ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

Contents
 
Introduction
 Release
 History
 Contact
 Overview
 Conventions
 Abbreviations
 Intro
 Scripting Tutorials
Reference Guide
Command Line User's Guide
References
Glossary
 
Index
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Notational conventions
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The following notational and typographical conventions are used throughout the manual.
  • Bold. Command names may appear in bold in syntax descriptions. (e.g. montecarlo ). Type them as they appear in the text.
  • Typewriter font is used for command words, examples and ICM-shell prompts. This text can also be copied into the shell.
  • Italic font is used for command or function arguments which should be replaced with actual values. For example, if you see /whatever/your/ICM/directory/ and your ICM directory actually is /usr/pub/icm the latter is what you should actually type. Short prefixes shown in parentheses may be used to specify argument type: integer (i), real (r), string (s), logical (l), preference (p), iarray (I), rarray (R), sarray (S), parray (P), date array (e), parray of chemical molecules (X), matrix (M), sequence (seq), profile (prf), alignment (ali), map (m), graphics object, or grob (g), structure factor (sf), atom selection (as), residue selection (rs), molecule selection (ms), object selection (os), variable selection, e.g. a subset of torsion angles, (vs), and table (T). chemical table (X). These prefixes are also used to construct formal argument names for macros. For example, I_Color would mean an integer array with color information, or s_ObjName would mean a string variable or constant (e.g. "crn" ) specifying the object name.
  • Optional arguments appear in square brackets [ ].
  • Braces { } are used for mutually exclusive groups or arguments. For example: set charge as { r_Charge | add r_Increment } means either set charge as r_Charge or set charge as add r_Increment
  • The default values in ICM macros are shown in parenthesis and in typewriter font: icmPocketFinder as_receptorMol r_threshold (3.) l_display (yes)

Sometimes the dimension of an array is shown after the underscore symbol, e.g. R_3xyz, means that this is a 3-membered array.


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