Jul 1 2004
Contents
 
Introduction
Reference Guide
User's guide
 ICM-shell
  How to get help
  Customization
  How to write a nice demo with menus to impress the boss
  How to boost learning process while reading the ICM manual
  How to get the list of the command words
 ICM graphics
 Structure analysis
 Sequence, searches and alignments
 Energetics and electrostatics
 Manipulations with molecules
 Animation
 Transformations and symmetry
 Maps and factors
 How to plot
 How-to: Docking and Virtual Ligand Screening
 Example scripts
References
Glossary
 
Index
Prev
3.1 ICM-shell		Next

[ hg | customization | ms | il | icw ]

3.1.1 How to get help

[Top]
This entire book can be searched from the command line. You may just type help and use /searchString to find what you want, or use help commands or help functions to find out about the syntax. If you want help on a multi-word term, e.g. read pdb, merge the words, e.g. help readpdb . The web version of this book with links is also available ( man.tar.gz file contains about 2000 html files ). See also: help, help commands, help functions.

3.1.2 Customization

[Top]
There are several mechanisms of helping you to customize your ICM environment:
!_ ICMHOME
Define UNIX environmental variable ICMHOME in your .cshrc file, e.g. 
 
 setenv ICMHOME /opt/icm/
This will be the directory from which ICM program takes all necessary libraries, databases, etc.
!_ USER environment: $HOME/.icm and $HOME/icmprojects files and directories In contrast to $ICMHOME directory which may be installed under root for several users, the $HOME/.icm directory contains files which can be changed by a user. Under Windows the directory is $USERPROFILE/.icm . The icm-user directory contains the following files and directories:
dir/filedescription
blastdb/ contains blast-formatted files for ICM sequence searches (see also s_blastdbDir )
config/ contains icm.cfg and icm.rc files with startup preferences.
../icmprojects/ contains subdirectories with icm files for saved project (see also s_projectsDir.
inx/ default location for database index files (see also s_inxDir )
log/ contains session logs, (see also s_logDir )
_startup if present, overrides the global _startup in $ICMHOME.
user_startup.icm user startup files. Executed in addition to _startup
Notice that the icmprojects is a subdirectory of the user $HOME directory rather than the $HOME/.icm directory. As a result, the whole $HOME/.icm directory can be removed and automatically recreated with the default settings by icm without loosing any of the project information.
!_ general _startup Adjust _startup file to your needs. Define directories, PostScript viewer, help engine, database directories, etc.
Examples are given below. 
 
 s_pdbDir     = "/data/pdb/" # set it to the place where PDB lives 
 s_helpEngine = "icm"        # default, web-browser is an alternative 
 s_prositeDat = s_icmhome+"prosite.dat" # you may have your own updated file 
 s_psViewer   = "/usr/opt/bin/gs -q"    # xpsview may be more standard 
 s_tempDir = "/tmp"       # better be accessible only for you
Set $BLASTDB system environment variable for searches in the blast-preprocessed sequence databases (see the find database command).
!_ individual user_startup.icm , gui-controls and menus :
additional personal custom commands can be stored in $HOME/.icm/user_startup.icm file under UNIX and $USERPROFILE/.icm/user_startup.icm under Windows . This allows to have your own additional setup which follows a general $ICMSCRIPTDIR/_startup[.icm] file execution. We also recommend that you create a .icm directory in your home directory and store all additional files, such as your personal icm.clr , GUI-setup and color file, and other custom files. Example personal user_startup.icm file in which we use personal GUI files: 
 
LIBRARY.clr = Getenv("HOME")+"/.icm/icm.clr"  # USERPROFILE under Windows 
LIBRARY.men = Getenv("HOME")+"/.icm/icm.gui"  # now gui will invoke your file 
read color   # updates your GUI-control and color setup

!_ aliases : Define aliases convenient for you.
!_ hotkeys : Use, define new or modify old keystrokes. Set key command allows you to create efficient keystrokes to control graphics
!_ macros: Create macros for all frequently used interactive operations and their combinations.

3.1.3 How to write a nice demo with menus to impress the boss

[Top]
See example in the description of the menu command and the _demo family of scripts.

3.1.4 How to boost learning process while reading the ICM manual

[Top]
  • Start ICM, mark (copy) all the example lines from the manual with the mouse and paste them to the ICM-shell text window. Try each line as you read it! You will immediately see the result and will be able to play around. Note: in principle you may mark several lines, but sometimes the buffer gets overflown. In this case paste lines in smaller chunks or one by one.
  • Use HTML cross-references.
  • Write to support@molsoft.com if you have questions or need an ICM-shrink.
  • Always use TAB key while typing the command.

3.1.5 How to get the list of the command words

[Top]
Use list command to see the whole list of valid ICM words. If you need a list of all available ICM functions, use list function command instead.
help commands and help functions will give all the syntax lines too.
Prev
usersguide		Home
Up		Next
icmgraphics

Copyright© 1989-2004, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.