interface

 

Function

Reads coordinate files and writes files of inter-chain residue-residue contact data

Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

Usage

Here is a sample session with interface:

% interface

Command line arguments

   Mandatory qualifiers:
  [-in]                infile     Name of protein coordinate file for input
                                  (embl format)
   -vdwf               string     Name of data file with van der Waals radii
   -thresh             float      Threshold contact distance
  [-out]               outfile    Name of contact file for output
   -conerrf            outfile    Name of log file for the build

   Optional qualifiers:
   -ignore             float      If any two atoms from two different residues
                                  are at least this distance apart then no
                                  futher inter-atomic contacts will be checked
                                  for for that residue pair . This speeds the
                                  calculation up considerably.

   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-in]
(Parameter 1)
Name of protein coordinate file for input (embl format) Input file Required
-vdwf Name of data file with van der Waals radii Any string is accepted Evdw.dat
-thresh Threshold contact distance Any numeric value 1.0
[-out]
(Parameter 2)
Name of contact file for output Output file test.con
-conerrf Name of log file for the build Output file interface.log
Optional qualifiers Allowed values Default
-ignore If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. Any numeric value 20.0
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

Data files

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
contactsReads coordinate files and writes files of intra-chain residue-residue contact data
dichetParse dictionary of heterogen groups
hmmgenGenerates a hidden Markov model for each alignment in a directory
profgenGenerates various profiles for each alignment in a directory
psiblastsRuns PSI-BLAST given scopalign alignments
scopalignGenerate alignments for families in a scop classification file by using STAMP
scoprepReorder scop classificaiton file so that the representative structure of each family is given first
scopresoRemoves low resolution domains from a scop classification file
seqalignGenerate extended alignments for families in a scop families file by using CLUSTALW with seed alignments
seqsearchGenerate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments
seqsortReads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file
seqwordsGenerate file of hits for scop families by searching swissprot with keywords
siggenGenerates a sparse protein signature from an alignment and residue contact data
sigscanScans a signature against swissprot and writes a signature hits files

Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (date) - author.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments