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QUANTA 2006 Basic Operations |
Who should read this book
What this book contains
How to use the QUANTA introductory documentation set
Documentation set roadmap
Related documentation
Conventions
1. Using QUANTA
Online help
QUANTA design, layout, and basic functions
Understanding files
Setting the QUANTA environment
Setting up to run the tutorials
Starting QUANTA
Understanding QUANTA windows
Molecule window
Viewing area
Menu bar
Command line
Message line
Textport
Molecule Management table
Palettes
Dial emulator
Using the mouse
Understanding menus
Menu types
Using dialog boxes
Selecting information in a dialog box
Data-entry boxes
Scrolling list
Using an action button
Using the File Librarian
Using the Molecule Management table
Displaying structures
Display defaults
Picking an atom
Moving structures
Using dial emulators
Using the mouse and keyboard
Using palettes
Defining menu and window colors
Using the keyboard
Using the keyboard with data entry boxes
Keyboard commands
Command-driven QUANTA
Binding commands to function keys
Executing system commands
Window access to the operating system
Command line access to the operating system
Exiting QUANTA
Summary
2. Manipulating Molecular Displays
Starting your QUANTA session
Displaying structures and substructures
Using proximity tools
Customizing display colors
Customizing atom colors
Using menu functions to customize atom colors
Assigning structure colors
Atom property coloring
Define properties
Property
Normalization
Spectral colors
Electrostatic colors
Toggle Legend
Toggle blended bonds
Status of properties
Labeling atoms
Selecting active atoms
Specifying and saving active atom selections
Using selection commands
Customizing defaults
Summary
3. QUANTA Scripting Language
Contents
Introduction
Command Logging
Creating a QUANTA log file
Playing back a script
Script Modification
Script simplification
Adding new commands to a script with a text editor
Introduction to TCL Scripting Control
Variable definitions and usage.
Branching and looping
Lists creation and modification
List extraction
Operations
Input / Output
Appendix
Commonly used QUANTA keyboard commands:
TCL documentation
Sample TCL/rec scripts
Binding commands to function keys
A. Main Menus
B. External Devices for Silicon Graphics Machines
Using a button box
Default settings
Customizing the button box
Using a dial box
Using a graphics tablet
Global transformations
Fragment and atom movement
Rotating torsions
Miscellaneous transformations
User-defined transformations
Using a spaceball
C. File Formats
Molecular structure files
Display parameter file
External file formats
Protein Data Bank format
CHARMm/CNX/X-PLOR PDB variant
CHARMm ASCII format
Konnert format (command mode only)
Diamond format (command mode only)
CHARMm binary format
CHARMm binary property files
Fractional coordinates (old Cambridge database format)
Cambridge database FDAT format
Gromos atom format
QM coordinate file format
Dictionary files
Nohpro.dic file
Generic.dic file
Template files
Hydrogen atom addition template file for Protein Design
Dummy atom file
Brick map file
Special value
QUANTA plot file
ChemNote data files
Atom type files for ChemNote and the Molecule Editor
Atom typing rules example
D. Residue Topology Files
Amino acid residue topology files
Nucleic Acid Residue Topology File
Carbohydrate residue topology file
Metal ions topology file
Porphyrin topology file
Protein Data Bank topology file
E. Tool Command Language (TCL)
Overview
Interpreters
Data Types
Basic Command Syntax
Comments
Grouping arguments with double-quotes
Grouping arguments with braces
Command substitution with brackets
Variable substitution with $
Separating commands with semi-colons
Backslash substitution
Command summary
Expressions
Lists
Regular Expressions
Command Results
TCL_OK
TCL_E`RROR
TCL_RETURN
TCL_BREAK
TCL,_CONTINUE
Procedures
Variables-scalars and arrays
Built-in TCL Commands
append varName value ?value value ... ?
array option arrayName ?arg arg ... ?
break
case string ?in? {patList body ?patList body...?}
catch command ?varName?
cd ?d!rName?
concat arg ?arg ...
continue
catch {...} errMsg set savedInfo $errorInfo ... error $errMsg $savedInfo
errorinfo
eval arg ?arg ... ?
exec arg ? arg .
exit ?returnCode?
expr arg
file option name ?arg arg ...?
flush fileId
for start test next body
foreach varname list body
format formatString ?arg arg ...?
gets fileId ?varName?
glob ?-nocomplain? filename ?filename ...?
global varname ?varname ...?
history ?option? ?arg arg ...?
history add command ?exec?
history change newValue ?event?
history event ?event?
history Info ?count?
history keep count
history nextid
history redo ?event?
history substitute old new ?event?
history words selector ?event?
if test When? trueBody ?else? ?falseBody?
incr varName ?increment?
info option ?arg arg ... ?
join list ?JoinString?
lappend varName value ?value value...?
linsert list Index element Ulement element ... ?
list arg ?arg...?
llength list
Ireplace list first last ?element element...?
Isearch list pattern
open fileName ?access?
proc name args body
puts fileId string ?nonewline?
pwd
read fileId, read fileId nonewline, read fileId numBytes
regexp ?-Indices? ?-nocase? exp string ?matchVar? ?subMatchVar ...?
regsub ?-all? ?-nocase? exp string subSpec varName
rename oldName newName
return ?value?
scan string format varnamel ?varname2 ... ?
seek fileId offset ?origin?
set varname ?value?
source fileName
split string ?splitChars?
string option arg ?arg ...?
tell fileId
time command ?count?
trace option ?arg arg ...?
unknown cmdName ?arg arg ... ?
unset name ?name name ... ?
uplevel ?level? command ?command ... ?
upvar ?level? otherVar myVar ?otherVar myVar...?
while test body
QUANTA Script Examples