ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
May 17 2024

Reference Guide
 ICM options
 Alignment Editor
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Flow control
 Energy Terms
 Chemical Functions
 Gui programming
 Icm shell functions
Command Line User's Guide
PrevICM Language Reference
ICM command line options

Option Description
-a arg_string initialize s_icmargs string with arg_string
-b inhibit Buffered output
-c clean: do not save _seslog
-e 'commands' execute semi-colon separated icm commands and quit
-g [menuFile] start GUI menu bar, using menu file [default=icm.gui]
-G [menuFile] start GUI menu and keep the original terminal window
-i Input Icb file from the stdin pIpe
-n do Not execute _startup file
-ng no-gui: open in shell only, do start GUI/graphics after reading the file
-R[] # Redirect standard text/info output into stderr to enable piping binary content
-s Silent mode (l_warn=no l_commands=no l_info=no l_confirm=no)
-p set path for ICMHOME, e.g. -p/opt/icm/
-w web cgi mode: combination of -p and -s, e.g. -w/opt/icm/
-d(or -display) address sets/redirects the X display (default is $DISPLAY)
-24 enforce high quality 24-bit image mode at the expense of double buffering
-B[max_beeps] no more than max_beeps on errors (default=300)
-X report the computer identification number for a node-locked license GUI options:
-style={motif windows platinum cde} sets the GUI style
-session=session restores the earlier session
-geometry WxH+X+Y sets the client geometry of the main widget, e.g. -geometry 200x200+150+700
-fn or -font font defines the GUI font
-bg or -background color sets the default background color
-fg or -foreground color sets the default foreground color
-btn or -button color sets the default button color
-name name sets the GUI name
-title title sets the title (caption)
-visual TrueColor forces to use a TrueColor visual on an 8-bit display
-ncols count limits the number of colors on a 8-bit display
-cmap causes to install a private color map on an 8-bit display


  icm -g                      # run in the interactive gui mode
  icm -g -p/home/yoda/icmd/   # temp path to ICMHOME
  icm 1crn.pdb 2ins.pdb       # opened these two files
  icm script.icm > script.out # runb
  icm -G  # keep the terminal window separate
  icm -a "4.2 3" # the string copied into s_icmargs variable
  icm -s  # no startup, just ICM in a quiet mode
  icm -24 # if you intend to save high-resolution images
  icm <<EOF
#command1     # ICM reads from standard input
  "print 123\nprint 432" | icm -s

Reference Guide

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