[ unique | unix | Virtual | volume | vrestraint | vrestraint type | wire | xstick | ZEGA ]
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).
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.
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)
.
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.
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.
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
a combination of ball and stick representations of atoms and bonds.
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.