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

source {selection of atoms}

Selection of source atom set.

target {selection of atoms}

Selection of target atom set.

mindist <mind>

Minimal contact distance (in A), default 0.0

maxdist <maxd>

Maximal contact distance (in A), default 4.0

seqdist <seqd>

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 same residue).

sort [off|source|target|distance] [inc|dec]

('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.

cells [off | 0 | 1 | 2 | symm | inter]

('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)
symm: 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
inter: 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 source atom.

symmetry <spgname>

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.

geometry <a> <b> <c> <alpha> <beta> <gamma>

Input of the unit cell dimensions (space-separated real numbers). This parameter is mandatory if coordinate file does not specify the cell parameters.

ATOM SELECTION SYNTAX

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.