contacts reads coordinate files and writes files of intra-chain residue-residue contact data.

Here is a sample session with contacts:

% contacts Reads coordinate files and writes contact files Location of coordinate files for input (embl-like format) [./]: Extension of coordinate files (embl-like format) [.pxyz]: Location of contact files for output [./]: Extension of contact files [.con]: Threshold contact distance [1.0]: Name of data file with van der Waals radii [Evdw.dat]: Name of log file for the build [contacts.log]:

Mandatory qualifiers:

[-cpdb] (string)

Location of coordinate files (EMBL format input).

[-cpdbextn] (string)

Extension of coordinate files.

-vdwf (string)

Name of data file with Van der Waals radii.

-thresh (float)

Threshold contact distance.

[-con] (string)

Location of contact files for output.

[-conextn] (string)

Extension of contact files.

-conerrf (outfile)

Name of log file for the build.

Advanced qualifiers:

-ignore (float)

If any two atoms from two different residues are at least this distance apart, no further interatomic contacts are checked for that residue pair. This option speeds the calculation up considerably.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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