ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 24 2018

Contents
 
Introduction
Reference Guide
 ICM options
 Editing
 Graph.Controls
 Alignment Editor
 Constants
 Subsets
 Molecules
 Selections
 Fingerprints
 Regexp
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Arithmetics
 Flow control
 MolObjects
 Energy Terms
 Integers
 Reals
 Logicals
  l_antiAlias
  l_autoLink
  l_bpmc
  l_breakRibbon
  l_bufferedOutput
  l_bug
  l_caseSensitivity
  l_commands
  l_confirm
  l_easyRotate
  l_info
  l_minRedraw
  l_neutralAcids
  l_out
  l_print
  l_racemicMC
  l_readMolArom
  l_showAccessibility
  l_showMC
  l_showMinSteps
  l_showResCodeInSelection
  l_showSpecialChar
  l_showSites
  l_showSstructure
  l_showWater
  l_showTerms
  l_updateLists
  l_warn
  l_wrapLine
  l_writeStartObjMC
  l_xrUseHydrogen
 Strings
 Preferences
 Tables
 Other
 Chemical
 Smiles
 Soap
 Gui programming
 Commands
 Functions
 Icm shell functions
 Macros
 Files
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Logical variables
Next

[ l_antiAlias | l_autoLink | l_bpmc | l_breakRibbon | l_bufferedOutput | l_bug | l_caseSensitivity | l_commands | l_confirm | l_easyRotate | l_info | l_minRedraw | l_neutralAcids | l_out | l_print | l_racemicMC | l_readMolArom | l_showAccessibility | l_showMC | l_showMinSteps | l_showResCodeInSelection | l_showSpecialChar | l_showSites | l_showSstructure | l_showWater | l_showTerms | l_updateLists | l_warn | l_wrapLine | l_writeStartObjMC | l_xrUseHydrogen ]

ICM-shell logical variables are the following.

l_antiAlias


if yes, invokes anti-aliasing for lines displayed in the graphics window. This feature is not supported on all the platforms.
Default ( no ).

l_autoLink


if yes, tries to link molecules and alignments/sequences automatically. In case of degeneracy, i.e. identical sequences exist with different names, a molecule can be linked to two different alignments containing its sequence etc., the autolink procedure chooses the first occurrence. Use the link command to impose links explicitly, and the show link command to see them. Links can be used by the following commands and functions:
Default ( yes ).

l_bpmc


if yes, use Biased Probability Monte Carlo moves in the Monte Carlo procedure. See Abagyan and Totrov, 1994 for reference. Important: the probability zones are described in the icm.rst file and should be assigned to a peptide before the montecarlo command with the
set vrestraint a_/*
command.
Default ( yes ).

l_breakRibbon


if yes, break too the ribbon if the distance between the reference atoms is larger than GRAPHICS.ribbonGapDistance

Default ( yes ).



l_bufferedOutput


if no, suppresses pagination in the output of ICM commands (including the show command). Useful in batch jobs.
Default ( yes ).

l_bug


if yes, print some debug information
Default ( no ).

l_caseSensitivity


active in most commands and functions using string comparisons.
Default ( no ).

l_commands


if no, do not show commands in batch mode
Default ( yes ).

l_confirm


if no, overwrite the contents of an existing file; ask permission to overwrite it otherwise.
Default ( no ).

l_easyRotate


allows faster handling of images in the graphics window. If yes, then the currently displayed solid representations (e.g., ribbon, skin, cpk, etc.) are temporarily hidden if an operation like rotation or translation is undertaken. Only the wire representation remains allowing quick manipulation with the object in use. The previous type of display is restored when rotation or translation is completed. The parameter can be toggled by a keystroke if you assign the l_easyRotate = !l_easyRotate with the set key command.
Default ( no ).

l_info


if yes, print info messages
The default value is yes.



l_minRedraw


if no, suppresses redrawing of a displayed structure at each minimization step. The new minimized structure will be redrawn only at the end of minimization. Useful when the graphics is slow or the structure is heavy.

l_neutralAcids


Several commands such as read mol, read mol2, build smiles and set bond auto include automated assignment of aromatic systems as well as some resonance structures in O-C=O, O-S=O, PO3, O-N=O, and NO3. The automated conversion invoked with the l_readMolArom variable set to yes reassigns the bonds in the group to be equivalent. For the acidic groups it leads to the charged form with two partial charges of -1/2 or -1/3. If you want to suppress this transformation for the CO2,SO2 and PO3 groups only set the l_neutralAcids flag to yes . In this case the acidic groups will be kept unchanged.
Example:
 
 l_neutralAcids = yes 
 read mol s_icmhome+"ex_mol.mol" 
 wireStyle=2 
 display only a_  # the acidic group is uncharged 
 build hydrogen 

Default ( no ).
See also: l_readMolArom,`read-mol{read mol}, read mol2, build smiles and set bond auto.

l_out


a logical variable similar to i_out and r_out .
Default ( yes ).

l_print


if yes, show print command with arguments as well as the result of its action.
Default ( no ).

l_racemicMC


Activate switching between stereoisomers at chiral centers during montecarlo . This flag can also be dynamically activated with the chiral option of the montecarlo command. To reset the chirality status of an atom use the set chiral command
Example:
 
build string "se nter his cter" 
set chiral a_/his/ca 3  # set chirality flag to 3 (means a racemic mixture) 
unfix V_//FC    # unfix phases for stereoisomeric rearrangements 
compare a_//*  
vicinity = 1. 
 
l_racemicMC = yes 
montecarlo v_//!?vt*   # will switch between stereoisomers 
 
display 
display atom label type=6   # to see the isomers 
# now you can browse the stack solutions 

l_readMolArom


if yes, automatically assigns aromatic rings and resonant structures (CO2,SO2,PO3,NO2,NO3) from patterns of single and double bonds upon reading objects, mol and mol2 files or build from smiles. The automated assignment module is also called by the set bond auto command.
If this flag is set to no , the build hydrogen command will have problems with resonant structures, such as carboxyl groups, - a hydrogen will be attached to the oxygen connected with a single bond to the carbon.
Example of a recommended best conversion procedure for chemical library files:
 
 l_readMolArom = yes # it is the default, but just in case  
# you also want to use l_neutralAcids = yes 
 read mol s_icmhome + "ex_mol" 
 for i=1,Nof(object) 
   build hydrogens   # may have problems if l_readMolArom = no 
   set type mmff     # also improves the aromatic system assignment 
   set charge mmff 
   convert           # makes an ICM object  
 endfor 

Default ( yes ).
See also: l_neutralAcids which allows one to keep acidic groups unchanged and uncharged.

l_showAccessibility


show the residue accessibility string assigned to a sequence generated from a three dimensional structure in the commands show sequence , show alignment, write alignment . The relative residue accessible area is expressed by an integer number in a scale from 0 to 9 (0-fully buried, 9-fully exposed). Example:
 
 read pdb "1crn" 
 show surface area   # calculate atomic and residue accessibilities 
 make sequence a_1   # generate a sequence  
 l_showAccessibility=yes 
 show 1crn_m 
Default ( yes ).

l_showMC


display one-line info about each Monte Carlo trial conformation.
Default ( yes ).

l_showMinSteps


display every step of the local minimization procedure.
Default ( no ).

l_showResCodeInSelection


if yes, shows one-letter code for amino-acid residues in residue selections, e.g. a_/^F12:^A23 instead of a_/12:23 . The amino-acid code is preceded by a caret symbol ^. In versions older than 3.1 the amino-acid code was not shown.

l_showSpecialChar


if yes, displays unprintable characters with the show string and list string commands in text format (like \a \t \n). This flag does not apply to the print command.
Default ( no ).

l_showSites


show the site string assigned to a sequence in the commands show sequence, show alignment, write alignment. The one-letter site codes are given below.
Default ( yes ).

l_showSstructure


show the secondary structure string assigned to a sequence in the commands show sequence, show alignment, write alignment.
Default ( no ).

l_showWater


if yes, all water molecules are shown in the output of commands such as show molecule or show a_* . Set it to no to skip the usually long lists of water molecules in PDB structures.
Default ( yes ).

l_showTerms


Obsolete. Now you can achieve the same via s_icmPrompt variable.
Examples:
 
 s_icmPrompt = "icm/%o/%e> "  # equivalent to l_showTerms=yes 


l_updateLists


if yes, updates the atomic interaction lists during minimization once the maximal displacement reaches listUpdateThreshold . The interaction lists are lists of atom pairs involved in van der Waals, electrostatic or hydrogen bonding interactions and within the vwCutoff or hbCutoff distance. If this parameter is set to no , the lists are not recalculated. To trigger a recalculation, use the


delete list
command.

Default ( yes ).

l_warn


if yes, print warning messages. If you want to see warning messages (i.e. l_warn = yes ), but suppress some of the messages, use the s_skipMessages variable (e.g. s_skipMessages = "[147][148]" ) .
Default ( yes ).



l_wrapLine


wrap long lines if yes. If no truncate long lines and add a dollar sign ($) to indicate that truncation has occurred.
Default ( yes ).

l_writeStartObjMC


write the starting object in the montecarlo command to a file. This object will have the same fixation (set of free and fixed variables) as in your montecarlo simulation. In case the variable is set to no, the same object can be generated if you repeat the fix and unfix command as in your simulation script.
Default ( yes ).

l_xrUseHydrogen


defines whether hydrogen atoms are used in calculations of crystallographic structure factors from atom coordinates (the term).
Default ( yes ).

Prev
xrWeight
Home
Up
Next
Strings

Copyright© 1989-2018, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2018, 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.