NCONT (CCP4: Supported Program)
- analyses contacts between subsets of atoms in a PDB file.
[Key-worded input file]
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
Input coordinate file.
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 further residues, but not in the
('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.
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).
Input of the space group symmetry name, e.g. 'P 21', 'P 1 21 1'
or 'P21'. The program should accept a variety of naming
conventions, but it does not currently accept spacegroup number.
This parameter is mandatory if coordinate file does not
specify the space group symmetry on the CRYST1 card.
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
- generates only one (primary) unit cell, in which
the source and target atoms are originally found
- generates the primary cell +/- 1 cell in all
directions (27 cells in total)
- generates the primary cell +/- 2 cells in all
directions (125 cells in total)
- same as 2 except that only symmetry-generated
target atoms are included, i.e. contacts to the target
atoms in the input file are excluded
- same as 2 except intra-chain contacts are
excluded from the contact listing, though they remain in
the overall statistics. Here "intra-chain" means target
atoms for which no symmetry operation or unit cell translation
has been applied, and which have the same chain ID as the
The program currently gives a short summary of the commands received, and
a list of the contacts found.
pdbcur - MMDB application for manipulating PDB files.
act - traditional contact program.
contact - traditional contact program.
Eugene Krissinel, European Bioinformatics Institute, Cambridge, UK.