ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Oct 18 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
  autoSavePeriod
  defSymGroup
  i_out
  i_2out
  maxColorPotential
  maxFileSizeMb
  maxMemory
  minTetherWindow
  mnSolutions
  mncalls
  mncallsMC
  mnconf
  mnhighEnergy
  mnreject
  mnvisits
  nLocalDeformVar
  nSsearchStep
  nProc
  randomSeed
  segMinLength
  sequenceBlock
  sequenceLine
  surfaceAccuracy
  windowSize
 Reals
 Logicals
 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
Integer shell parameters
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[ autoSavePeriod | defSymGroup | i_out | i_2out | maxColorPotential | maxFileSizeMb | maxMemory | minTetherWindow | mnSolutions | mncalls | mncallsMC | mnconf | mnhighEnergy | mnreject | mnvisits | nLocalDeformVar | nSsearchStep | nProc | randomSeed | segMinLength | sequenceBlock | sequenceLine | surfaceAccuracy | windowSize ]

Here is the alphabetically sorted dump of integer parameters defined in the ICM-shell. These parameters are used by various commands and functions and can be changed interactively, e.g.
 
 mncallsMC= 10000 
 montecarlo 
ICM-shell integer variables are the following.

autoSavePeriod


In the course of a montecarlo or ssearch procedures which may run for days, the current stack of conformations which accumulates the best energy representatives of different conformational areas is saved periodically to allow access to intermediate results of the simulations. The above parameter defines the number of stack changes after which it is saved to a disk file. Set autoSavePeriod to 1 if you want to be conservative.
If you set autoSavePeriod to 0 , the stack will not be saved at all.
Default (10).

defSymGroup


defines a crystal space group number. To find the group name and symmetry operations use the Symgroup function. Default (0) means that the group is not defined.
Examples:
 
 defSymGroup = 19  # direct assignment. You know group 19, don't you?  
 
 defSymGroup = Symgroup("P212121") # Oh, you do not! ..  
 
 defSymGroup = Symgroup("P61 2 2") # This one you do not remember for sure 


i_out


an integer where some commands or functions store their integer output:
  • Rmsd saves the number of aligned equivalent points;
  • Srmsd saves the number of aligned equivalent points;
  • convert saves the number of heavy atoms missing from the pdb-template (e.g. atoms of the flexible lys side-chain are not given in the pdb-file).
  • superimpose saves number of aligned equivalent points;
  • set tether saves the number of tethers imposed;
  • set drestraint saves the number of distance restraints imposed;
  • set vrestraint saves the number of variable restraints imposed;
  • make disulfide bond saves the number of imposed disulfide bonds;
  • minimize saves the number of function evaluations;
  • montecarlo saves the total number of function evaluations during minimization;
  • show area skin saves the total number of triangles in the Connolly construction.

Default (0).

i_2out


the second variable for additional integer output. (see also i_out and I_out )


maxColorPotential


local electrostatic potential in kcal/e.u.charge units at which the surface element is colored by extreme red or extreme blue. All higher values will have the same color. This absolute scaling is convenient to develop a feeling of electrostatic properties of molecular surfaces.
If the maxColorPotential is set to 0. the color grob potential command will perform automated scaling to the absolute maximal value of the potential.

See also: color grob potential [heavy], dsRebel , Potential , make grob potential , TOOLS.rebelPatchSize ,
Example:

 
 build string "se glu arg"  # dipeptide  
 maxColorPotential = 3. 
 dsRebel a_ yes 
 maxColorPotential = 6. 
 TOOLS.rebelPatchSize = 0.5 # do not do it for very large objects
 dsRebel a_ yes 

maxFileSizeMb


maximal file size in Megabytes that can be read in ICM. Increase this limit if needed. Example:


maxFileSizeMb = 10000
read table mol "giant.sdf"

See also: write index

maxMemory


maximal memory size requested by the program in megabytes. It is used to read blocks of databases in the search commands. Make sure that this parameter is reasonable. If your maxMemory is larger than what your computer actually has, expect serious delays. However, usually computers can handle it by swapping memory onto disk, which can be slow.
Recommendation: divide your available RAM by a factor from 2 to 4. Current memory resources are reported by the chkdsk command on a PC or by the top command on a UNIX workstation. Do not forget that ICM itself will additionally allocate some BufferSpace specified in the icm.cfg file.
Default (10.0) Mb



minTetherWindow


maximal number of preceding torsions strictly speaking rigid bodies which are locally minimized during the chain growth procedure (the minimize tether command) to create an ICM-object with ideal geometry on the basis of a set of arbitrary atom coordinates (often referred to as the regularization procedure).
Default (30).

mnSolutions


this parameter limits the number of hits retained by the program after a search. It is used in several icm-search functions:
  • find molecule - chemical substructure search
  • find pattern - find sequence pattern in sequences of mol. objects.
  • find database - advanced sequence similarity search
  • align ms_1 ms_2 - alternatives solutions for 3D superposition
  • find profile - find protein Prosite profiles in a sequence
  • find prosite - find protein Prosite patterns in a sequence
  • Table( profile P_seqArray [ threshold ] )

Default (500).

mncalls


maximal number of function calls in local minimization performed in minimize, and as a part of one step of a multistep procedure in montecarlo, ssearch, convert . The number of function evaluations required to find the local minimum varies widely depending on the terms used (i.e. the "tz" term makes minimization very slow, if structure is far from its target). If the minimum is found according to the tolGrad criterion, the procedure will be terminated anyway.
Default (100).
See also: minimizeMethod , tolGrad , drop .

mncallsMC


maximal number of function calls in the montecarlo command. Since the procedure performs random steps accompanied by local minimization (controlled by the mncalls parameter), the number of function evaluations for the whole procedure can be roughly evaluated as a product of mncalls and the number of MC iterations. mncallsMC should be sufficiently large to ensure convergence of the global optimization procedure and may range from 10,000 for a single side-chain, 100,000 for a 3-4 residue peptide to several million calls for 15-20 residue peptide or a large protein loop.
Default ( 1000 ). The default value is small to minimize damage of the unintentional calls of the montecarlo command.
See also: montecarlo , mncalls .

mnconf


maximal number of conformations in the conformational stack . The stack stops growing after this number is achieved and starts replacing representative conformations with higher energy values by new conformations with superior energies, if the latter are found.
Default (50)
See also: montecarlo , ssearch .

mnhighEnergy


maximal number of consecutive accepted trial conformations which do not change the conformational stack because their energies are higher than energies of the stack conformations. Therefore, the montecarlo procedure is walking in the high energy area and is probably wasting its time. When this threshold is reached the procedure acts according to the highEnergyAction parameter.
Default (50)
See also: mnvisits , mnreject , stack .

mnreject


maximal number of consecutive rejections (due to the Metropolis criterion) of trial conformations generated by the montecarlo procedure. When this threshold is reached the procedure acts according to the rejectAction parameter (which usually increases the simulation temperature).
Default (10)
See also: mnvisits , mnhighEnergy .

mnvisits


maximal number of visits to the same slot of the conformational stack in the course of a montecarlo procedure. When this threshold is reached the MC procedure acts according to the visitsAction parameter. A visit is an event when a newly generated conformation finds a slot with a similar conformation in it, but the stack conformation is not replaced by the new one because it has a better energy.
The optimal mnvisits parameter grows with the size of the problem (it may be several hundred for a 15-20 residue peptide).
Default (50)
See also: mnreject , mnhighEnergy .

nLocalDeformVar


Number of backbone torsion angle variables (excluding omegas) which are changed simultaneously to provide local deformation. This parameter can be less than the actual number of backbone torsion angles in the loop. In other words it is OK if the loop contains more than nLocalDeformVar variables, however, if it contains less than nLocalDeformVar variables, it will not be deformed.
Default (10), minimal number (8).
See also: montecarlo local.

nSsearchStep


number of steps per variable for ssearch . Normally the whole [-180., 180.] range is divided into nSsearchStep parts. In the local mode (i.e. the search is performed around a particular conformation) the total search range around each variable is defined by the ssearchStep parameter (30. deg. by default)
Default (3) .

nProc


This variable can be used as a hint to run an ICM command in parallel if possible. The current list of ICM commands which supports this option is below:

Example:


read mol table "big.sdf" name="t"
set charge formal auto nProc=8    # run in 8 threads



randomSeed


is a seed used by the random-number generator in the montecarlo , randomize , Random function. Helpful if you need to reproduce exactly a calculation which uses random number(s). If the variable has its zero default value, the random function is seeded from the current time plus the process id. Otherwise, if you explicitly redefine it before, let us say, a montecarlo run, it will use the specified number.
Note that the randomSeed parameter can be set only once in the very beginning of the session. If you redefine its value in the middle of the session, it will not be used. To push the new value of the seed, use the set randomize i_newRandomSeed command.
Default (0).
Examples:

 
 randomSeed=2493059372  # this number you took from the previous run 
 montecarlo             # simulation will reproduce the previous one 
# 
... 
# 
 set randomize 2493059372 
 montecarlo 


segMinLength


secondary structure segments shorter than this threshold will be ignored when a simplified quantitative representation of the polypeptide fold is constructed using the assign sstructure segment command.
Default (3).

sequenceBlock


length of the contiguous sequence block in sequence output.
Default (10).
See also: sequenceLine .

sequenceLine


maximum sequence length printed on each line. Usually sequence is additionally subdivided into smaller blocks.
The same parameter also controls the size of alignment block as saved by the write alignment command.
Example:
 
 read alignment s_icmhome+"sh3" 
 sequenceLine=1000 
 write sh3 "aaa" 

Default (60). Values >= 1 .
See also: sequenceBlock

surfaceAccuracy


integer accuracy level used in surface calculations (not graphics) and boundary element electrostatics. By reducing the level, you can speed up the accessibility calculation in the show area surface command. It may be important to increase surfaceAccuracy to 5 in the rebel and make boundary calculations. The corresponding number of dots per sphere is the following:
  • Level 1 ( 89 dots )
  • Level 2 ( 144 dots )
  • Level 3 ( 233 dots )
  • Level 4 ( 377 dots )
  • Level 5 ( 610 dots )

Default (3)
See also: show area surface, "sf" energy term .

windowSize


number of elements used for sliding window averaging by the Smooth function.
Default (7).

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