[ database | Depth cueing | distance | distance geometry | Ssbond | drestraint | drestraint type ]
a format for storing entries containing several different types of information.
The
column
format (multicolumn representation) is the alternative.
The database should have the following format:
FieldName1 Number|String
FieldName2 Number|String
FieldName3 Number|String
FieldName1 Number|String
FieldName2 Number|String
FieldName3 Number|String
...
Fields can contain integers, reals and multiline strings.
Example:
id jur1
iq 24
addr LA
addr California
id jur2
iq 17
addr LA
a visual effect which makes objects disappear in a fog according to the screen Z-coordinate.
Press
Ctrl-D
to invoke the effect and move the back clipping closer with MidMB to make
the effect more dramatic. Also more the front clipping plane with Ctrl-MidMB to
make the front brighter.
|
|
If you use gui adjust the front and back clipping planes using the buttons in the
graphics tool bar and vertical movements with the left-mouse-button
Two parameters influence the fog effect:
- fogStart determines the relative Z-position
at which the linear fog effect starts (the distance between the front and the back planes is 1.)
- color volume color command allows to color fog differently from the background (by default they are the same).
a measure of proximity in three-dimensional or multidimensional space for
all kinds of objects, including sequences and real arrays. Sometimes it means a special
array ( parray to be exact) consisting of batches of interatomic distances. This objects
are shown in the GUI and are interactive.
See also:
is often used to calculate a set of Cartesian coordinates of a series
of objects given all (or even a subset of) the inter-object distances
(Crippen and Havel, 1988).
ICM function Disgeo() allows to solve this sort of problems.
See also Distance().
(or SS-bond) a covalent bond between sulfur atoms of two cysteine residues.
In the PDB objects loaded by the
read pdb
command these bonds are automatically imposed on the basis of SSBOND
records. Upon conversion of a PDB structure into the ICM-object with the
convert
command, the disulfide bonds are inherited. Important: commands
make disulfide bond
and
delete disulfide 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. In addition, SS-bonded
cys residues are renamed to cyss.
Therefore, to count the number of disulfide bonds you may simply count the cyss
residues: show Nof(a_/cyss)/2 .
Distance restraints imposed to form such a bond are defined in the file icm.cnt .
a distance restraint (sometimes abbreviated as cn ) which
imposes a penalty function on the distance between two atoms of the same object
( in contrast, tether imposes a restraint to an atom in another object ) .
Distance restraints may have different characteristics and types.
A drestraint is a basin with flat bottom between the upper and lower bounds ( Du and DL )
and quadratic walls:
P( d ) = w*( d - Du )2 /Du | if d > Du (upper wall)
|
P( d ) = 0 | if DL < d < Du (flat bottom)
|
P( d ) = w*( d - DL )2 /DL | if d < DL (lower wall)
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drestraints are mostly used in structure determination using the NMR NOE data.
The weight, w, is the product of the weight for all distance restrains ( cnWeight )
and a specific weight for a given drestraint type.
Drestraints may be read, written,
made, setn, shown,
and displayed.
The parameters of drestraints are written in *.cn files.
See also: icm.cnt drestraint type file description.
To activate the drestaint penalty term, use the set terms "cn" command.
a type of distance restraint(s).
It describes well depth, lower and upper boundaries and has two forms:
global and local. Local restraints become weaker and vanish
as the distance between the corresponding atoms grows (similar to the van der
Waals forces), while global restraints become stronger as you deviate further
from the required distance range. Local type has an additional characteristic such as
sharpness. The types are given in *.cnt files.
The main list of types consists of general user-defined global and local
types as well as a number of fixed named types used to impose
disulfide bonds or
peptide bonds.
Drestraint types may be
read,
written,
set,
and
shown.
See also: *.cn file description.