Jul 1 2004
Contents
 
Introduction
Reference Guide
 ICM command line options
 Command line editing
 Graphics controls
 Editing pairwise sequence-structure alignments
 Constants
 Subsets and index expressions
 Molecule intro
 Selections
 Arithmetics
 Flow control
 ICM molecular objects
 Energy and Penalty Terms
 Integer shell parameters.
 Real shell variables
 Logical variables
 String variables
 Preferences
 Tables (structures)
 Other shell variables
 Commands
 Functions
 Macros
 Files
User's guide
References
Glossary
 
Index
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2.1 ICM command line options
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OptionDescription
-a arg_stringinitialize s_icmargs string with the arg_string
-binhibit Buffered output
-cclean: 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
-n do Not execute _startup file
-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)
-Xreport the computer identification number for a node-locked license GUI options:
-style={motif|windows|platinum|cde}sets the GUI style
-session=sessionrestores the earlier session
-geometry WxH+X+Ysets the client geometry of the main widget, e.g. -geomerty 200x200+150+700
-fn or -font fontdefines the GUI font
-bg or -background colorsets the default background color
-fg or -foreground colorsets the default foreground color
-btn or -button colorsets the default button color
-name namesets the GUI name
-title titlesets the title (caption)
-visual TrueColorforces to use a TrueColor visual on an 8-bit display
-ncols countlimits the number of colors on a 8-bit display
-cmapcauses to install a private color map on an 8-bit display


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