the Atom Expression field to be useful, you must first understand what
atom ID numbers are and how SYBYL defines them.
¾ In the D1 row, press the Atom Labels column (it currently says
None).
¾ Select Id.

Atom ID numbers are unique numbers that SYBYL uses to identify atoms.
All atoms are labeled with an ID #.
¾ Select a single 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
parentheses.
¾ Press Clear and press 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, Booleans, and defined sets directly
into the field.
¾ Replace * with 1+2+3 and press 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” Boolean.
¾ Press Clear.
Select By Atom Types
¾ In the D1 row, set the Atom Labels to Type.
¾ In the Atom Expression dialog, press 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 Press 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 N.am atoms and
turn off N.2 atom.
¾ Change the Union operator to Difference.
¾ Press 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 Press Clear.
Select via Predefined Sets
SYBYL also has a wide variety of unique “Sets” available. Sets can be used to
highlight unique characteristics of a molecule. Various pre-defined 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 Press Sets to display the Sets dialog.
¾ Turn on the Aromatic check box and 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 Press Clear.
2. Locate all rings within this molecule.
¾ Change the Difference operator to Union.

¾ Press Sets.
¾ In the Sets dialog, turn on 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 Change the Union operator 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 Press Atom Types.
¾ In the Atom Types dialog, check N and 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, press Cancel.
Clear all molecules.
Select by Substructure
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 simply the one chosen for this example.
¾ In the textport window, type take $TA_DEMO/tut_big.spl.
¾ In the D2 row, set the Atom Labels to Subs.
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 Press Substructures to display the Substructures dialog.

All substructures in the protein are listed.
¾ In the Residues list, click on A/THR1 and A/PRO41.
¾ Press OK.
All atoms that are part of the two substructures are highlighted.
¾ In the Atom Expression dialog, press Clear.
Select by Monomer
¾ In the Atom Expression dialog, change the option menu from 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 by

clicking on CYS3 in the list and dragging the cursor through CYS4
and into PRO5. (Note: 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 highlighted.
Residue selection can also be done via the Monomer Types button.
¾ Change the option menu from Atoms to Monomers.
¾ Press the Monomer Types button.
¾ Click on TYR in the list and press OK.

All tyrosines are now highlighted.
Select via Predefined Sets for Proteins
1. Color atoms that are in a helix and in the backbone.
¾ In the Atom Expression dialog, press Sets.
¾ In the Sets dialog, select HELIX_H1 and HELIX_H2, and press OK.

¾ In the Atom Expression dialog, change the operator from Union to

Intersection.
¾ Press Sets.
¾ In the Sets dialog, click on the Backbone check box and press OK.
Since you used the Intersection operator, 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 and press OK.

All selected atoms are colored magenta.
2. Highlight the sheet in the protein:
¾ In the Sets dialog, select SHEET_S1, and press OK.
¾ Change the operator to Intersection.
¾ Press Sets.
¾ In the Sets dialog, click on Backbone and press OK.
¾ Select Green and press OK.

At this point the sheet is colored green.
3. Undisplay sidechains to have a better view of the protein backbone.

¾ View >>> Undisplay Atoms
¾ Click on the Sidechain check box and press OK.
4. When finished, reset the atom colors and Atom Expression dialog:
¾ View >>> Display Atoms
¾ Press the All button and press OK.

¾ View >>> Color >>> By Atom Type
Conclusion
At this point, you should have a good idea how to select atoms, sets of atoms,
and substructures. To understand how this can benefit your work, try the
following exercise.
Crambin Protein Exercise:

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
5.3 Bond Selection Tutorial

• Simple Bond Selection on page 123
• Select via Predefined Bond Sets on page 124
• Select by Bond Types on page 124
• Select by Substructure on page 125
• Clear the Bond Color on page 125
Setup
Clear the SYBYL screen of all molecules and background images.
¾ Type: take $TA_DEMO/tut_big.spl to load the structure for

crambin.
Simple Bond Selection
¾ View >>> Color >>> Bonds
¾ In the Bond Selection dialog, select two atoms that are connected to a
bond.
The entire bond is highlighted green and the bond number appears in the
Bond Expression field.
¾ Press Clear.

Select via Predefined Bond Sets
¾ Press Sets to display the Sets dialog.
¾ From the list of predefined sets in the MACROMOL dictionary, select

ACIDIC and press OK.
All bonds in residues of type ASP, GLU, and TYR are selected and the
equation in the Bond Expression field states: M2({ACIDIC}).
¾ Press Clear.
Select by Bond Types
¾ Press Bond Types to display the Bond Types dialog.
All possible bonds in the molecule are listed. Highlighting one or more of the
bond types and pressing OK selects all bonds in the molecule of the selected
type(s).
¾ In the Bond Types dialog, press Cancel.

Select by Substructure
¾ Press Substructures to display the Substructure dialog.
The Substructures dialog enables you to select all bonds within selected
substructures.
¾ Press Cancel.
You can also obtain a list of bonds by selecting atoms or monomers in the
option menu (upper left corner of the Bond Expression dialog).
¾ Set the option menu to Atoms.
Although identical to the Atom Expression dialog, selections are interpreted in

relationship to bonds instead of atoms.
¾ Click on any three atoms in the crambin protein and press OK.
¾ In the Option dialog, choose magenta and press OK.
All bonds directly connected to atoms you selected are colored 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 you have just done.
¾ View >>> Color >>> Bonds
¾ Select All and press OK.
¾ Select TRANSPARENT and press OK.
Conclusion:
At this point, you should have a good idea how to select bonds, sets of bonds,
and substructures.

Substructure Selection Tutorial
5.4 Substructure Selection Tutorial

• Select from Chain on page 126
• Select via Predefined Sequence Sets on page 127
• Select by Monomer on page 128
Select from Chain
With the crambin structure still on the screen, display the Sequence Expression
dialog. (If crambin is not on the screen, type: take $TA_DEMO/
tut_big.spl.)
¾ Biopolymer >>> Composition>>> Excise Monomer
Unlike the Atom and Bond Expression dialogs, this dialog only has one option
available in the upper left menu: Monomer.
Select residues ILE33 through ALA38.
¾ Use the scroll bar below the field showing the chain residue list to
move to ILE33.
¾ Highlight ILE33 through ALA38 in the chain list by clicking on ILE33
and dragging the cursor through the other residue names and into
ALA38. (Note: As long as any portion of the residue’s name in the list
is highlighted, it is considered to be selected.)
This field lists the monomer sequence in the selected molecule area. It is empty
if the molecule has no monomer sequence.

All atoms in the 6 selected residues are highlighted.
¾ Press Clear.
Select via Predefined Sequence Sets
¾ While still in the Sequence Expression dialog, press Sets to display the
Sets dialog.
Predefined sets available in the 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.

All atoms in residues considered to be hydrophobic are selected.
¾ Press OK.
Note the equation in the Sequence Expression field now says:
M2({HYDROPHOBIC}).
¾ Press Clear.
Select by Monomer
¾ In the Sequence Expression dialog, press Monomer Types.
The Residue Types dialog lists all possible monomer types available in the
dictionary. Highlighting one or more of the types and pressing OK selects all
residues in the molecule of the specified type(s).
¾ In the Residue Types dialog, select ALA in the list and press OK.
All of the alanine residues are highlighted.
¾ In the Sequence Expression dialog, press Cancel.
Conclusion
At this point, you should have a good idea how to select protein substructures
by chain, by set, and by monomer. This concludes the Selection Tutorial.

Chapter 6.
Molecule Databases
• Database Tutorial on page 132

• Open/Close Databases on page 138
• Obtain Information on Databases on page 143
• Retrieve Molecules on page 144
• Managing Database Content on page 148
• Save Database Molecules to MOL2 or MOL Files on page 153
• Connect to External Relational Databases on page 154
• DATABASE Command List on page 163
Database Formats
There are currently two different formats for molecular 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.
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 SGI and IBM workstation 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 will usually eliminate such
errors.
Users 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 an example of this, see the Database
Tutorial on page 132. 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 6. 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://leadquest.tripos.com
• 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
6.1 Database Tutorial

This tutorial shows 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.
For purposes of clarity, a small database containing amino acids has been
created and is used in this tutorial.
Set Up
2. Copy a file from the demo account to the working directory. Be careful to
include the space and period at the end of the line.
¾ Type: dcl cp -r $TA_DEMO/aa.mdb .
Open the Database
Open the database of amino acids and examine its contents.

¾ File >>> Database >>> Open
¾ Select aa.mdb (press OK).
¾ Select UPDATE (press OK).
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.
¾ File >>> Database >>> List

Database Tutorial
¾ Select MOLECULE (press OK).
¾ Accept * as the Object Name (press OK).
The names of the molecules that make up the aa database are listed in the
textport.
Define (Static) Sets of Molecules
1. Enter the DATABASE mode.
¾ Type: MODE DATABASE
The MODE command is used 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, thus the outer command is not repeatedly entered. When
you are in this mode, any command not available as an option can be invoked
by preceding it with the word COMMAND.
2. Partition 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:

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 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, which appear below.
The group membership of database sets is static.

Database Tutorial
3. Examine the contents of the newly created sets.
¾ Type: 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.

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
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”).
Build a New Molecule
In this section of the tutorial, hydroxyproline is added to the database.
1. Retrieve proline from the database to use as a template.
¾ File >>> Database >>> Get Molecule
¾ Select PROLINE (press OK).

Database Tutorial
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.
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.
¾ Build/Edit >>> Name Molecule
¾ Enter hydroxyproline (press OK).
¾ File >>> Database >>> Put Molecule
Redefine a Set and its Effect on the Class
1. Since hydroxyproline is an uncharged polar molecule, add it to the

POLAR_NEUTRAL set.
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 *

Database Tutorial
Notice that hydroxyproline has been automatically added to the definition of

HYDROPHILIC. Since the class “hydrophilic” was defined in terms of the
groups “acidic”, “neutral”, and “basic”, hydroxyproline automatically becomes
a member of “hydrophilic”.
Search the Database
The next few sections will each present a different way of accessing database
molecules. Recall that the simplest way was to retrieve by molecule name. If
you do not know the name, either at all or exactly, you can use a wildcard to
search the database (by name) for any matching string. The wildcard (*) alone
selects all of the molecules.
¾ Type: SEARCH NAME *
¾ Change the display to Quartered mode.
1. Select leucine from the database.
¾ Type: SELECT leucine M2
This command takes either the molecule’s full or partial name (with wildcards).
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.

Database Tutorial
¾ Select M4 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 Type: SELECT glu* M4
Any combination of union, intersection, difference, and negation of property

groups and name specifications (with or without wildcards) can be used to
select molecules for retrieval. These facilities, coupled with the ability to
organize molecules into groupings meaningful to you, allow arbitrarily complex
structures to be manipulated with ease.
Close the Database
1. Exit the DATABASE command mode.
¾ Type: ENDMODE
2. Close the database.
¾ File >>> Database >>> Close
Continue reading

Open/Close Databases
6.2 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 139
• Open Database via Command Line on page 140
• Open a New, Empty Database on page 140
• Copy Database Contents to New Database on page 141
• Define Alias for Database via Command Line on page 141
• Specify a Default Database on page 141
• Close Database via the Command Line on page 141
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.
6.2.1 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 Pick sub-directory containing database to open.
Other Directo- Lists your home directory and SYBYL’s default direc-
ries tory, if it is different from your home directory.
Databases Databases available in the selected directory. Clicking
once on a database in this list highlights it and places it
in the Database Name field, for possible editing.
Clicking twice on a database opens it.
Show Databases Turn on check box(es) for type(s) of databases to show
in the list. By default, both types are listed.
Database Name Shows full path of database selected in the list. Alter-
nately, enter the full path of the database directly in this
field.

6.2.2 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.
6.2.3 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.

6.2.4 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.
6.2.5 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.
6.2.6 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.
6.2.7 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
6.3 Obtain Information on Databases

• List All Open Databases on page 143
• Show Status for Database on page 143
• List Contents of Open Database on page 143
• List Molecule and Group Information for Open Database on page 143
6.3.1 List All Open Databases

DATABASE ALLOPEN
Full database names are listed along with aliases given in parentheses. The
default user database is denoted.
6.3.2 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.
6.3.3 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).
6.3.4 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
6.4 Retrieve Molecules

• A Note on Query Expressions on page 144
• Retrieve a Molecule on page 146
• Search for Molecule(s) to Retrieve on page 147
• Create/Modify a Table of Data on page 147
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
6.4.1 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 144.

Retrieve Molecules
6.4.2 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.
6.4.3 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
6.5 Managing Database Content

• Add Molecule(s) on page 148
• Delete Molecule(s) on page 149
• Organize Molecules into Groups (Sets and Classes) on page 149
6.5.1 Add Molecule(s)

Notes:
• The molecule being added must have a name. (See MODIFY MOLECULE
NAME to give the molecule a name, or General Naming Conventions on
page 84 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).

6.5.2 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.
6.5.3 Organize Molecules into Groups (Sets and Classes)

• Grouping Mechanisms on page 149
• Define/Modify Definitions of Groups on page 150
• Rename Group or Molecule on page 150
• Reorganize and Compress Database Contents on page 151
• Align Molecules in Database on page 152
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-hydroxyproline)
• Database Classes—Molecules matching a specified database query
expression. Once defined, the class is reevaluated each time it is refer-
enced, 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 132 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.

Align Molecules in Database
License Requirement:
Requires a QSAR license.
Menubar: File >>> Align Database

Command Line: DATABASE MATCH_ALIGN old_db mol_list tem-
plate query orientation new_or_old [db]
• old_db—Database from which to get molecules and
template.
• mol_list—Comma-separated list of names of database
molecules to align.
• template—Name of database molecule to use as a
template.
• query—UNITY query describing core structure to use
for alignment.
• orientation—
AS_IS—Do not change the orientation.
INERTIAL—Inertially align template molecule to get a
more robust CoMFA with a good q2.
• new_or_old—What to do with the molecules:
EXISTING—Store in existing database.
NEW—Store in new database.
NONE—Leave in molecule areas.
• db—Database to put aligned molecules into if previous
argument is EXISTING or NEW.
All molecule areas are cleared, including the one containing the core structure.
Upon completion, all occupied molecule areas are written into the designated
new database in REPLACE mode. If new database does not yet exist, it is
created. For multiple occurrences of core in the template or in the molecules
being aligned, you are prompted to select the appropriate substructure.
Be aware that the core is only used to determine the connectivity of the
substructures to be matched. Conformational information (e.g., chair vs. boat) is
not utilized.
• Database Align dialog in the QSAR Manual.

Save Database Molecules to MOL2 or MOL Files
6.6 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
6.7 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.
6.7.1 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
6.7.2 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
6.7.3 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
.
.
6.7.4 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
6.7.5 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.
6.7.6 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
6.7.7 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
6.7.8 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

6.7.9 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
6.8 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
MATCH_ALIGN OPEN RENAME
REORGANIZE SAVE_AS SEARCH
SHOW STATUS SYSTEM
TABLE TO_MOL2DB WRITE_FILE
WRITE_FILE2 XADD XCLOSE
XCREATE XSTATUS

Chapter 7.
Expert’s Corner
The following information may be found helpful when working with SYBYL
• Manage Input/Output Formats on page 166
• Generate 3D Coordinates on page 166
• SMILES Strings on page 167
• SD/MACCS Files on page 168
• AMPAC Status Files on page 169
• MOPAC Status Files on page 169
• CSSR files on page 169
• Record and Play SYBYL Sessions on page 171
• Modes for SYBYL on page 176
• Command Modes and Execution Options on page 178
• Execute Operating System Commands from Within SYBYL on page 181
• Markush Atoms on page 182
• Textport Output Presentation on page 183
• Keyboard Shortcuts on page 184
• Control Characters on page 185
• Menubar Shortcuts and Comments on page 186
• Libraries of Chemical Groups and Fragments on page 187
• Edit Text Files with the Text Editor on page 192

Chapter 7. Expert’s Corner
Manage Input/Output Formats
7.1 Manage Input/Output Formats

7.1.1 Generate 3D Coordinates
The CONCORD™ program rapidly generates high quality approximate 3-
dimensional molecular structures. It is distributed by Tripos as an optional
addition to SYBYL. CONCORD can also be executed as part of the SKETCH
CLEAN_UP procedure. (See TAILOR SET SKETCH CLEAN_UP.)
Specify Molecule Build/Edit >>> Clean-Up Molecule >>> CON-

Area via the CORD Clean-Up
Menubar: Updates molecule coordinates. If there is an error, orig-
inal molecule is not modified.
Specify Molecule CONCORD MOLECULE mol_area
Area via Command Updates molecule coordinates. If there is an error, orig-
Line: inal molecule is not modified.
Specify SLN via Build/Edit >>> CONCORD SLN
the Menubar:
Specify SLN via CONCORD SLN mol_area sln_string
Command Line: • mol_area—Area to hold resulting structure.
• sln_string—SYBYL line notation string.
Specify SMILES Build/Edit >>> CONCORD SMILES
String via the If SMILES string is valid, molecule is displayed. Other-
Menubar: wise, an error message is issued reporting location of
first non-acceptable character in the string.
Specify SMILES CONCORD SMILES mol_area smiles_string
String via Com- • mol_area—Area to hold resulting structure.
mand Line: • smiles_string—Chemical line notation string.
If SMILES string is valid, molecule is displayed. Other-
wise, an error message is issued reporting location of
first non-acceptable character in the string.
Exit via the CONCORD EXIT
Menubar: Terminate CONCORD process. A log file is written
and closed.
References:
[1] R. S. Pearlman, “Rapid Generation of High Quality Approximate 3-
dimension Molecular Structures,” Chem. Des. Auto. News, 2,1, (1987).
[2] CONCORD/StereoPlex Manual, Tripos Inc., St. Louis MO, 1998.

7.1.2 SLN Files
Menubar: File >>> Read

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

Convert the supplied SMILES string into a SYBYL molecule. If CONCORD is
available, it is used to generate a 3D structure. If CONCORD does not exist, an
internal SMILES converter is used to generate 2D coordinates. This structure
should be minimized or otherwise converted to 3D for modeling purposes.
SMILESTOMOL smiles
Reference:
[3] Weininger, D., SMILES, a Chemical Language and Information
Systems. 1. Introduction of Methodology and Encoding Rules, Chem.
Inf. Comput. Sci., 28, 31-36 (1988).
• CONCORD command description.
• %smiles_to_mol expression generator.

7.1.4 SD/MACCS Files

MACCS is the format used by Molecular Design Ltd. 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 on page 168
• Convert MACCS Files to Molecular Spreadsheet or UNITY Hitlist on
page 168
Read/Write SD Files

File >>> Save As (specify the Format as 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.
Convert MACCS Files to Molecular Spreadsheet or UNITY Hitlist
MACCS is the format used by Molecular Design Ltd. 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.
7.1.5 AMPAC Status Files

Command Line: FILES AMPAC_STATUS mol_area filename
Multiple molecules in the AMPAC file (.arc extension is implied) are

displayed in successive molecule areas. Any existing molecule in the designated
molecule area (and all subsequent areas used), is overwritten. Connectivity
information is derived from minimum (0.90 Å) and maximum (1.65 Å)
distances of atoms. Atom types are converted to SYBYL atom types. Verify all
atom type assignments.
7.1.6 MOPAC Status Files

Command Line: FILES MOPAC_STATUS mol_area filename
Multiple molecules in the MOPAC file (.sta extension is implied) are displayed
in successive molecule areas. Any existing molecule in the designated molecule
area (and all subsequent areas used), is overwritten. Connectivity information is
derived from minimum (0.90 Å) and maximum (1.65 Å) distances of atoms.
Atom types are converted to SYBYL atom types. Verify all atom type assign-
ments.
7.1.7 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.

Record and Play SYBYL Sessions
7.2 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 172
• Record Output from a Single Command on page 173
• Record Terminal Dialog of Session on page 173
• Insert a Pause in a Recorded Session File on page 174
• Play Recorded Session on page 174
• Read Command Input From Text File on page 175
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.

7.2.1 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 173
• Insert a Pause in a Recorded Session File on page 174

7.2.2 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.
7.2.3 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 173

• Play Recorded Session on page 174
7.2.4 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.
7.2.5 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.
7.2.6 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.

Modes for SYBYL
7.3 Modes for SYBYL

There are three basic modes in which SYBYL can be run:
• Menubar Mode on page 176
• Command Mode on page 176
• Object Picking Mode on page 177
The most commonly used mode is menubar and most of the documentation for
SYBYL is written from the perspective of running in this mode.
7.3.1 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 simply typing the command:
MENUBAR
Follow it with the command SET PICKING command (discussed in the

Graphics Manual).
7.3.2 Command Mode

When in command mode, commands are typed at the SYBYL prompt. There are
three variations of the command mode available, depending on your level of
expertise with the program:
• Type only the command name and press <return>. 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 entire command and all arguments on a single line.
Notes:
• In menubar mode, you may also enter commands without changing
picking modes. To return to the command mode from another mode,
type: set picking no_picking.

Modes for SYBYL
• 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).
Default Values
When entering a command, the computer prompts for the arguments you must
supply. After each prompt, a set of angle brackets occurs containing a word,
numeric value, or phrase. This is the current default which will be accepted if
you simply hit the <return> key.
Special Characters
?—The help character may be entered at any time to obtain information about a
command, legal values of an argument, or 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.
7.3.3 Object Picking Mode

In this mode, every time an object (atom, bond, substructure, or molecule) is
requested, a menu or dialog appears and you may pick that object from that
menu or from the molecule(s) displayed on the screen. All other input is
accepted from the keyboard in normal command line.
To use object picking mode, type: set picking object_only.

Command Modes and Execution Options
7.4 Command Modes and Execution Options

• Command Mode on page 176
• Automatic Command Execution on page 178
• Execute Command on Multiple Molecules on page 179
• Monitor Performance of SYBYL Command on page 180
7.4.1 Command Modes in SYBYL

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 (|).
7.4.2 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 will be
executed each time SYBYL starts.
TA_SYSTEM_STRT is used 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"
TA_USER_STRT is 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 collect (Log

Commands) and photo (Log Session) files and to set the error reporting to
traceback. See Record and Play SYBYL Sessions on page 171 for a description
of the files and their purpose.
7.4.3 Execute 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 must then 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>)
7.4.4 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 then re-issues the
command to the program. When the command terminates, the elapsed time
during the command, time spent in the system, and time spent in execution of
the command (in seconds) are displayed in the textport. This command can 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.

Execute Operating System Commands from Within SYBYL
7.5 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.

Markush Atoms
7.6 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
Define via the Menubar: UNITY >>> Markush >>> Define

Define via Command MARKUSH DEFINE name definition
Line • name—Name for new Markush atom.
• definition—SLN defining the Markush (refer
to the SLN Manual).
Delete via the Menubar: UNITY >>> Markush >>> Delete
Delete via Command MARKUSH DELETE name
Line
List via the Menubar: UNITY >>> Markush >>> List
List via Command Line MARKUSH LIST
Load via the Menubar: UNITY >>> Markush >>> Load
Load via Command Line MARKUSH LOAD filename
Modify via the UNITY >>> Markush >>> Modify
Menubar:
Modify via Command MARKUSH MODIFY name definition
Line • name—Name of Markush to modify.
• definition—New SLN defining the Markush.
Save via the Menubar: UNITY >>> Markush >>> Save
Save via Command Line MARKUSH SAVE filename
This is identical to the UNITY MARKUSH command, except that it does not start
the server and, therefore, does not require a UNITY license.

Textport Output Presentation
7.7 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. SYBYL solves this problem by monitoring the number of lines
written to your screen, and suspending output when the screen is full.
The prompt: “Additional Output Available [C,G,Q]” appears at the

bottom of the screen, and lists the three actions available at that point:
• C—Continue with output until the screen is once again filled with text, at
which point the prompt is issued again. The <return> key may also be
used to perform this function.
• G—Go until the current operation is finished. This is useful when the
output does not warrant close inspection. No further prompts are issued,
regardless of the number of output lines.
• Q—Quite the current operation and return to the command level.
These single characters can be in upper- or lowercase, and need not be followed
by a <return>.
For time-consuming operations, such as minimization, you may not wish to

remain by the terminal while the computation takes place. To prevent the
program from halting after the first screen-full of information, a timer is used. If
no response is given to the “Additional Output Available” prompt within
two minutes, output continues as if you had pressed the C key. To avoid even
these delays, set the time to zero with the command SET CGQ_TIMEOUT 0 or
run the operation in batch mode.

Keyboard Shortcuts
7.8 Keyboard Shortcuts

Several keyboard keys have been assigned a particular function is SYBYL.
Below is a summary of the functions available:
Key Action
F1 Push textport window back to view entire graphics screen;
press it again to put text on top.
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 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 Raise/lower SYBYL graphics window. When full screen hard-
ware stereo is active, the menubar is also raised/lowered.
F9 Toggle between Global and D1.
Up arrow Rotate +90° about the X-axis.
Down arrow Rotate –90° about the X-axis.
Left arrow Rotate +90° about the Y-axis.
Right arrow Rotate –90° about the Y-axis.
Control Use in combination with a left mouse pick to select a mole-
cule or background for object transformation.

Control Characters
7.9 Control Characters

^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.

Menubar Shortcuts and Comments
7.10 Menubar Shortcuts and Comments

Several shortcuts exist with the menubar interface, some of the most frequently
used ones are listed below:
• Commands can be typed at the keyboard while in menubar mode.
• Pull-down menus remain visible if you click on the menu item and
release the mouse button.
• Control-click selects the molecule to rotate, without using the widget to
change the display area or altering the default molecule area.
• Control-right-click on an atom labels that atom according to the tailor
variable GRAPHICS MOUSE_LABEL.
• Dialogs can often be resized to expand the fields. The procedure depends
on your X window environment.
• Double clicking on an item in a pop-up menu (a single choice list in a
dialog) is equivalent to clicking once on the item and clicking once on
OK or End.
• Press the tab key to skip to the next field or list in the dialog.
• In a list, the arrow keys move the pointer up and down.
• Once an operation has been initiated by clicking on 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.
• Beware of the hidden dialog. Given the complexity of some operations
and the flexibility of the modern Motif windowing environment, it is
possible for one window to cover a dialog waiting for input. If you
suspect such a situation click on the Restack graphic icon or succes-
sively lower or iconify each window large enough to cover a dialog.
Warning: Closing the SYBYL or Spreadsheet window by clicking on the

window’s close box causes a SYBYL crash.

Libraries of Chemical Groups and Fragments
7.11 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 accom-
plished once you know a little about the SYBYL file structure.
In this section, you will find:

• Group Library Structure and Contents on page 187
• Fragment Library Structure and Contents on page 188
• Using the Fragment Library (Refer to the FRAGMENT command)
7.11.1 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.

7.11.2 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 149.
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

7.12 Edit Text Files with the Text Editor

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.
Edit Text Files with the Text Editor
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.

SYBYL Basics Index
A Attach
chain 48, 56
Abort a command 177
Attributes
Access help 11 all atom
Acidic global se 98 remove 53
all bond
Add
atom 47
remove 55
stereo atom
bond 53
remove 69
chain 48
stereo bond
features and constraints 76
remove 69
group 56
hydrogens 48 Automatic command execution 178
rawatom 48 Average molecule 70
ADD_PSEUDOATOMS 49
Aggregate B
sets 95
Backbone
Alignment built-in set 102
database on a template 152
Basic global set 98
ALLMOLS 179
Bibliography
Alternate atom types 51 chirality assignment 67
Amide bond 86 SHAKE algorithm 69
Amino acid BIOPOLYMER
global sets 98 sets 97
AMPAC Block global set 98
read status file 169 Bond
Angle add 53
between planes 27 angle list 21
measure 27 attributes 67
modify 55 expression rules 86
Aromatic bond 86 length
list 21
Aromatic built-in set 102 naming conventions 86
Atom remove 55
add 47 stereo attributes 67
chirality attribute 67 type
expression rules 85 modify 55
modify 49 Building
naming conventions 85 small molecule 41
rawatom 48
remove 53 101
Built-in sets
Atom expression Bulky global set 98
dialog 112 Bumps
field 115 built-in set 102
Atom types
alternate set 51 C
modify 50
C-alpha carbon global set 98
Atomic coordinate
topography 21 Cambridge
SYBYL 7.0 (Fall 2004) SYBYL Basics Index-195

read/write CSSR files 169 D
Cap global set98 Database
CAPTURE 173 add molecules 148
Center of mass 71 align molecules 152
align on a template 152
Centroid 72
classes 149
CGQ prompt 183 close 141
Chain copy contents to new database 141
of atoms 48 copy database directories 131
create empty database 140
Change
create table 147
molecule name 58, 150
DATABASE command list 163
substructure name 57
define alias 141
Charge define class or set 150
built-in set 102 example 133
modify 49 delete 149
Chiral built-in set 102 deleting database directories 130
get a molecule 146
Chirality
grouping mechanisms 149
atom attribute 67 list contents of open database 143
check 39
list molecule and group information 143
invert 68
list open databases 143
Class open 140
define in a database 149 open system database 140
Collect commands into a file 172 rename 150
reorganize contents 151
Color
reorganizing mol2 databases 151
dynamic hydrogen bonds 101
save as 148
static hydrogen bonds 107
save to MOL2 or MOL file 153
Command search 147
mode 176 example 136
default values 177 sets 149
special characters 177 show status 143
unique string 177 specify default database 141
CONCORD 166 tutorial 132
unlocking 138
Conformation
naming conventions 90 dbtranslate Unix utility
SCAN 69 see UNITY manuals
valid state names 91 use in MACCS conversion 168
Connectivity dbunlock Unix utility 138
quick bonds 54 DCL 181
Conventions (see Names) Default molecule area 10
Coordinates Defining
list 21 center of mass 71
MODIFY 49 centroid 72
Copy molecule area contents 24 dynamic set 100
extension point 73
Creating
global set 96
small molecules 41 line 74
normal 75
plane 76
Index-196 SYBYL Basics SYBYL 7.0 (Fall 2004)

static set 106 center of mass 71
UNITY features 77 centroid 72
Deleting extension point 73
all atom attributes 53 line 74
all bond attributes 55 normal 75
atom 53 plane 76
bond 55 Exit
center of mass 72 SYBYL 32
centroid 72 Extension point 73
dynamic hydrogen bonds 101
extension point 73 Extract structures
global set 97 from molecule area 24
line 74
local set 100 F
molecule in a database 149
non query atoms 77 Features
normal 75 center of mass 71
plane 76 centroid 72
static hydrogen bonds 107 extension point 73
stereo atom attributes 69 line 74
stereo bond attributes 69 normal 75
substructure 57 plane 76
UNITY feature 78 UNITY 77
Difference File formats
operator .demo file 175
in a database 144 File selection dialog 16
in object expressions 92 Files
Dipole moment 28 edit 192
Directory Files created
list database contents 143 CAPTURE 173
Display area COLLECT 172
diagram 15 DATABASE 140
WRITE_FILE2 153
Distance
FILES
measure 27
CSSR 170
modify 55
MOPAC 169
Disulfide global set 98 MOL2 and MOL 18
DNA global set98 SD files 168
Double bond 86 Files, reading/writing
AMPAC 169
Dynamic set 100
CSSR 169
(see also Local sets)
MOPAC 169
SD file 168
E SLN 167
Edit Fill valences 48

text files 192 Findconf built-in set 103
End SYBYL 32 Fragment
Environment variable FRAGMENT command 13
TA_HIDE_UNLICENSED_PRODS 9 library 188
access from sketcher 45
Evaluating structure and contents 188

Freeze
coordinates
J
before merging 25 Join
groups or molecules 66
Fuse ring 59
tutorial 60 Journal
COLLECT command 172
PHOTO command 173
G
Geometry
measure 26
K
modify 55 Kollman atom types 51
display 51
Global
dictionary set 97
set 96 L
Grid Libraries 187
SKETCH 46
License requirements
Group library 187 SYBYL basics 5
add 56
SKETCH 45 Line 74
structure and contents 187 List
object information 22
H Load
molecules 13
Hardcopy 23
Local set 99
Hbond built-in set 103 Log out of SYBYL 32
Height measurement 27
Logical operators in object expressions
Help 11 difference 92
special characters 177 grouping 94
Hide menu options 9 intersection 92
negation 92
Hydrogen bonds
union 92
dynamic
color, delete, resize 101 Lone pair
static MODIFY 50
color, delete, resize 107 LQSample database 131
Hydrogens
add 48
M
Hydrophobic
global set 98 MACCS
convert to molecular spreadsheet 168
convert to UNITY hitlist 168
I read into SYBYL 168
write from SYBYL 168
Information
report on atom, bond, or substructure 21 MARK_RS isomerism 67
Interacting MARK_ZE isomerism 67
with SYBYL 7 Markush 182
Intersection operator Match
in a database 144 align database on a template 152
in object expressions 92 Measure
Invert chirality 68

angle 27 Montype built-in set 103
distance 27 MOPAC
height 27 read/write status files 169
plane angle 27
torsion 27 MREAD 18
UNITY features 28
Menubar 9 N
command 176
Name
shortcuts 186
atom 85
Merge atoms
structures 24 modify 50
Mode 178 bond 86
chain 90
Modified amino acid global set 98
conformation specification 90
Modify general conventions 84
angle 55 local set 99
atom 49 molecule area 88
bond 55 molecules 88
distance 55 monomer sequence 89
global set 97 generic 89
local set 99 specific 89
molecule 58 set 88
substructure 56 substructure 87
torsion 55
NCI_2000 database 131
UNITY feature 77
Negation operator
MOL 18
in a database 144
write multiple files 153 in object expressions 92
MOL2 18 Neutral global set 98
Molecular Spreadsheet
Non-bonded
MACCS file conversion 168 list 21
Molecule
defining features 71
Normal 75
deleting in a database 149 Notebook
evaluating features 71 COLLECT command 172
expression rules 88 PHOTO command 173
extracting atoms 24
modify 58
naming conventions 88
O
reading a file(s) 16 Object
save in a database 148 definition 80
split 53 expression 92
type 59 picking mode 177
writing a file(s) 16 selector 92
Molecule area 80 Operator
default 10 difference 92, 144
naming conventions 88 grouping 94
Monomer intersection 92, 144
sequence expression rules 89 negation 92, 144
sequence naming conventions 89 precedence 145
union 92, 144
Monprop built-in set 103

P normal 75
plane 76
Pause 174 stereo atom attribute 69
PHOTO 171, 173 stereo bond attribute 69
substructure 57
Plane 76
UNITY feature 78
measure angle 27
reflect through 68 Replace chain 48, 56
Play back session Resize
COLLECT and TAKE files 171 dynamic hydrogen bonds 101
command file 174 static hydrogen bonds 107
Polar global set 98 Retrieve molecules 146
Possible_hbond built-in set 103 Ring
built-in set 104
Printing 23
external 81
PRO RS isomerism 67 fusion 59
Purine global set 98 internal 81
list 22
Pyrimidine global set 98 ring fusion tutorial 60
RNA global set 98
Q Root atom 58
QUICKBOND command 54 Rotation
Quit 32 modify center 58
of molecules 25
R RS isomerism 67
Rawatom, adding 48
RDBMS 154 S
Read file dialog 16 Saving
in the memory stack 30
Read/save database molecules 153 molecules in a database 148
Recording sketch 40
COLLECT command 172 Scanning
PHOTO command 173 torsions 69
Recover contents of molecule area 30 Scrolling text region 183
References SD file
chirality assignment 67 read/write files 168
SHAKE algorithm 69
Search
Reflect atoms 68 database 147
Remove Sequence
all atom attribute 53 built-in set 104
all bond attribute 55
atom 53 SET
bond 55 PICKING 176
center of mass 72 Sets 95
centroid 72 aggregates 95
extension point 73 built-in 101
global set 97 database 149
line 74 dialog 127
local set 100 dynamic 100
non query atoms 77 for biopolymers 97

global 96 SYBYL/Advanced CoMFA
local 99 database align 152
naming conventions 88 SYBYL/TRIAD
static 106 See the TRIAD Manuals
user-defined 96
SHAKED command 69
T
Sidechain built-in set 104
TABLE
Single bond 86
DATABASE 147
Sketcher 41
Tailor
add Z coordinate 44
ATOM_TYPE
branching 43
FIX_NAMES 50
change atom types 43
CENTROID 72
check chirality 39
CHIRAL 68
draw a ring 44
CONNECT 54
draw multiple bonds 44
DATABASE 129, 139
menu items 45
FUSE 59
move an atom 45
GENERAL
save 40
ANGLE_RANGE 26
techniques 42
ATOM_IDENTIFIER 22, 23
tutorial 34
HELP 11
SLN JOIN 66
read/write file 167 MERGE 25
Small molecule building (see SKETCH) 41 MOL
COORD_PLACES 138, 151, 153
SMILES to MOL conversion 167 FILE_FORMAT 19, 20, 153
SPAWN command 181 NORMAL 75
Sphere built-in set 105 PLANE 76
SCAN 70
Spiro fusion 59
TABLE 155
Split molecule 53 UNITY 76
Standard amino acids Tailor variables
global set 98 HBONDS
Starting MAX_DISTANCE 101
SYBYL 8 MIN_DISTANCE 101
Static set 106 TAKE 174
manage hydrogen bonds 107 TAKE51 175
Store molecules 148 Template
Subst_sphere built-in set 105 152
aligning database
Substructure Terminate SYBYL 32
expression rules 87 Textport window
modify 56 SYBYL 9
naming conventions 87
Time performance of command 180
remove 57
root 57 TMPDIR environment variable 151
selection example 118 To_atoms built-in set 105
type 57
Toolbox icons
Sugar global set 98 overview 9
SYBYL 5.1 Topography 21
COLLECT/TAKE files 175
Torsion

list angle 21
measure 27
modify 55
Triple bond 86
TTY command 175
Tutorials
atom expression 112
building a small molecule 34
DATABASE 132
file format 175
interacting with SYBYL 7
ring fusion 60
sketching a small molecule 34
small molecule sketching 34
U
Undo last action 30
Union
operator
in a database 144
in object expression 92
UNITY
defining features 77
MACCS file conversion to hitlist 168
modify feature 77
remove features and constraints 78
remove non query atoms 77
Unix utilities
dbtranslate
see UNITY manuals
use in MACCS conversion 168
dbunlock 138
User-defined sets 96
Z
ZAP 29
ZE isomerism 67

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SYBYL® Basics Manual

Tripos Inc. Phone: +1.314.647.1099

hint! is a registered trademark of eduSoft LC.

SYBYL 7.0 (Fall 2004) SYBYL Basics TOC-3

TOC-4 SYBYL Basics SYBYL 7.0 (Fall 2004)

SYBYL is a state-of-the-art program in molecular modeling which uses

Required License for SYBYL Basics

SYBYL 7.0 (Fall 2004) SYBYL Basics 5

The Very Basics

• Start SYBYL on page 8

SYBYL 7.0 (Fall 2004) SYBYL Basics 7

2.1 Start SYBYL

2. Start the SYBYL program.

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

8 SYBYL Basics SYBYL 7.0 (Fall 2004)

SYBYL’s menubar is similar to that of a PC application’s menubar. The

SYBYL 7.0 (Fall 2004) SYBYL Basics 9

Default Molecule (Work) Area

Menubar: Options >>> Set >>> Default Molecule

10 SYBYL Basics SYBYL 7.0 (Fall 2004)

2.2 How to Get Help

SYBYL 7.0 (Fall 2004) SYBYL Basics 11

Type a question mark (?), when prompted by the program for

12 SYBYL Basics SYBYL 7.0 (Fall 2004)

2.3 Work with Molecules

2.3.1 Load Molecules from the Fragment Database

Menubar: Build/Edit >>> Get Fragment

SYBYL 7.0 (Fall 2004) SYBYL Basics 13

Load Multiple FRAGMENT NAME name_expr

1. Load 1,3-DIOXANE into SYBYL.

¾ Build/Edit >>> Get Fragment

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

A display area is where your molecule is going to be displayed on the screen.

Note that molecule areas have rules:

14 SYBYL Basics SYBYL 7.0 (Fall 2004)

• M1 is always in display area D1.

The figure below demonstrates this pattern:

2. Change the characteristics of your loaded molecule.

¾ Press Q to close the Display Options dialog.

3. Load another molecule into SYBYL.

¾ Build/Edit >>> Get Fragment

SYBYL 7.0 (Fall 2004) SYBYL Basics 15

M1 is already being used by 1,3-dioxane. However, the other molecule

2.3.2 Read/Write Files of Molecules

Additional information on using different input formats in SYBYL is available

16 SYBYL Basics SYBYL 7.0 (Fall 2004)

Read in Structure from File via the Menubar

¾ To open a file for reading, select File >>> Read.

Directory Current directory.

SYBYL 7.0 (Fall 2004) SYBYL Basics 17

A subset of this dialog, is accessed from several other dialogs.

Write out Structure from File via the Menubar

Read/Write MOL/MOL2 Files via Command Line

MOL2 direction [mol_area] [filename]

MOL direction [mol_area] [filename]

MREAD direction [mol_area] [filename]

18 SYBYL Basics SYBYL 7.0 (Fall 2004)

direction • DIRECTORY—Report if specified file has MOL or MOL2

SYBYL 7.0 (Fall 2004) SYBYL Basics 19

bond information, rotatable bond definitions and plane equations. To

2.3.3 Obtain Information on SYBYL Objects

20 SYBYL Basics SYBYL 7.0 (Fall 2004)

Report Information on an Individual Atom, Bond, or Substructure