ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Aug 16 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
  addBfactor
  alignMinCoverage
  alignOldStatWeight
  axisLength
  clashThreshold
  cnWeight
  consensusStrength
  dcWeight
  COLOR.bg
  COLOR.distanceAtom
  COLOR.label
  CONSENSUS_strength
  densityCutoff
  dielConst
  dielConstExtern
  drop
  fogStart
  gapExtension
  gapOpen
  gpWeights
  hbCutoff
  lineWidth
  listUpdateThreshold
  mapSigmaLevel
  mapAtomMargin
  mcBell
  mcJump
  mcShake
  mcStep
  mfWeight
  mimelDepth
  mimelMolDensity
  r_out
  r_2out
  resLabelShift
  rsWeight
  selectMinGrad
  selectSphereRadius
  sfWeight
  shininess
  ssThreshold
  ssWeight
  ssearchStep
  surfaceTension
  tempLocal
  temperature
  timeLimit
  tolGrad
  tolFunc
  tzWeight
  vicinity
  vwCutoff
  vwExpand
  vwExpandDisplay
  vwSoftMaxEnergy
  waterRadius
  wireBondSeparation
  xrWeight
 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
Real shell variables
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[ addBfactor | alignMinCoverage | alignOldStatWeight | axisLength | clashThreshold | cnWeight | consensusStrength | dcWeight | COLOR.bg | COLOR.distanceAtom | COLOR.label | CONSENSUS_strength | densityCutoff | dielConst | dielConstExtern | drop | fogStart | gapExtension | gapOpen | gpWeights | hbCutoff | lineWidth | listUpdateThreshold | mapSigmaLevel | mapAtomMargin | mcBell | mcJump | mcShake | mcStep | mfWeight | mimelDepth | mimelMolDensity | r_out | r_2out | resLabelShift | rsWeight | selectMinGrad | selectSphereRadius | sfWeight | shininess | ssThreshold | ssWeight | ssearchStep | surfaceTension | tempLocal | temperature | timeLimit | tolGrad | tolFunc | tzWeight | vicinity | vwCutoff | vwExpand | vwExpandDisplay | vwSoftMaxEnergy | waterRadius | wireBondSeparation | xrWeight ]

ICM-shell real variables are the following.

addBfactor


additional B-factor which may be added to the current atomic B-values to create a smoother electron density map from a set of atoms. See also:
Default (0.0)

alignMinCoverage


a threshold for the ratio of the aligned residues to the shorter sequence length. All alignments shorter than alignMinCoverage*minLength will not be reported by find database command.
The default value is 0.5. However the parameter can be tuned with the respect to the database and the nature of the query sequence.
  • Search against the protein domain sequence database: use 0.5 or higher
  • Search a multidomain sequence against long multidomain sequences: use 0.1 or lower

See also: 'alignMinMethod , find database .
Default (0.5)

alignOldStatWeight


a parameter influencing the statistical evaluation of sequence comparison significance in the find database command.
Statistical significance can be evaluated in two ways: first, a priori, i.e. before the database search and based only on the individual score of an alignment of interest and its theoretical distribution, or, second, a posteriori, i.e. on the fly and on the basis of all empirically observed scores of other alignments in the course of the database search.
The parameter ranges from 0. to 1. and sets how two different statistical criteria of alignment significance, a precomputed (the old one) and a run-time, should be mixed. Zero corresponds to only the run-time measure ( the new way) in which the significance is evaluated on the run-time statistics of the observed alignment scores, while one corresponds to the statistics evaluated before the search using the formula from Abagyan and Batalov, 1997 . If the database is small then the run-time score statistics may be incomplete and alignOldStatWeight closer to 1. is a better choice. On the other hand, the run-time statistics has several principal advantages:
Precomputed statistics (1.) based on individual alignment score and length Run-time statistics (0.) based on distribution of scores
works always relies on database diversity
is trained only in 64 condition sets and ZEGA alignment automatically adjusts to any set of conditions, e.g. gapFunction, or alignMinCoverage
does not reflect compositional bias automatically reflects all seq. properties
does not reflect extra terms to the score accounts for solvent accessibility correction (see accFunction )
The run-time statistics will fit the scores to an optimized empirical function. This function avoids the problems of the normal distribution, and certain pitfalls of a popular EVD function. The resulting P-value is a reliable estimate of the false positive rate if the database is sufficiently diverse, i.e. the fraction of sequences similar to the query is small. For example, searching a tyrosine kinase through a database of tyrosine kinases will yield incorrectly low pP-values (pP = -Log(P)).
Reliable expect-values: P * Nof(sequences) <= 0.1 .
Example:
  • Swissprot has N=89,000 sequences. LogN = 4.95
  • Reliable pP = LogN + 3, twilight pP is from LogN + 1. to LogN + 3.


axisLength


length (in Angstroms) of the X,Y,Z axes of the coordinate frame. The axes can be displayed by the display origin or display virtual command. The axes are marked X Y Z . Example:
 
 build string "ala ala his his" 
 display 
 axisLength=10. 
 display origin 

Default (1.5)

clashThreshold


a clash is defined as an interatomic distance less than a sum of van der Waals radii of two atoms of interest multiplied by the clashThreshold parameter. For hydrogen bonded atoms, the distance threshold is additionally reduced by 20% .
See also: display clash , show clash, GRAPHICS.clashWidth
Default (0.82)

cnWeight


weighting factor for the interatomic distance restraints penalty term. See also: tzMethod , drestraint and Bfactor .
Default (1.0)

consensusStrength


a real parameter between 0. and 1. controlling the percentage of sequence identity in an alignment column required to establish a consensus. This parameter r is applied to the C0 parameters defined in the CONSENSUS table according to this formula:
 
C = C₀ + (100-C₀)*2*(r-0.5) 
The 0.5 value corresponds to the percentage in the table. Default (0.5)


dcWeight


weighting factor for the density correlation term "dc".
Default (1.0)

COLOR.bg : background color in 3D graphics


user preference for the background color (overwrites icm.clr preference) E.g.


 COLOR.bg = "grey"
 write system preference
See also:

COLOR.distanceAtom : default colors of interatomic distances


interatomic distance is shown by a dotted line of this default color. These colors and styles can be changed individually.

COLOR.label... default colors of labels.


  • COLOR.labelAtom : atom labels
  • COLOR.labelResidue : residue labels
  • COLOR.labelSite : site labels
  • COLOR.labelVar : variable labels
they overwrite the colors specified in icm.clr

CONSENSUS_strength


regulates the strength of consensus modifying the CONSENSUS.fraction values. The CONSENSUS table controls the rules of consensus derivation from an alignment . This table may look like this:

 
#>T CONSENSUS 
#>-symbol------fraction----residues--- 
   A           80          A 
   C           90          C 
   D           85          D 
   d           60          ND 
... 
... 
The CONSENSUS_strength (denoted S ) parameter can increase or decrease the fraction values f according to the following formula: f1 = f + (100-f)*(S-0.5) Therefore if S = 1. all fraction values become equal to 100% . This affects the Consensus function and the GUI representation of alignment consensus in ICM versions above 3.0.
To color structures according to the consensus, use the color alignment rs_command, or, interactively, left-click on a color icon and select Color_By followed by alignment.
Default (0.5)


densityCutoff


The neglected fraction of the total atomic electron density in the course of calculation of the grid electron density from atomic positions. Atomic density distribution is approximated by two Gaussian functions which need to be truncated for computational efficiency. See also:
  • make map cell command and related operations with the electron density,

Default (0.1)

dielConst


dielectric constant of the solute used in Coulomb, distance-dependent, MIMEL, and boundary element electrostatic calculations. If electroMethod="distance dependent" the actual dielectric constant is a product of dielConst and a distance from a change.
See also: dielConstExtern, term "el"
Default (4.0)

dielConstExtern


dielectric constant of the solvent exterior used in MIMEL and boundary element, REBEL, electrostatic calculations.
Default (78.5)

drop


expected initial function drop in local minimization. The parameter is used to evaluate initial step size. If your function is already very close to its minimum, it is a good idea to reduce the parameter, otherwise the procedure will start with an inappropriately large step.
Default (10.0)

fogStart


relative Z-depth with respect to the front clipping plane at which fogging starts. With this parameter you can keep some area in front without any fog and than start gradually increasing the effect until the back clipping plane.
To activate fog use Ctrl-D , or click on the FOG GUI button, or use the display volume command. Clipping planes can be moved with Ctrl-MiddleMB (front plane) and MiddleMB - left 5% margin (back plane). Actually the mapping of these operations to particular keystrokes is flexible and is defined in the icm.clr file. For Linux it is useful to redefine the back-clipping plane movements to
 
 mode   9  Right5-Mid                # Move rear clipping plane       
Right5 means that you use the 5% right margin of your window.
Usually the fog color is the same as the background color. You can change the fog color with the
color volume Color
command. From the command line the fog can be switched on and off with the display volume and undisplay volume command

The value of fogStart is saved and restored as a system preference. If its value is negative, the fog is not activated, if the value is a positive number between 0. and 1., ICM sets the fog flag on.


Default (0.3)



gapExtension


Relative gap extension penalty used in an alignment procedure. The absolute gap penalty is calculated as a product of gapExtension and the average diagonal element of the residue comparison table
Default (0.15)
See also gapFunction , Align .

gapOpen


Relative gap opening penalty used in an alignment procedure. The absolute gap penalty is calculated as a product of gapOpen and the average diagonal element of the residue comparison table You may vary gapOpen between 1.8 and 2.8 to analyze dependence of your alignment on this parameter. Lower pairwise similarity may require somewhat lower gapOpen parameter. A value of 2.4 (gapExtension=0.15) was shown to be optimal for structural similarity recognition with the Gonnet et. al.) matrix, while a value of 2.0 was optimal for the Blosum50) matrix ( Abagyan and Batalov, 1997).
Default (2.4).
See also gapFunction , Align .

gpWeights


the rarray of seven weighting factors for the property grid penalty term in the energy function.

Example:


 gpWeights = Rarray( 7, 1. )  # seven weights of 1. each 

See also:


hbCutoff


(Angstroms) cutoff radius for hydrogen bonding interactions.
Default (3.0)

lineWidth


the real width of lines used to display the 3D wire representation of chemical bonds. See also IMAGE.lineWidth parameter which controls line thickness in molecular images generated by the write postscript command, and the PLOT.lineWidth which controls the width for the plot command. For bond width in chemical drawings in tables, see IMAGE.lineWidth2D
Default (1.0)
Example:
 
 build string "se nad"  # NAD molecule  
 lineWidth = 3.   
 wireStyle="chemistry" 
 display 

See also: GRAPHICS.grobDotSize , GRAPHICS.grobLineWidth , GRAPHICS.mapLineWidth , IMAGE.lineWidth (3D display), IMAGE.lineWidth2D (chemical tables) PLOT.lineWidth , PLOT.gridLineWidth .


listUpdateThreshold


the real maximal displacement of an atom during local minimization which triggers the recalculation of the interaction lists. This mechanism can be suppressed by setting the l_updateLists variable to no

See also: l_updateLists , minimize .

Default (1.5)



mapSigmaLevel


(in Rmsd values over the mean value). Margin value used for making graphical objects contouring the 3D density map .

See also: map
Default (1.5)


mapAtomMargin


Margin in Angstroms around selected atoms. The margin is added to the positional boundaries to define a submap index box in the Map ( map_source , as_ ) function.

Default (3.0)

mcBell


average relative size of normally distributed montecarlo step from the center of an ellipsoid surrounding the multidimensional variable restraint zone.
Example:

 
 mcBell = 1.0       # places one standard deviation at the rs border 
 mcBell = 2.0       # distribution is two times broader etc.  

Default (1.0)

mcJump


maximum value (in degrees) of random angular distortion per variable during a stack action (as opposed to mcStep that is a part of a regular random step). The mcJump local random perturbation occurs if visitsAction, highEnergy or rejectAction ICM-shell variables are set to "random" . Randomization is a possible action in three problematic situations in montecarlo procedure.
Default (30.0)

mcShake


amplitude [Angstrom] of Brownian type the montecarlo random move applied to a molecule when one of the 6 variables defining its relative position is picked. Usually these variables may be selected by v_myMolecule//?vt*selection. The center of mass of the molecule randomly moves in an xyz sphere of mcShake radius. The molecule is also randomly rotated around a random axis with an amplitude equal to mcShake divided by the MolecularRadius . This parameter is also used as a default amplitude for the randomize command where the six position/orientation variables are selected.
Default (2.0)

mcStep


montecarlo step size (degrees). Maximum random change of one variable. This parameter is also used as the default amplitude for the randomize command
Default (180.0)

mfWeight


the overall weighting factor for the "mf" penalty term. This term may contain any user-defined energy or penalty function depending on pairs of atom types and interatomic distances. The parameters for the term are stored in the icm.pmf file and loaded with the read pmf s_pmfFile command.
The weighting factor will determine the "mf" term contribution with respect to the energy terms.
See also: "mf" term, cnWeight, dcWeight, rsWeight, ssWeight, tzWeight, ssWeight, gpWeights .
Default (1.0)

mimelDepth


The fraction of an estimated molecular radius which is taken as a radius of the probe sphere used by the MIMEL algorithm. The accessible surface of this probe sphere is used to calculate the distance between a charge and the effective dielectric boundary. Described in detail on p. 991-992 of (`ato94{ Abagyan and Totrov, 1994}). For small molecules mimelDepth = 0.3 is recommended.
See also: Default (0.5).

mimelMolDensity


a coefficient used to calculate the effective molecular radius from a number of atoms. Recommendation: do not touch it, unless you are an advanced user. See also the description of the MIMEL method.

See also:


Default (1.0).

r_out


a real variable where some commands and functions (e.g. show area, show volume, superimpose, minimize tether, Corr , Axis , Align ) store their output. Also, in the electrostatic calculations with the MIMEL or REBEL method, the solvation energy part of the electrostatic energy is returned in r_out.
Default (0.0). See also: r_2out.

r_2out


a real variable where some commands and functions (e.g. Axis ) store their output.

Some r_2out outputs:

  • Align or align : for 2 sequences: percent sequence alignment identity
  • Axis( R_12transform ) : helix rise in
  • Energy( rs simple ) : rmsd of normalized residue energies
  • convert : maximal positional deviation upon conversion

Default (0.0). See also: r_out .

resLabelShift


is the screen Z-translation towards the viewer (normal to the graphics screen) used to display a label in front of cpk's or skin's rather than bury the label under them. The recommended values are 2. to 4. See also:
Default (0.0) to be used with more popular wire representation.

rsWeight


weighting factor for the multidimensional variable restraints penalty term.
Default (1.0).

selectMinGrad


default minimal gradient vector length for gradient atom selection ( a_//G). This parameter is also used by the montecarlo fast command, which requires a value of 2. to 10. for optimal performance.
Example:
 
 read pdb "1fox" 
 convertObject a_ yes no yes no 
 show energy 
 selectMinGrad=80. 
 show a_//G    
 display 
 display a_//G cpk 

Default (1.5).

selectSphereRadius


default sphere radius (in Angstroms) for atom selections in Sphere( ) function, as well as the Gaussian 3D averaging radius in the color ribbon command with ribbonColorStyle="reliability".
This parameter is also used in the compare surface command.
Default (5.0).

sfWeight


the overall weighting factor for the surface solvation energy term. If surfaceMethod is "constant tension" it can also be controlled by the surfaceTension parameter.
Default (1.0).

shininess


parameter defining the shininess of solid surfaces such as cpk, ribbon, ball, stick, xstick, and skin when they are displayed. Only values in the range [0.,128.] are accepted.
Example in which we generate a high quality CPK image:
 
build string "ASDW" 
GRAPHICS.quality = 15. 
shininess = 100. 
display cpk 

Default (20.0). Range: from 0. to 128.

ssThreshold


threshold distance between two Sg atoms of cysteine residues. This distance controls the automatic formation of disulfide bonds in some commands (e.g. read pdb).
Default (2.35).

ssWeight


weighting factor for the disulfide bridge ( "ss" ) penalty term.
Default (1.0).

ssearchStep


angular increment (in degrees) for variables in the systematic search ( ssearch command ) in so called "local" mode when the search is performed around the current conformation.
Default (30.0).

surfaceTension


surface energy density in kcal/mole/A2. The surface energy which is a product of this parameter by the total solvent accessible area will be stored in the "sf" term, if surfaceMethod preference is set to "constant tension" .
Note, that if a part of the system is represented with grid potentials, one needs a special m_ga grid map for correct calculations of the surface accessibilities.
Default (0.012)

tempLocal


montecarlo simulation temperature for local deformation random moves. This temperature can be set higher than the normal temperature since a local deformation includes a larger number of variables and may require a higher temperature for efficient sampling. To set the same simulation temperature, specify:
tempLocal=temperature
in your script.
Default (5000.).

temperature


montecarlo simulation temperature. A new trial conformation with a higher energy than the current one is accepted with the probability of exp(-(Etrial - Enew)/RT)). RT is 0.6 kcal/mole for T = 300 Kelvin.
The effect of temperature on the montecarlo procedure is the following:
  • to find the global minimum successfully one needs a combination of persistence if a chosen place with a good sense of when to stop searching in this place and move along to the next one.
  • if the temperature is too high, the acceptance ratio improves (gets higher) and wider sampling becomes easier since more high energy conformations are accepted. The downside of this is the low "persistence" (or "lack of patience") of the search procedure. Instead of spending more time in each conformational vicinity to find the real global minimum, the procedure just tries a couple of sub-optimal conformations and jumps away.
  • if the temperature is too low the procedure may not cover the global conformational space of interest.

* tempCycle (need to create a variable with that name) If you want to set a cooling temperature schedule, or even a periodic PCR-like temperature schedule, you can define a new rarray array called tempCycle which contains { tempMax, tempMin, period, phase } . For a simulated annealing schedule, set the period to be twice the value of the mncallsMC parameter. Tcurr = 0.5(T1 + T2) + 0.5 ΔT cos( 2π ( phase + x / period )), x = [0:1]


tempCycle = {10000.,600.,2.,0.}  # the whole period is 2 times longer than the simulation
# it will start from t=10000. finish at about 600. 
montecarlo

Default (300.).

timeLimit


the real running time of ICM in hours (wall time) before a long simulation is interrupted. This limit can interrupt a montecarlo procedure (another exit condition is mncallsMC),
Example:
 
timeLimit = 2.  # two hours  
montecarlo    # will interrupt the simulation in 2 hours 

Default (99999.0).

tolGrad


gradient tolerance criterion for local minimization. Minimization is stopped if the gradient root-mean-square deviation from zero is less than the parameter value.

See also: tolFunc , mncalls , minNumGrad , l_updateLists , listUpdateThreshold .
Default (0.05).


tolFunc


exit criterion for local minimization by looking at the amplitude of the function value decrease during the last four steps of minimization. Minimization is stopped if the function does not decrease more than the parameter value during the last four steps. The negative value means that this criterion is ignored. All criteria, namely tolGrad, mncalls and tolFunc , are checked simultaneously.

See also: tolGrad , mncalls , minNumGrad , l_updateLists , listUpdateThreshold .
Default (-0.01).



tzWeight


the overall weighting factor for the tether penalty term. You may need to increase it while minimizing a highly energetically strained molecule resulting from the initial steps of the conversion or regularization procedure. Additional atom specific weights can be introduced through atomic bfactors with tzMethod="weighted"

See also: TOOLS.tsWeight , term ts
Default (1.0).



vicinity


maximum angular root-mean-square deviation per variable (degrees) or cartesian root-mean-square deviation per atom (Angstroms) when two structures are still considered belonging to the same conformational family in conformational stack manipulations. The type of comparison is defined by the compare command.
Examples:
 
 compare a_//ca,c,n  # compare by Cartesian RMSD 
 vicinity = 3.0      # conf. are similar if RMSD< 3 A 
 
 compare v_//phi,psi # compare by angular RMSD 
 vicinity = 40.0     # conf. are similar if aRMSD < 40 deg 

Default (15.0) . Do not forget to set it to a lower value if Cartesian RMSD is compared.

vwCutoff


(Angstroms) cutoff radius for van der Waals interactions and Coulomb electrostatics .
Default (7.5).

vwExpand


radius of a probe sphere used to display a dotted surface of a molecule. All van der Waals radii are expanded by this value. vwExpand=0 corresponds to the CPK surface, vwExpand=1.4 corresponds to the water-accessible surface. Be aware of the difference between the waterRadius , vwExpand and GRAPHICS.surfaceProbeRadius parameters: The waterRadius parameter is used in
  • show energy "sf"
  • show [area|volume] skin
  • display skin
while vwExpand is used in
  • show [area|volume] surface
  • Xyz( as_ r_distance surface) # sampling points above the surface
and GRAPHICS.surfaceProbeRadius is used in

display surface
Default (1.4).


vwExpandDisplay


Obsolete. Replaced by GRAPHICS.surfaceProbeRadius . See also: GRAPHICS.surfaceDotDensity, GRAPHICS.surfaceDotSize



vwSoftMaxEnergy


Parameter defining maximal energy value of van der Waals repulsion at r -> 0. for the finite approximation van der Waals function ( vwMethod = "soft" ). This parameter must be greater than 0. kcal/mole.
Note that in the "soft" mode, the electrostatic energy will be automatically buffered to avoid singularities. You will see that the electrostatic term "el" changes upon switching from vwMethod=1 to vwMethod=2 .
Default (7.0).



waterRadius


radius of water sphere which is used to calculate an analytical molecular surface (referred to as skin) as well as the solvent-accessible surface (centers of water spheres). Because of the complexity of skin calculations, it is not recommended that one play's with this parameter (of course, you rushed to do exactly that). Be aware of the difference between the waterRadius and vwExpand parameters: waterRadius is used in
  • show energy "sf"
  • show [area|volume] skin
  • display skin
while vwExpand is used in
  • display surface
  • show [area|volume] surface

Default (1.4).

wireBondSeparation


the distance between two parallel lines representing a chemical double bond if wireStyle = "chemistry".
Default ( 0.15 Angstroms).

xrWeight


the overall weighting factor for the structure factor correlation penalty term. See also: xrMethod .
Default (1.0).

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