ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
References
Glossary
 A
 B
 C
 D
 E-H
 I-N
 O-R
 S
 T
 U-Z
  unique
  unix
  Virtual
  volume
  vrestraint
  vrestraint type
  wire
  xstick
  ZEGA
 
Index
PrevICM Language Reference
U-Z
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[ unique | unix | Virtual | volume | vrestraint | vrestraint type | wire | xstick | ZEGA ]

unique


an option of the group sequence command used to exclude from the group identical sequences (which may result from, e.g., from a set of PBD structures with the same sequence, but somewhat different conformation).


unix


See the sys function ( unix was too discriminatory against other operating systems).

virtual atoms and variables


Additional immaterial geometrical points (referred to as "virtual atoms") attached to each molecule for technical reasons, and internal coordinates ("virtual bonds, angles, torsions and phases") associated with them. These points help to have a standard yet flexible treatment of parameters defining absolute position (translation and rotation) of each molecule with respect to the coordinate frame. Each molecule is connected to the origin via two virtual atoms attached to it. This part of the ICM-molecular tree is built in the following way:

  • o2, o1, o three points with coordinates 1,0,1, 0,0,1 and 0,0,0, respectively. They are the same for all molecules
  • vt1 the first virtual atom of a molecule. It is attached to the origin ( o ) via virtual bond length bvt1, planar angle avt1 (o1-o-vt1) and a dihedral angle. The dihedral angle is a torsion angle tvt1 (o2-o1-o-vt1) for the first molecule in the tree, but it is a phase angle fvt1 (a difference between dihedrals o2-o1-o-vt1( current-molecule) and o2-o1-o-vt1( 1st-molecule)) for all molecules but the first one.
  • vt2 the second virtual atom attached to vt1 via virtual bond length bvt2 (usually fixed), planar angle avt2 (o-vt1-vt2) and a a torsion angle tvt2 (o1-o-vt1-vt2).
  • the first real atom of a molecule. Torsion angle leading to it is called tvt3.
The absolute position of the first molecule as a rigid body is defined by six virtual variables:
 
   Name StdValue Type  Definition 
1. tvt1 180. torsion   **o2-o1-o-vt1 
2. avt1  90. angle     **o1-o-vt1 
3. bvt1   1. bond      **o-vt1 
4. tvt2 180. torsion   **o1-o-vt1-vt2 
5. avt2  90. angle     **o-vt1-vt2 
6. tvt3 180. torsion   **o-vt1-vt2-1stAtom 
The
 
 set a_1//vt1 
command sets the first virtual atom to the center of mass of the corresponding molecule. After that you can control the distance to the origin by vt1. To understand it better, try the following short session (just paste it line by line):
 
 build string "se ala\nml a\nse his" # two molecules 
 display virtual 
 varLabelStyle = "name" 
 display variable labels 
 display virtual atom labels a_//vt* 
 connect a_1   # move the 1st molecule with the mouse 
 connect a_2   # move the 2nd molecule with the mouse 
 set a_1//vt1 
 set a_2//vt1 
 set v_1//bvt1 2. 


volume


measured in cubic Angstroms. One can calculate the van der Waals volume (see Volume function), the volume confined by solvent-accessible surface (see show volume surface) , or by molecular surface referred to as skin (see show volume skin) .

vrestraint


a multidimensional variable restraint (often abbreviated as rs ) which restrains one or several geometrical variables (usually torsions) to certain ellipsoidal zones, described by Abagyan, Totrov and Kuznetsov (1994). Variable restraints may have different characteristics and types. The vrestraints are marked either for energy calculations or for description of probability distributions (fields 'rse' and 'rs', respectively). See also: icm.rs and icm.rst files.

vrestraint type


a type of multidimensional variable restraint. Each type specifies to which variables this type may be assigned, the average values and standard deviations (or well dimensions), and the well depth. The types are described in *.rst files. There are two kinds of vrestraint types depending on what they will be used for: energy kind marked with the 'rse' field and the probability type marked with the 'rs' field. The first kind will be used as an "rs" penalty term, while the second kind will be used for the BPMC random step.

wire


a default representation of a molecule, fast and simple. Bonds are shown by lines or arrows according to the wireStyle preference. Double bonds in the wireStyle "chemistry" mode are shown according to the wireBondSeparation parameter. Isolated atoms are shown according to the atomSingleStyle preference (usually by a small tetrahedron); line thickness is controlled by the lineWidth parameter.
Examples:
 
 display a__1crn./n,ca,c  # displays a wire model of crambin.  
                          # (note, display command can also  
                          # read in the 3D coordinates  
                          # if double "_" used)  
You would need to mention "wire" explicitly to undisplay it when other types of graphical representation are also present.
Examples:
 
 display                 # wire is the default  
 display cpk a_/1:5      # adds CPK  
 undisplay wire          # remove wires, leave only CPK  


xstick


a combination of ball and stick representations of atoms and bonds.

ZEGA


a Zero End-gap Global Alignment, that is a pairwise alignment method based on the Needleman and Wunsch algorithm modified to use zero gap end penalties. This type of alignment was first described by Michael Waterman, who called it the "fit" alignment. The paper of Abagyan and Batalov, 1997 describes the statistics of the structural significance of the alignment score and optimization of the alignment parameters for the best recognition of structurally related proteins. This statistics is used in database search (see the find database command) to evaluate the significance of hits. This pairwise alignment algorithm is used in the Align function, align command, and database searching.

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