NCONT (CCP4: Supported Program)
NAME
ncont
- analyses contacts between subsets of atoms in a PDB file.
SYNOPSIS
ncont xyzin
foo_in.pdb
[Key-worded input file]
DESCRIPTION
ncont analyses contacts between subsets of atoms in a PDB file.
The program is written using the new MMDB
library for coordinate data, and thus works with a hierarchical view
of the atomic model. This hierarchy is visible for example in the
atom selection syntax used.
INPUT AND OUTPUT FILES
XYZIN
Input coordinate file.
KEYWORDED INPUT
Selection of source atom set.
Selection of target atom set.
Minimal contact distance (in A), default 0.0
Maximal contact distance (in A), default 4.0
Minimal "sequence distance", or difference in indices
(_not_ in sequence numbers) of residues between those
containing the contacting atoms. The default value is
1, which means that contacting atoms may be found in
the neighbouring and farer residues, but not in the
same residue).
('off' and 'inc' default).
This parameter specifies
the subject and order for sorting the contacts on
output. For example, 'sort source dec' means sorting
by decreasing index of the source atoms (index is
essentially the atom's serial number in a correct PDB
file). Subject 'off' (default) means no sorting.
('off' default).
If cells is set to 'off', the program
seeks contacts only between the atoms found in the
coordinate file. Other values induce construction of
unit cell(s) and looking for contacts also between source
atoms and target atoms generated in the cell(s).
- 0
- generates only one (primary) unit cell, in which
the source and target atoms are originally found
- 1
- generates the primary cell +/- 1 cell in all
directions (27 cells in total)
- 2
- generates the primary cell +/- 2 cells in all
directions (125 cells in total)
Input of the space group symmetry name, e.g. 'P 21 21 21'
(without quotation marks, spaces _are_ significant).
This parameter is mandatory if coordinate file does not
specify the space group symmetry.
Input of the unit cell dimensions (space-separated
real numbers). This parameter is mandatory if coordinate
file does not specify the cell parameters.
See the description in the pdbcur
documentation.
PROGRAM OUTPUT
The program currently gives a short summary of the commands received, and
a list of the contacts found.
EXAMPLES
Runnable example
ncont.exam
SEE ALSO
pdbcur - MMDB application for manipulating PDB files.
act - traditional contact program.
contact - traditional contact program.
AUTHORS
Eugene Krissinel, European Bioinformatics Institute, Cambridge, UK.