ICM Manual v.3.9 by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Nov 14 2024

Contents


Introduction
Reference Guide
Command Line User's Guide
References
Glossary
A
B
C
D
E-H
I-N
O-R
Object
only
parray
pattern
png
Pdb
peptide bond
pharmacophore
profile
prosite
rarray
Psa
REBEL
real
regularization
residue
rgb
ribbon
S
T
U-Z

Index

ICM Language Reference
O-R

object, 3D molecular objects

A pdb file or a chemical molecule with 3D coordinates, or a newly build group of molecules that can co-exist in space are called objects in ICM. Please do not confuse this specific use of the word with general shell objects that include other data types. A session may contain any number of molecular objects.Each object (i.e. molecular object) in turn consists of three levels or organization:

molecules
residues
atoms

ICM understands expressions specifying different selections in objects, see object selections. There are two main classes of objects:

ICM objects
non-ICM objects

ICM objects have the assignment of rotatable bonds, partial charges and atom types for energy calculations. Conversion to an ICM object type is a necessary prerequisite of many commands including show energy , minimize and montecarlo .

The non-ICM objects (from the second line on) may have subtypes such as

"ICM" ready for energy calculations. Those objects are either built in ICM or converted to the ICM-type.
"X-Ray" determined by X-ray diffraction
"NMR" determined by NMR
"Model" theoretical model (watch out!)
"Electron" determined by electron diffraction
"Fiber" determined by fiber diffraction
"Fluorescence" determined by fluorescence transfer
"Neutron" determined by neutron diffraction
"Ca-trace" upon reading a pdb, ICM determines if an object is just a Ca-trace.
"Simplified" special object type for protein folding games.

Each object contains the following information:

Molecules (with their own internal structure, including residues and atoms)
name ( changed by rename and returned by the Name ( os ) function )
remark (set by set comment and returned by the Namex ( os ) function )
header ( returned by the Header (~~os ) function )
filename ( returned by the File( os ) function )
date ( return by the Date function )
resolution ( returned by the Resolution function )
type (returned by the Type ( os 2) function )

Functions on molecular objects. os_ means object selection for other abbreviations see the link.(note that some functions that also operate molecules, residues and atoms are not included).

`Cell ( { os | m_map } )

`Charge ( { os | ms | rs | as } [ formal | mmff ] )

`Date ( os )

`Field( { rs | ms | os } [ i_fieldNumber ] )

`Field( { as | rs | ms | os } [ s_fieldName ] )

`Field ( os i_fieldNumber ) # see also set field os_ i_number

`File ( os )

`Label ( os_objects )

`Mass( as | rs | ms | os )

`MaxHKL( { map | os | [ R_6CellParameters ] }, r_minResolution ) → I3

`Mol ( { os | rs | as } )

`Name ( s_hint os unique )

`Name ( os )

`Name ( s_root os_1 unique )

`Namex ( os )

`Next ( { as | rs | ms | os } )

`Nof( { os | ms | rs | as | vs } )

`Nof( { os | ms | rs } [ atom ] )

`Parray ( object [os] )

`Res ( { os | ms | rs | as } [ append ] )

`Resolution ( os_object ) → R_array_of_resolutions

`Select ( as_sourceSelection os_targetObject )

`Select ( os_sourceObject S_residueSelStrings )

`Select ( os_sourceObject I_atomNumbers )

`String( { os | ms | rs | as } [ i_number ] )

`Symgroup ( { s_groupName | os_object | m_map } )

`Symgroup ( { i_groupNumber | os_object | m_map } string )

`Transform( s_group|iGroup|os_1|map ) → R_12N_all_fract_transformations

`Transform( s_group|iGroup|os_1|map iTrans ) → R_12_fract_transformation_i

`Type ( os_object , 2 )

`dsCellBox os_

Commands acting on objects

append stack os_ligandObject

clear graphic [ os_ ]

convert [ exact ] [ charge ] [graphic] [ tether ] [ os_non-ICM-object ] [ s_newObjectName ]

copy [ strip ] [ tether ] os [ s_newObjectName ] [ delete ]

delete { object | os }

find pdb rs_fragment os_objectWhereToSearch s_3D_align_mask [ s_sequencePattern [ s_SecStructPattern ] ] [ r_RMSD_tolerance]

find pattern [ number ] [ mute ] s_sequencePattern [ i_mnHits] [ { os_objectWhereToSearch | seq_Name | s_seqNamePattern } ... ]

find segment ms_source [ os_objectWhereToSearch_2] [ r_maxRMSD ] [ i_minNofAlignedResidues [ i_accuracyParam ] ]

move ms_MoleculesToMove os_destination

move os_ObjectToMove os_destination

rename { os [ full ] | ms | rs | as } s_newName

rotate [ os | ms | g_grob ] M_rotation

set comment [ append ] os_Object s_comment # returned by the `Label() function

set object [ os_newObjName ]

set symmetry os_object R_6cell s_symgroup | i_symgroup [ i_NofChains ] # set symmetry os s_crysym_record

set type os s_type

set [ atom ] type mmff [ os]

show { os | ms | rs | as | vs }

sort object R|I # reorder objects by arrays, e.g. --{sort object Resolution(a_*.)}

sort object os_ i_pos # move selected OBJECTS to specified position

sort os [ field = i_Field ] # sort MOLECULES in selected objs by field

strip os_object [ virtual ]

superimpose os_static I_atomNumbers1 os_movable I_atomNumbers2

translate { os | ms | g_grob } [ add ] [ symmetry ] R_3translationVector

Important macros working on molecular objects.

convertObject ms l_delete_water l_optimize_hydrogens l_replace_the_original l_display

convert2Dto3D os l_build_hydrogens (yes) l_fixOmegas (yes) l_display (no) l_overwrite (yes)

icmPmfProfile os ( a_ ) l_accessibilityCorrection (yes) l_display ( no )

makeSimpleModel seq ali os

makeSimpleDockObj [ os_object ] [ s_newObjName ]

only

frequent option in commands which means disregard or delete the previous status. Without only commands usually add or append to the current settings.
Examples:

 
 display only g_icos      # undisplay everything which is in the 
                          # graphics window (if any) 
                          # and display icosahedron

parray

[ Object parray | Sequence parray | Image parray ]

pointer array, abbreviated as P. An array of pointers to objects. Currently there are several types of parrays, that consist of the following data types:

chemical
image
sequence
distances (e.g. interatomic distances, hbonds, angles, torsions)
3d labels
object
slide

Chemical arrays of chemical compounds created by reading a mol or sdf file. These compounds do not exist outside this array as independent molecular objects, but can be converted to molecular objects.
creating mol-arrays To create a molarray use the read table mol command and first column of this table will be such an array. Example:

 
read table mol "Maybridge.sdf"

You can also use the Chemical function.

Molecular objects in arrays and tables

ICM molecular objects (both converted and unconverted) can be grouped into arrays and shown in tables.

See the following functions:

Array of sequences

ICM sequences may be grouped into arrays and placed into tables. Some functions supporting sequence arrays:

Array of images

ICM provides multiple ways of generating images and performing advanced operations with them: See

pattern

a sequence consensus pattern like this, "[AG]?[!P]W", or this "C?G?\{2,3\}C". A pattern can be extracted from an alignment and searched against a sequence database. Allowed elements:


*       # anything until the next element, e.g. Find( "*[!A]?SI*" sequence )
?       # any symbol
[XY..]  # any one of the listed one-letter codes, e.g. [DE] for asp or glu.
!       # negation, e.g. [!PG] anything except P or G
\{l\}, or \{l1,l2\}  # anything of length l, or from length l1 to l2, e.g. \{0,5\}
#
# Example:
#
Find( "*A[LV]\{0,5\}*[!DE]?\{8\}C*" sequence )

png

[ pattern-matching ]

graphics image format. Stands for Portable Network Graphics and was designed to replace the GIF format and, to some extent, the much more complex TIFF format. While GIF allows for only 256 palette colors, PNG can handle a variety of color schemes like TIF (1,3,8, 24, etc. bit colors). Furthermore, PNG is free, while GIF is subject to licensing fees. PNG also supports alpha-channel. Since 1998 most browsers correctly display PNG images.

To write a png with transparent background use write png transparent

pdb or Protein Data Bank

a repository of macromolecular structures solved by crystallography or NMR (occasional theoretical models are frowned upon). It used to be at the Brookhaven National Laboratory, Now it is shared between UCSD and Rutgers University. The old citations: Bernstein et al., 1977; Abola et al., 1987). The new citations can be found at http://www.rcsb.org/pdb/ . On November 20th, 2001 it contained 16596 entries. On August 21st, 2007 if contained 45368 Structures.
An example ATOM record:

 
ATOM     52  N   HIS D  18      53.555  24.250  49.573  1.00 32.59

peptide bond

a covalent bond between C=O and N-H groups, which is imposed in ICM-objects as an extra set of distance restraints. These groups may belong to the terminal groups as to the amino acid side chains. Important: commands make peptide bond and delete peptide bond are valid for ICM-type molecular objects only (and have no effect on, say, PDB structures). Both commands change the covalent structure of the modeled molecular object and expel/add hydrogens. Distance restraints imposed to form such a bond are defined in icm.cnt file.

pharmacophore

Pharmacophores in ICM are special objects of the non-ICM type. A pharmacophore can combine special ph4 centers and disconnected chemical fragments.

The ph4 centers have the following atom types and names:

code:
315 Qa HBA
316 Qd HBD
317 Qm aromatic
318 Qh hydrophobic
319 Qp positive
320 Qn negative
321 Qx ExVolume
322 Qv a point defining the direction vector from Qa,Qd and Qm, or a pseudo atom

Creating a pharmacophoreA pharmacophore can be created from an object with the makePharma macro,

macro makePharma ms s_name ("pharm") l_points (yes) l_display

The l_points logical defines if the pharmacophoric centers or fragments are created from the source molecule.

The new object gets type pharmacophore (see the set type os "pharmacophore" command ).

Note the following issues:

for polar atoms with hydrogens and lone pairs, both Qa and Qv centers are created at the s
the directions of Qa-Qv or Qd-Qv vectors need adjustment
the direction atoms (Qv) can be selected and removed. In this case the direction will not be matched.
two or more ph4 objects can be merged into a single pharmacophore object. For example one can merge some ph4-centers with some fragments.
the properties of points can be edited interactively or with the set as_ commands.

Commands to change properties of ph4 centers:

set bfactor as1_ r_radius # to change the tolerance radius
```
 set bfactor a_pharma.p5/5/Qv10 0.8
```
resetting the radius (stored in the bfactor field) for the direction point Qv will change the width of the direction tolerance.

you can also change point type and name, e.g.


set type a_pharma.//Qa3 316
rename a_pharma.//Qa3 "Qd4"

the coordinates can be reset with the set atom command.

prosite

a dictionary of protein sites and patterns distributed by the Swiss Institute of Bioinformatics, http://ca.expasy.org/prosite/ , Copyright by by the Swiss Institute of Bioinformatics (SIB). it is also one of possible formats for string patterns. ICM converts prosite patterns to standard string patterns containing regular expressions, like "C?\{4,5\}CCS??G?CG????[FYW]C".
Included in ICM is only the old release 13 (1995). Until the 15th release the files were fully open for redistribution and said this.


CC   *************************************************************************
CC
CC   This file may be copied and redistributed freely,  without advance
CC   permission. You are allowed to reformat it for use with a software
CC   package,  but you should not modify its content without permission
CC   from the author).
CC
CC   *************************************************************************

If you want to use a newer version of prosite and your organization is non-profit or has a license from SIB, you can download prosite.dat from, e.g.:


unix wget ftp://us.expasy.org/databases/prosite/release_with_updates/prosite.dat
read prosite "./prosite.dat"  # read the newer version in
readUniprot "IL2_HUMAN"
find prosite IL2_HUMAN

rarray

ICM class for arrays of real numbers: { -1.6 , 2.150 3., -160.} An array can be formed dynamically from simple reals with the double slash (concatenate) operator, e.g. 1.3//-1.//dielConst//14.

Real arrays also support special values (see rarray constant )

ND (not defined)
>r_value
<r_value
INF : infinity
-INF : infinity

Example:


add column t {1.}//ND//Real(">2.")//Real("<3.")//Real("INF")//Real("-INF")//2.3
add column t

Predicting Polar Surface Area

Polar surface area or PSA is a parameter important for predicting transport properties of drugs. It correlates with intestinal absorption and blood brain barrier penetration. (e.g. see Polar Surface Area by Peter Ertl in Molecular drug properties: measurement and prediction, Raimund Mannhold, Ed, Wiley-VCH, v 37, 2008 )

Single conformation 3D PSAPSA is calculated as the exposed van der Waals surface of oxygens and nitrogens as well as the hydrogen atoms attached to them. For a converted and current ICM object PSA can be calculated with the following command:


 show surface area a_//n*,o* | ( a_//h* & Next( a_//n*,o* bond )) a_  mute  vwExpand = 0.
 PSA = r_out     # the previous command returns the value in r_out

The conversion is needed only to make sure that all hydrogens are in place. If they are, the conversion is not really needed and the same command can be applied.

Multiple conformation 3D PSAThis measure obviously depends on the conformation of the molecule. An average PSA can be calculated with the following script from a stack on conformers generated by a montecarlo command, e.g.:


  for iconf=1,Nof(conf)
     load conf iconf
     show surface area a_//n*,o* | ( a_//h* & Next( a_//n*,o* bond )) a_  mute  vwExpand = 0.
     avPSA += r_out  
  endfor
  avPSA /= Nof(conf)

This script can also be easily modified to include Boltzmann weights of individual conformer contributions. A similar look can be written to process the results of the _confGen script.

Fast and accurate estimate of PSA from chemical topology only ( TPSA or MolPSA )

Ertl et al. (see the reference above) proposed a way to estimate the PSA value directly from a two dimensional topology of a molecule without a need to convert it to 3D and sample its geometrical states. The ICM MolPSA function uses a similar method to estimate PSA, ( e.g. Predict( Chemical("CCO"),"MolPSA" ) ). The following method was used to derive a model (see the learn command ):

Six thousand drug compounds were converted to 3D, optimized and their real single conformation PSA values were evaluated
The chemical topologies were converted into Molsoft fingerprints and trained against the computed PSA values
The resulting model had a cross validated squared correlation coefficient of predicted vs training values of Q2=0.99 and the root mean square error of Rmse=1.56.

Example of using MolPSA in ICM:


read table mol s_icmhome+"/moledit/Dictionary.sdf" name="t"
add column t Predict(t.mol "MolPSA" ) name="MolPSA"
show Mean(t.MolPSA)

REBEL

a method to solve the Poisson equation for a molecule. REBEL is a new powerful implementation of the boundary element method with analytical molecular surface as dielectric boundary. This method is fast (takes seconds for a protein) and accurate. REBEL stands for Rapid Exact-Boundary ELectrostatics. The energy calculated by this method consists of the Coulomb energy and the solvation energy which is returned in the r_out system variable.
Related parameters and steps:

electroMethod = "boundary element";
.`TOOLS.rebelPatchSize (1., but can be smaller, say 0.3 or 0.5, it is a tradeoff between speed and accuracy)
dielConst (the default is usually OK);
dielConstExtern (the default is usually OK);
set charge as_ r_Charge (modify charges if you like);
make boundary (if you want to make several evaluations of energy or Potential( ) with the same boundary. The "boundary" parameters depend only on conformation and do NOT depend on charges. You can redefine charges afterwards and get a corrects energy evaluation);
delete boundary (if you do not need it);
show energy (make sure the "el" term is on);
Potential ( as_targets as_charges) (if the boundary exists, returns potentials from charges at the target atoms);
color grob potential [heavy] (create graphics object, say, with make grob skin actually it can be any grob and color it by the REBEL potential); option heavy results in better coloring.
Matrix(boundary) : returns the matrix solved to find the boundary element charges.
dsRebel : a macro for calculating the potential-colored electrostatic surface.

The polarization charges, or induced surface charges, can be returned by the Rarray( as_ ) function after the equation is solved, e.g.:

 
 electroMethod = 4 
 show energy "el" 
 Rarray( a_//* )  # returns polarization charges

Electrostatic troubleshooting

Problem: the electrostatic surface looks different before and after conversion to ICM .

Explanation: The unconverted PDB object has (i) an incomplete set of atoms ( lacking hydrogens for the X-ray entries, occasional missing side chains or loops, etc.); (ii) has formal charge ambiguities for his (hip), asp (ash) etc. , see below (iii) has no charges, i.e. the formal and partial charges are not assigned;

The dsRebel procedure (i) builds a full atomic model with hydrogens, (ii) resolves at least some residue charge ambiguities, and (iii) assigns to the atoms of the unconverted objects a simplified set of formal charges. See convertObject for further details.

The difference between the formal charges of the unconverted and the full distributed partial charges after conversion creates a small difference in electrostatic pattern.

If the conversion procedure charges a residue (e.g. a cysteine next to a metal ion), then the electrostatic patterns will differ much more in the vicinity of that residue.

Problem: the electrostatic surface looks different for different PDBs of the same protein

Explanation 1: Some residues can be charged or uncharged. In a specific PDB can be marked by a different 3-letter residue name or not. For example:

Amino Acid Frequent Rare
aspartate asp (-) ash (0)
cysteine cys (0) cym (-)
glutamate glu (-) glh (0)
histidine his (0) hip (+)
lysine lys (+) lyn (0)
tyrosine tyr (0) tym (-)
What may happen is, for example, that in one entry several histidines are marked as hip while in another they are simply marked as his . In this case the total charge will change and the dsRebel pictures will be different.

Problem: the numerical singularities are reported Sometimes numerical instabilities inherent to the REBEL calculation lead to singularities and strange values of electrostatic potential. This can be detected by looking at the polarization charge values. The ePotProtected macro in the _rebel file contains the code that checks for this type of instabilities.

real

number may exist in the ICM-shell as a named variable or a constant (e.g. 12.3, 2.0, -4.501 ). There are a number of predefined real variables. Reals can be concatenated into a real array like this: 12.3//2.0//-4.5

Reals may be mentioned in arithmetic expressions, commands and functions.
Examples:

 
 a = -1.2 
 b = Abs(Sin( 2.3 * a - 3.0 / a))

regularization

procedure for fitting a protein model with the ideal covalent geometry of residues (as represented in the icm.res residue library) to the atom positions of a target PDB structure (usually provided by X-ray crystallography or NMR). Regularization is required because the experimentally determined PDB-structures often lack hydrogen atoms and positional errors may result in the unrealistic van der Waals energy even if these structures were energetically refined (since the refinement of the crystallographic structures typically ignores hydrogen atoms and employs different force fields). The following steps are required to create the regularized and energy refined ICM-model of an experimental structure:

an extended all-atom model of a particular protein is generated with regular geometry characteristics (see the build command and the IcmSequence function);
the non-hydrogen atoms in the model are assigned to the equivalent atoms in the model (see set tether);
the regularized structure is built starting from the N-terminus by adding atoms one-by-one (see minimize tether);
methyl groups are rotated to reduce van-der-Waals clashes;
combined geometry and energy function is optimized;
polar hydrogen positions are adjusted;
optionally the model may be additionally minimized, now without tethers to observe a "stability" of the model in the local energy minimum.

See macro regul .

residue

a chemical building block or complete chemical compound, usually an amino-acid residue. The ICM hierarchy: atom -> residue -> molecule -> object. Individual small molecules may contain only one residue. Residues are described in the icm.res file. You may create your own residues with the write library command. Residues can be selected with the ICM-selection expression (e.g. a_/ala, a_/15, a_/15:20, a_/"RDGE" etc.), labeled with the display residue label rs_ command, by double clicking with the right mouse button, via a pop-up menu, or from * Added tothe registry{ Table( model chem [inverse] ) } function. the GUI menu.

rgb

red-green-blue. It is of interest, that the combination of these three can produce any other color. In addition, this is the name of the SGI image format used in the ICM commands write image and display trajectory . ICM also generates the fourth channel on top of the RGB information. This fourth number is called alpha-channel and generates the opacity index for each pixel of the image. This information is interpreted by a number of applications, i.e. the IRIX showcase and dmconvert (the SGI moviemaker). See also tif, targa, postscript.

ribbon

a graphical representation of a polypeptide chain backbone by a smooth solid ribbon. DNA and RNA can be also displayed in a ribbon style.
There are three types of elements of the ribbon display depending on the secondary structure assigned to a given residue.

Residues marked as alpha-helices ('H') will be shown by a flat ribbon, those marked as beta-sheets ('E') will be flat ribbon with an arrow-head, and the rest will be shown by a cylindrical "worm". The ICM-shell parameter GRAPHICS.wormRadius defines its radius. Default ribbon colors are defined in the icm.clr file. Note that minor secondary structure elements like 3/10 helix ('G'), Pi-helix ('I') are colored by the corresponding colors ( the threetenRibbn and piRibbon parameters in the icm.clr file), 'Y' type is colored by the alphaRibbon color, and 'L','P' and 'B' (isolated beta-residue) residues are colored by the "betaRibbon" color. DNA and RNA ribbons are colored according to the base type: A-red, C-cyan, G-blue, T or U - gold. Preference ribbonStyle allows one to display a simplified segment representation of the secondary structure elements instead of (or together with) the ribbon.

If the polypeptide chain has a break (missing residues) the ribbon shows bullets or nothing depending on the GRAPHICS.chainBreakStyle .
The DNA/RNA ribbons consists of two parts the backbone ribbon and the bases shown with the sticks and balls. To selectively display and undisplay the bases, you can do the following:
Example:

 
 read pdb "1dnk"         # contains 2 dna mol. 
 display ribbon a_1.2,3  # both bases and backbone 
 undisplay ribbon base a_1.2    # bases disappear 
 display ribbon base only a_1.2 # only bases 
 display ribbon a_1.2,3 yellow  # both bases and backbone 
 color ribbon a_1.3 magenta     # the second chain backbone 
 color ribbon a_1.2,3 bases     # default by base type 
 cool a_  # cool is a rich macro. View the whole thing