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Jun 5 2024
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[ _macro | _startup file | foldbank.db | Icm.cod | Icm.bbt | Icm.bst | Icm.cnf | Icm.cnt | Icm.cn | Icm.gro | Icm.htm | Icm.hbt | Icm.hdt | Icm.cfg | Icm.clr | Icm.map | Icm.trj | Icm.ob | Pmffile | Icm.res | Icm.var | Icm.rst | Icm.rs | Icm.col | Icm.tab | Icm.tot | Icm.vwt | Icm.pdb | Icm.seq | Icm.se | Icm.ali | Icm.all | Icm.cmp | Icm.prf | Icm.iar | Icm.sar | Icm.mat | Icm.rar ]
_macro file. A collection of ICM macros. |
This file contains a set of ICM macros. You can use them, modify them, or browse them to develop your own macros. _macro is downloaded by the call _macro command.
_startup. ICM startup file |
This ICM script contains a set of commands issued automatically upon invoking ICM. The file will be first searched in the current directory and then in the directory defined by the UNIX environmental variable ICMHOME. Read more about the _startup file in the customization: _startup section.
s_pdbDir = "/data/pdb/" # set it to the place where PDB lives
pdbDirStyle = "pdb1abc.ent" # style currently distributed by PDB
s_helpEngine = "icm" # reasonable default, HTML-help is
# an alternative
# you may have your own PROSITE updated file
s_prositeDat = Getenv("ICMHOME")+"/prosite.dat"
# xpsview may be more standard
s_psViewer = "/usr/opt/bin/gs -q"
# better be accessible only for you
s_tempDir = "/usr/tmp/"
#
read libraries # they will be read from $ICMHOME
call _aliases # by default it will be taken
# from the directory defined by
# environmental variable $ICMHOME
call _macro # by default it will be taken
# from the directory defined by
# environmental variable $ICMHOME
print "...ICM startup file executed..."
foldbank.db |
Bank of assigned secondary structures (foldbank.db) This text file may be created by _mkSegmentLib script and contains secondary structures for a non-redundant set of protein chains. Description of fields:
- NA - chain name ('m' usually stands for main or 'NO chain identifier')
- RZ - resolution. NMR entries get 9.99 (they may be actually worse than that).
- ER - all-atom RMSD-error upon PDB->ICM conversion. Beware of entries with ER > 0.5!!
- SE - amino acid sequence as extracted from the structure (not SEQRES)
- SX - authors' secondary structure assignment, all _____ if not provided (as in 1knt.m).
- SS - automatically assigned by ICM secondary structure using modified Kabsh and Sander algorithm.
Example two entries:
... ... ## 355 NA 4tpi.i RZ 2.20 ER 0.027 SE RPDFCLEPPYTGPCRARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA SX _______________EEEEEEEEEE__EEEEEEEEE__________HHHHHHHHHH__ SS ___GGG___________EEEEEEE____EEEEEEE_________B__HHHHHHHH___ ... ... ## 364 NA 1knt.m RZ 1.60 ER 0.015 SE TDICKLPKDEGTCRDFILKWYYDPNTKSCARFWYGGCGGNENKFGSQKECEKVCA SX _______________________________________________________ SS _GGGG______B____EEEEEEE____EEEEEEE__B______B__HHHHHHHH_ ... ...
Atom codes (icm.cod) |
This text file contains description of (1) atom types and references to (2) MMFF types, (3) van der Waals types, (type 0 or 9 to ignore) (4) hydrogen bonding types, (type 1 means no H-bonds) and (5) hydration types (0 to ignore). The real numbers are atomic mass (6) and surface (7). The character (8) is used to define atom color. Free-format. Two example lines:
# (1) (2) (3) (4) (5) (6) (7) (8) * Comment #> cd mmff vw hb hd wt sf na comment cod 63 6 18 6 6 16.000 40.77 o * o in r-c-oh (thr,ser) cod 71 32 19 6 8 16.000 36.79 o * o- in carboxylate ion cod 92 12 61 1 1 35.453 133.8 Cl * (MMFF) cod 223 38 13 4 3 14.007 61.16 n * pyridin nitrogen (MMFF)
Bond angle bending and improper torsion deformation parameters (icm.bbt) |
This text file contains a factor (kcal/mole) and an equilibrium angle in degrees for the bond angle bending deformation energy for different types of angles.
# Type Factor OptAngle(a0). E=Factor*(a-a0)<sup>2</sup> # bbt 1 160.7000 115.0000 ca-c#-n bbt 2 128.2000 120.5000 ca-c#=o ...
Bond stretching parameters (icm.bst) |
This text file contains a factor (kcal/mole) and an equilibrium bond length in Angstroms for the bond stretching energy for different types of bonds.
# E=Factor*(b-b0)<sup>2</sup> # Type Factor BondLength(b0). #> ity eybs eqbl bt comment # bst 1 500.0 1.4530 1 cn n-ca bst 2 1150.0 1.3250 1 cn c#-n bst 3 460.0 1.5300 1 cc ca-c# bst 4 430.0 1.5300 1 cc ca-cb ...
Conformational stack ( *.cnf ) |
This binary file contains descriptions of several conformations of the same molecule. You can not edit this file. The stack is automatically generated and saved in the course of Monte Carlo, or systematic search procedures. Alternatively the stack may be created directly by the store conf command. To read/write a stack use: read stack [s_StackName] write stack [s_StackName]
Distance restraint types ( icm.cnt or *.cnt ) |
The file describes legal types of drestraints to impose attraction or repulsion between atom pairs (e.g. NOE distance restraints derived from NMR data). This penalty term is called "cn". The system icm.cnt can be edited, however, user files (e.g. mydist.cnt) of the same format can be created and loaded with the read drestraint type command. The file contains:
# type weight lower upper sharpness # 4 special types for S-S bonds ssSS1 10.0 2.04 2.04 10.0 # Sharp well for S-S dist. ssSS2 2.0 2.04 2.04 1.0 # Wide well for S-S dist. ssSC 5.0 3.052 3.052 10.0 # S -Cb distance ssCC 3.0 3.855 3.855 10.0 # Cb-Cb distance global 1 1.0 0.0 3.0 # a global drestraint global 2 1.0 2.0 4.0 # a global drestraint local 12 1.0 2.5 2.8 1.0 # a local drestraintBoth local distance restraints and global ones force two atoms to stay between the upper and lower boundaries, however, the local restraints diminish at large distances (similar to van der Waals interactions), whereas the global restraints grow bi-quadratically as deviation from the target distance range increases. You can have and read several *.cnt files. If the type numbers overlap the previous types are redefined.
From version 3.6-2 self-sufficient harmonic drestraints that do not require a
separately defined type were introduced. However, the older drestraints with
external types continue to be supported.
See also related commands:
read drestraint type,
show drestraint type,
set drestraint type,
make drestraint type.
Distance restraints ( *.cn ) |
Contains list of atom pairs for which interatomic distances should be restrained according to specified types defined in a separate icm.cnt file. The .cn files are created by the user. Supplied icm.cn file is just an example.
# ml1 re1 at1 ml2 re2 at2 cn_type cn crn 1 val hg22 * 1 val ca 1 cn * 1 val hg23 * 1 val cg1 1 cn * 2 gln ca * 1 val hg11 1 cn * 2 gln ca * 1 val ha 1Molecule name and residue number (e.g. 14, 25A, etc.) are normally used to find an atom. An asterisk instead of the molecule name means that only the residue number should be matched. See also: read drestraint, show drestraint, set drestraint, and make drestraint (un)display drestraint
Graphics objects ( *.gro ) |
This text file contains streams of POINT coordinates (i.e. a triple of floats in one line, preceded by an integer reference number), LINE descriptors (i.e. pair of integer numbers of recently described POINTS in one line) and/or TRIPLES (or TRIANGLES, i.e. triples of integer numbers of POINTS). The order of streams is arbitrary, provided that referenced POINTS are already described. Either LINES or TRIPLES can be omitted. Graphics objects can be read, written, displayed , or made from a 3D map.
1 1.00 -1.00 0.00 2 1.00 1.00 1.00 3 0.00 2.00 0.50 1 2 1 3 2 3 1 2 3Check content of other .gro files in you icm directory. ICM also understands the Wavefront obj-format ( files *.obj and *.off ) as well as 3DXML from Dassault Systemes, and two Collada formats, namely .DAE and .KMZ. The .KMZ format is a zip file that contains .DAE files and additional texture files. You can create your own dot, wire or solid graphics objects either manually or automatically.
ICM HTML help file ( icm.htm ) |
contains this manual
Hydrogen bonding types ( icm.hbt ) |
A and B parameters for the A/r12 - B/r10 potential between HB donors and acceptors. See Nemethy et al. for reference.
Example lines:
# i j B A E r0 # hbt 2 4 8244.0 32897.0 0.550 2.190 * n-h...n hbt 3 4 8244.0 32897.0 0.550 2.190 * o-h...n
Hydration parameters ( icm.hdt ) |
Parameters to calculate solvation energy based on atomic solvent-accessible surfaces (see solvation term). The file contains the current ICM set and several currently inactive sets (e.g. Eisenberg and McLachlan (1986), Wesson and Eisenberg (1992) ) that are commented out.
Example lines:
rwater 1.4000 # water radius used to roll around the molecule # # 1 2 3 4 5 6 7 8 # ty, eyhd, ey_apolar, ra, exvo, ey_membrane hdt 1 0.0100 0.0151 1.950 21.15 -0.00824 c aliphatic hdt 2 -0.0090 0.0177 1.800 12.57 -0.02646 c aromatic hdt 4 -0.2800 -0.0548 1.700 13.63 -0.03390 n+ nz lys+
- reference type number
- solvation energy density from vacuum-water transfer experiments for a given hydration type
- solvation energy density from octanol-water transfer experiments for a given hydration type
- radius used to calculate accessible surface
- excluded volume
- membrane (lipophilic) implicit solvation parameters, see surfaceMethod = 4 and TOOLS.membrane array
- atom code name
- comment
The solvation parameters can be temporarily changed and the product of the current solvent accessible areas by the parameters can be returned with the Area ( as_ R_newParams energy ) function.
Configuration file (icm.cfg) |
This file contains limits and memory requirements for ICM. It will be searched in the current directory ( ./ ) first and, if not found, in the directory defined by the UNIX environmental variable $ICMHOME or $HOME/.icm/config/ directory ( $USERPROFILE/.icm/config/ for Windows), if present.
You may edit the file and change the limits. The MnArrays parameter controls sized of three types arrays: rarray , iarray and sarray .
# ICM configuration file. Free format # Mn stands for "Maximal Number of" # Mx stands for "Maximal Size of" BufferSpace 2097152 # ICM will not let you decrease BufferSpace less than 131072 MnResidueTypes 200 MnSequences 20000 MnAlignments 1500 MnProfiles 40 MnGrobs 200 MnArrays 600 MnTables 140 MnMaps 40 MnMacros 400 XTermFont *-fixed-medium-*-*-*-24-* # to set font in the terminal window Xterm xwsh # default for SGI # Xterm xterm # default for Linux and other UN*Xes
Colors ( icm.clr ) |
file contains default color and font settings. The default icm.clr file resides in the $ICMHOME directory. The LIBRARY.clr variable defines the default path and name of the icm.clr file.
Keep your own color and graphics controls file in ~/.icm directory. Example of ~/.icm/user_startup.icm file ( $USERPROFILE/user_startup.icm under Windows ):
LIBRARY.clr = Getenv("HOME")+"/.icm/icm.clr"
read color # load your custom settings
Modify the file if needed. The following lines are recognized (free format):
# CONFIGURABLE GRAPHICS.mode translation table # Use keywords Left Mid Right, Shift Ctrl Alt Dbl, At # TopNN LeftNN RightNN BottomNN, where NN is a percentage of the zone # Modes 0,3,4,5,14,15 require a hit in 'At' = (atom | grob) # otherwise control falls through to next best appropriate action # Some modes have submode switches listed in parentheses () # Users are encouraged to modify bindings to their needs # ---mode--combination------------- # equivalent GRAPHICS.mode preference mode 0 Right-At # popup (in GUI only) mode 1 (Shift)-Left # Rotation mode 2 (Shift)-Mid # Translation mode 3 (Ctrl)-Shift-Right-At # Label atoms mode 4 (Ctrl)-Dbl-Right-At # Label residues mode 5 (Shift)-Ctrl-Left-At # Change torsion angles mode 6 (Shift)-Bottom5-Left # Rotation of the view mode 7 (Shift)-Top5-Left # Z-axis rotation mode 8 Left5-Mid # Zoom mode 9 Alt-Mid # Move rear clipping plane mode 10 Ctrl-Mid # Move front clipping plane mode 11 Ctrl-Alt-Mid # Slab mode 12 (Shift)-Right # Rectangular selection mode 13 (Shift)-Ctrl-Left # Lasso selection mode 14 (Shift)-Ctrl-Alt-Right-At # Connect to molecule mode 15 Shift-Ctrl-Dbl-Right-At # Set alignment cursor mode 16 Ctrl-Mid-At # Drag atoms mode 17 Right5-Mid # Z-translate
#--------------{Colors}------------
# -----color------------RRGGBB--A_real_if_not_1
....
color lightgreen # 80ff80
color rita # ff1b00 0.3
color darkseagreen # 8fbc8f
...
#--------{ Atom/Grob/Font Colors }--------
atom c grey # c is the first character of chemical element.
background black
# color font size bold italic underline
atomFont rose times 12 0 0 0
varFont yellow symbol 12 0 0 0
residueFont green helvetica 18 0 0 0
grobFont green helvetica 18 0 0 0
stringFont green times 24 0 0 0
auxiliaryFont green symbol 28 0 0 0
fixedFont green courier 12 0 0 0
#
alphaRibbon red
piRibbon blue
threetenRibbon magenta
betaRibbon green
coilRibbon yellow
#- 0:127 rainbow colors (address them by number: color 15.5) -------
# ---------i-color----
rainbow 0 # 0000ff
rainbow 63 # ffffff
rainbow 127 # ff0000
....
Electron density map ( *.map ) |
This binary file contains a complete description of the electron density map, compatible with the format devised by Phil Evans. Maps are stored as a 3-dimensional array preceded by a header which contains all the necessary information about the map. See "The CCP4 Suite" manual for details.
A crystallographic electron density map can be converted to a rectangular equally spaced grid map with the make map potential m_source command.
To create an electron density map from an object in ICM use the make map potential command which by default creates a map called m_atoms . Example:
read pdb "1xbb" # Syk kinase with gleevec make map potential a_sti # density map only for the gleevec display m_atoms only
MC simulation trajectory ( *.trj ) |
This binary file contains a description of a set of geometric parameters (free variables, usually torsions and overall rotation/translation variables), participating in MC simulation, followed by a stream of their values for each conformation accepted during the simulation, together with the energy of each accepted conformation. Movies can be created or appended during MC simulation runs, and then played in any direction with optional smoothing, superimposition (to the initial conformation) and/or centering. These files tend to be large, watch them carefully and do not create them without a need. See also: display trajectory.
ICM-object ( *.ob ) |
a binary non-editable file describing one or several molecules forming an ICM-object. In addition to information available in a PDB-file it contains a description of atomic charges, tree-like connectivity, detailed atom codes, information about which internal coordinates are constrained, references to energy parameters, secondary structure, etc. The object can be read and written.
Parameters for "mf" mean force term ( icm.pmf ) |
Example lines:
# types: icm pmf pmft 50 5 pmft 53 6 pmft 54 6 pmft 55 6 ..... # midi mxdi steps (interpolation range) pmfh 0.0 9.0 46 # type1 type2 energy (interpolation points) pmf 1 1 4.253138 4.253138 4.253138 4.253138 ..........
Lines starting with "pmft" key define mapping of general icm atom types (as defined in icm.cod) to a (smaller) set of types of atoms for "mf" energy term. A single line starting with "pmfh" defines the range of distances and the number of interpolation steps for energy energy calculations using cubic spline. Lines starting with "pmf" key define energy function for a specific pair of atom types (first two integers), subsequent reals are function values at different distances, from minimal to maximal as defined in "pmfh" line.
See also:
Residue library ( icm.res or *.res ) |
The main residue library, describing all "residues" and molecules which can constitute a legal ICM-object. You can create your own entry either manually or using the write library command and add the entry to the icm.res file. You can also keep it in a separate file and append the file to the LIBRARY.res sarray (i.e. LIBRARY.res=LIBRARY.res//"usr" followed by the read library command). A example of an entry for a pro residue:
# resName 1-ch Type AccSurf Eentropy LongName nare pro P AMINO 150 0.0 proline rem rem _________atom_________ _dihedral_angles __bond_angles__ _bond_lengths rem / \ / \ / \ / \ rem at na cd lwat qu gu na fe vuva ey na fe vuva ey na fe vuva ey qfm # Fields: # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 # atre 1 n 216 0 -0.285 0 psi + 180.000 2 an . 118.000 1 bn . 1.340 31 atre 2 ca 113 1 0.050 0 omgp + 180.000 24 aca . 121.000 1 bca . 1.465 1 atre 3 ha 1 2 0.040 0 fha . 116.800 0 aha . 110.200 1 bha . 1.090 0 atre 4 cb 112 2 -0.025 0 fcb . -120.850 0 acb . 103.700 37 bcb . 1.530 4 atre 5 hb1 1 4 0.015 0 fhb1 . 120.200 0 ahb1 . 111.600 1 bhb1 . 1.090 0 atre 6 hb2 1 4 0.015 0 fhb2 . -120.200 0 ahb2 . 111.600 1 bhb2 . 1.090 0 atre 7 cg 112 4 -0.050 0 xi1 . 27.400 21 acg . 103.700 1 bcg . 1.502 4 atre 8 hg1 1 7 0.025 0 fhg1 . 120.450 0 ahg1 . 111.200 1 bhg1 . 1.090 0 atre 9 hg2 1 7 0.025 0 fhg2 . -120.450 0 ahg2 . 111.200 1 bhg2 . 1.090 0 atre 10 cd 114 7 0.100 0 xi2 . -35.600 21 acd . 105.300 39 bcd . 1.501 4 atre 11 hd1 5 10 0.010 0 fhd1 . -119.730 0 ahd1 . 111.600 1 bhd1 . 1.090 0 atre 12 hd2 5 10 0.010 0 xi3 . -90.760 21 ahd2 . 111.600 1 bhd2 . 1.090 0 atre 13 c 121 2 0.455 1 phip . -68.800 19 ac . 112.300 3 bc . 1.520 3 atre 14 o 81 13 -0.385 1 fo . 180.000 0 ao . 120.500 1 bo . 1.230 5 # F 20 lwat 13 # F 21 exbo 1 10Eentropy is the entropic contribution to the free energy for a fully accessible residue divided by the solvent accessible surface of this residue (in gly gly X gly gly environment) and multiplied by a factor of 1000.
Fields:
- relative atom number
- atom name
- main atom code (see icm.cod file). It in turn refers to other codes such as hydrogen bonding code, van der Waals code and hydration code.
- previous atom in a connectivity graph of the directed ICM-tree.
- electric charge
- groups of close charges (they should not be separated due to cutoffs distance in interaction lists)
- torsion name
- fixation status (+ free variable, . fixed)
- torsion angle (degrees)
- torsion energy type (see icm.tot file).
- bond angle name
- bond angle fixation status
- bond angle value (degrees).
- bond angle deformation energy type (see icm.bbt file).
- bond length name
- bond fixation status
- bond length (Angstroms)
- bond stretching energy type (see icm.bst file).
- (qfm) formal charge (may be +1, -1/3, -1/2 etc.), if any
- (lwat) exit atom of the residue
- (exbo) additional (non-tree) covalent bonds (atom1 atom2). Normal ICM-tree bonds form regular directed graph without cycles, therefore all the remaining bonds should be declared separately.
The following modified amino acids are also present in icm.res :
- cme C S,S-(2-hydroxyethyl)thiocysteine
- csd A 3-sulfinoalanine
- cso C S-hydroxycysteine
- kcx K lysine Nz-carboxylic acid
- hyp P 4-hydroxyproline
- ptr Y Aphosphotyrosine
- tys Y AO-sulfo-L-tyrosine
- llp K lysine-pyridoxal phosphate
- sep S phosphoserine
- tpo T phosphothreonine
Access to 250 modified amino acids.ICM also contains a table called AminoAcids with objects and codes for 250 amino acids. mutateResidue2 res code macro can be used to modify an amino acid to the specified one.
See also: LIBRARY.res , Table (residue)
Object Variables ( *.var ) |
Text file containing either a subset or a complete set of internal coordinates (variables). Usually created by the write vs_var command. It may also be typed manually. In contrast to an object file ( *.ob) which is a complete description of an object, icm.var may contain any selection of variables. These variables can be read and automatically assigned to a molecule according to molecule name, residue number and variable name.
Examples:
rem Va fx Atom Residue Mol Obj VaType Symm Value va psi + n 3 gln mol dl 2 1 180.00 va phi + c 3 gln mol dl 1 1 -60.00 va psi + n 4 met mol dl 2 1 120.00 va phi + c 4 met mol dl 1 1 180.00
Multidimensional variable restraint types ( icm.rst or *.rst ) |
define generic attraction zones in internal coordinate space (usually torsion space) in terms of residue name pattern (* for any residue type), relative residue number, and variable names. After the types are loaded, you may use them to assign specific vrestraints using the set vrestraint command. Three example restraint types (the third one marked with 'rse' will be used as a penalty term, the first two will be used for BPMC steps):
------------------------------------ Two-variable vrestraint rs aa -3.300 0.700 0.542 va ala* 1 phi -63.200 22.500 va * 2 psi -38.540 25.500 ------------------------------------ One-variable vrestraint rs vt -3.511 0.700 0.670 va val* 1 xi1 174.690 29.225 -------------------------------------- rse fmr -3.267 0.700 0.525 va phe* 1 xi1 -66.780 29.700 va * 1 xi2 98.680 75.100Explanation of fields:
- aa - rs-name (not longer than 4 characters). Usually the first character is a 1-char residue name, and the second is the zone character (a - alpha, b-beta, g-gamma,d-delta,t-trans,p-plus 60, m-minus 60,n-null)
- -3.300 - well depth ( should be negative )
- 0.700 - flat fraction of the well
- 0.542 - occupancy (probability) of the well with respect to other wells which could be assigned to the same set of variables.
- ala* - residue name pattern
- 1 - relative residue number
- phi - variable name
- -63.2 - center of the well for 1 phi
- 22.5 - size of the well (well is -63.2 +- 22.5 )
- * 2 psi - residue name pattern (* means any), relative residue number (psi formally belongs to C atom of the next residue, that is why the relative number is 2) and variable name
Multidimensional variable restraints ( *.rs ) |
This file has similar format to the icm.rst file. The differences are:
- rse and rs fields indicate whether the zone will be used for energy or probability, respectively.
- .rs file contains specific residue numbers rather than the relative ones.
- instead of the residue name pattern the file should contain molecule name or "*".
Example:
------------------------------------ Two-variable vrestraint rs aa -3.300 0.700 0.542 va 1crn 1 phi -63.200 22.500 va 1crn 2 psi -38.540 25.500 ------------------------------------ One-variable vrestraint rse vt -3.511 0.700 0.670 va * 3 xi1 174.690 29.225 -------------------------------------- rs fmr -3.267 0.700 0.525 va 1crn 4 xi1 -66.780 29.700 va 1crn 4 xi2 98.680 75.100
A sample *.col file |
The file shows an example of a multicolumn file which can be read with the read column command. Arrays r, e s and ent will be created.
# Entropies of several amino acids #>-r---e------s--------ent--- arg 2.13 184.920211 11.5181 asn 0.81 99.516352 8.1393 asp 0.61 89.629773 6.8057 cys 1.14 85.947233 13.263 gln 2.02 129.68481 15.576 glu 1.65 119.957333 13.75 his 0.99 121.124577 8.173 ile 0.75 132.717054 5.651
A sample *.tab file |
The file shows an example of a .tab file which can be read with the read table. It is similar to the previous file but additionally command. Table t consisting of header string t.titl and arrays t.r, t.e t.s and t.ent will be created.
#>s t.titl Entropies of several amino acids #>T t #>-r---e------s--------ent--- arg 2.13 184.920211 11.5181 asn 0.81 99.516352 8.1393 asp 0.61 89.629773 6.8057
Torsion parameters ( icm.tot ) |
The file contains torsion parameters according to Momany et al., 1975. Parameters for type 21 for pro taken from Venkatachalam et al., (1974), Macromolecules, 7, 212, parameters for types 22-23 for cooh taken from Karplus et al., J.Comp.Chem., (1983),4,187-217, DNA parameters are from Veal and Wilson, 1991. We added extra terms and modified the original Momany et al. parameters (psi and xi3 of Met). The format is free.
# +----symmetry-----+ # maxEner sign fold exact heavy Pseudo selChar phase # tot 0 0.00 0 0 1 1 1 - 0. # fixed dihedrals tot 2 0.25 1 1 1 1 1 S 90. # psi tot 44 0.50 1 1 1 1 1 S 90. # psi : removing the ECEPP alpha bias tot 3 10.00 -1 2 1 1 1 S 0. # omg tot 4 1.35 1 3 1 1 1 H 0. # xi CH2-CH2 tot 8 0.90 1 3 3 3 3 M 0. # nh3 term.group of lys,lysn tot 14 0.00 0 2 1 1 2 H 0. # xi2 of his (+-90) tot 5 1.00 1 3 1 1 1 H 0. # xi3 met tot 5 1.17 -1 1 1 1 1 H 0. # xi3 met additional torsionTorsion energy is calculated as: maxEner*(1 + sign*Cos(fold * torsion_angle)) Symmetry is a rotational symmetry in different situations: Exact is the exact symmetry (implies presence of all atoms, including hydrogens), Heavy implies presence of only the heavy atoms (no hydrogens) but uniqueness of different atom types. Pseudo implies that all heavy atoms are equivalent, and hydrogens are ignored. The last character is a short reference name which can be used in vs_var. For example: v_//M specifies all the torsions rotating terminal hydrogen atoms with symmetry higher than 1, v_//H side-chain torsions rotating heavy atoms, etc.
Van der Waals parameters ( icm.vwt ) |
The file contains ECEPP/2 parameters for peptides ( Momany et al., 1975, Nemethy et al., 1983), parameters for DNA atoms: Veal and Wilson, 1991 and other parameters (unpublished).
Example lines:
# type pzat n_el energy Deq Rvw Rvwel electroRadii # vwt 1 0.42 0.85 0.0370 2.92 1.200 1.200 * h aliphatic vwt 2 0.42 0.85 0.0610 2.68 1.200 0.808 * h amide,amine vwt 7 1.51 5.20 0.1400 3.74 1.700 1.700 * c carbonyl vwt 39 0.00 0.00 0.55 5.911 2.631 2.631 * pseudo atomEach line contains:
- type reference number (see icm.cod file)
- atomic polarizability *1024 (cm cubed);
- effective number of electrons
- -e(kk), kcal/mol - depth of energy minimum at the optimal inter-atomic distance
- r(kk), a - equilibrium (optimal) distance between two atoms of the same type
- van der Waals radius (used in graphics,electrostatics,etc)
- electrostatic radii, used to calculate geometrical surface boundary in boundary element method and MIMEL calculations
Protein databank file ( or *.ent ) |
Protein Data Bank formatted files consist of x,y,z coordinates, occupancies, and B-factors.
Examples:
ATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19This file does not provide a complete and unambiguous description of a molecular object. Therefore an object resulting from the read pdb command has a special type and needs conversion in order to become a full-scale ICM-object for which energy calculations are possible.
See also: convert and minimize tether commands .
Sequence ( *.seq *.pir *.gcg *.msf *.gb ) |
Acceptable formats of sequence files: FASTA and ICM format ( *.seq the simplest and the most natural):
> Name1 comment1 comment2 AGFDSTREMNH-FQW > Name2 RTPIYQWSCCVANMKL
PIR format: ( *.pir )
>P1;Azur_Pses4
Length: 80
AECSVDIQGN DQMQFSTNAI TVDKACKTFT VNLSHPGSLP KNVMGHNWVL TTAADMQGVV
TDGMAAGLDK NYVKDGDTRV*
//
>P2;Azur_Pses3
Length: 50
AECSVDIQGN DQMQFSTNAI TVDKACKTFT VNLSHPGSLP KNVMGHNWVL*
GCG format ( difficult to generate and impossible to edit because of the CheckSum):
Azur_Alcfa Length: 69 Check: 4484 ..
1 ACDVSIEGND AMQFNTKSIV VDKTCKEFTI NLKHTGKLPK AAMGHNVVVS
51 DGMKAGLNND YVKAGDERV
MSF format - obsolete multiple sequence format for alignments. Noneditable, contains CheckSums.
GB-Gene Bank format
Entries start with field names followed by a tabulation and the value. NCBI allows one to save in this format.
LOCUS (entry code)
..........(other fields) ...
ORIGIN ...(then the sequence)
1 tctaaataag ttttacacaa aataagttat ..
ICM-sequence file ( *.se ) |
contains molecular names and sequences. A simple example with two peptides:
ml a se gly ala ser pro tyr his se phe trp tyr ml b se ala ala ser asnA more advanced example with numbering, N- and C-termini and D-amino acids:
ml sub1 se 0 nter 1 gly 2 ala 2A Dglu 4 asp cooh ml water se 18 hohml field followed by molecule name signals that a new molecule is started. se field indicates sequence lines (free format). Residue names should correspond to entries in the icm.res residue library (or icmff.res library if you intend to use ICMFF forcefield). Residue numbers (if any) may be arbitrary, negative and may contain additional characters (e.g. 15A, 15B, etc.). Terminal modifiers (nter, nh3+, cooh, coo-, conh, etc.) may be explicitly specified. Cystein bridges may be specified as in cys(1) .... cys(1) .... cys(2) ... cys(2) Certain modules (ligand/peptide docking _dockScan and conformer generation _confGen) )further understand modres fields that can follow se field:
modres 6 c1ccccc1 modres 7/og OC
This allows creation of various modified or unnatural aminoacids. In the above example phenyl ring will be placed instead of Cbeta of residue 6 (and anything that follows in the sidechain), and methoxy group will replace Ogamma of residue 7. _confGen and _dockScan further understand special terminal groups nvtr and cvtr as an indication that N- to C- cyclization is to be applied.
ICM-alignment file |
ICM-format for sequence alignments. The consensus string contains the following symbols:
| symbol | description |
|---|---|
| space | gap in at least one of the sequences |
| character | this amino acid is conserved in all the sequences |
| + | positively charged amino acids ( R,K ) |
| - | negatively charged amino acids ( D,E ) |
| ^ | small amino acids: ( A,S,G,S ) |
| % | aromatic residues ( F,Y,W ) |
| # | hydrophobic amino acid (F,I,L,M,P,V,W) |
| ~ | polar amino acid ( C,D,E,G,H,N,Q,S,T,Y ) |
| dot | the rest (no consensus, no gap) |
# comments # Consensus: .C~.~I.^ND.MQ.~.K~#.V~K~CK~FT#~LKH.GK#.K..MG Azur_Alcde MLAKATLAIVLSAASLPVLAAQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMG Azur_Alcfa ---------------------ACDVSIEGNDSMQFNTKSIVVDKTCKEFTINLKHTGKLPKAAMG Azur_Alcsp --------------------AECSVDIAGNDQMQFDKKEITVSKSCKQFTVNLKHPGKLAKNVMG # Consensus: FCSFPGH#^#MKG.# Azur_Alcde FCSFPGHWAMMKGTLKLSN Azur_Alcfa FCSFPGHWSIMKGTIELGS Azur_Alcsp FCSFPGHFALMKGVL----
Residues can be colored by consensus with the color alignment rs_ command.
ICM all-file: a file with multiple icm objects. |
a file containing several ICM-shell objects divided by the following separators:
#> type1 ICM-shell-object-name1 .... obj1..... .... obj1..... .............. #> type2 ICM-shell-object-name2 .... obj2..... .... obj2..... .............. etc.Legal separators:
- #>i integer_name
- #>r real_name
- #>s string_name
- #>l logical_name
- #>p preference_name
- #>I iarray_name
- #>R rarray_name
- #>S sarray_name
- #>M matrix_name
- #>seq sequence_name
- #>prf profile_name
- #>ali alignment_name
- #>m map_name
- #>g grob_name
- #>T table_name # the column layout
- #>col table_name # the column layout
- #>db table_name
# the database layout
- #> brk # a protein-data-bank file content
- #> var # internal variables (torsions, angles, bonds) for the current ICM-object
#>i numberOffset 0 #>r lineWidth 1.00 #>l logo yes #>R boxx 0. 0. 1. 1. #>brk ATOM 1 n leu m 1 2.602 -12.770 -6.750 1.00 20.00 ATOM 2 ca leu m 1 2.423 -11.442 -7.311 1.00 20.00 ATOM 3 cb leu m 1 0.947 -11.187 -7.625 1.00 20.00 ATOM 4 cg leu m 1 0.758 -11.068 -9.138 1.00 20.00 ATOM 5 cd1 leu m 1 1.487 -9.824 -9.649 1.00 20.00 ATOM 6 cd2 leu m 1 1.335 -12.309 -9.822 1.00 20.00 #>s tt.h this is a header string of table tt. The arrays follow. #>i tt.i 15 #>T tt #> a b c d 1 2. bla 13 3 5. bli 13
Residue comparison table ( icm.cmp or *.cmp ) |
A triangular matrix with relative residue exchange frequencies (see actual file). The amino acid character line serves as a ruler. Use your favorite comparison matrix.
Protein profiles ( *.prf ) |
A profile table contains residue preferences for each residue type in each sequence position. The preferences may be derived from a multiple sequence alignment or from three-dimensional structure.
Examples:
Cons A B C D E F etc. Z Gap Len .. C 35 -32 143 -42 -52 -12 etc. -62 100 100 P 55 17 6 17 17 -71 etc. 26 100
Integer array ( *.iar ) |
File looking like this (free-format):
# everything which is not a number will be skipped 1 2 4 9 numbers may be in a row, or column or be in an arbitrary order. -14 9
String array ( *.sar ) |
Actually any text file. Each line will be a separate element of a string array
Matrix ( *.mat ) |
File looking like this:
1 0 0 0 1 0 0 1 1or like that
# my matrix 0. 1. 1. 2.2 1. 0. blu 1. 2. # text will be skipped # 1. 1. 0. 3. this line is commented outIn the latter case the result of read matrix command is a matrix of two rows {0. 1. 1. 2.2 } and {1. 0. 1. 2.} . Lines can be commented out with # sign. All the fields which do not look like numbers are skipped. If you matrix is symmetric, you may specify only the upper left or the lower right triangle like this:
1. 1. 2 1. 2 -1. 1. 2 3. 5.
Numerical data (real arrays) ( *.rar ) |
File may contain arbitrarily mixed numbers and strings. Strings will be skipped and numbers will form an array. A hash sign # at the beginning of a line comments this line out.
Examples:
# 1.2 1.4 1.8 rem 2.2This array will lead to {1.4 1.8 2.2} array.
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