Subject: Inter-residue contact matrix

From: Francois Sampieri <sampieri.f..at..jean-roche.univ-mrs.fr>
Date: Fri, 13 Jun 2003 10:46:39 +0200

Hi all,

Is there any free program (executable for SGI Irix 6.5, or Mac OS X) that
could make a graphical representation of matrix of protein inter-residue
contacts?

Thank you and best regards!

Frangois Sampieri

____________________________________________
UMR 6560 CNRS-Universite de la  Mediterranee
Laboratoire de Biochimie - IFR Jean Roche
Faculte de Medecine Nord, Bd Pierre Dramard
13916 Marseille Cedex 20
E-mail: sampieri.f..at..jean-roche.univ-mrs.fr
Tel: (33) 4 91 69 88 44
Fax: (33) 4 91 65 75 95

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From: Marc Baaden <baaden[at]smplinux.de>
Date: Fri, 13 Jun 2003 12:42:40 +0200

sampieri.f[at]jean-roche.univ-mrs.fr said:
>> Is there any free program (executable for SGI Irix 6.5, or Mac OS X)
>> that could make a graphical representation of matrix of protein
>> inter-residue contacts? 

There are such tools in the gromacs package (www.gromacs.org),
which is free and can be compiled on linux, SGI, MacosX and windows.
I think there are even binaries for some of these platforms.

The precise tool you are looking for is g_mdmat, I believe. Here
goes its description: 

g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames these distance matrices can be stored as a function of time, to be able to see differences in tertiary structure as a funcion of time. If you choose your options unwise, this may generate a large output file. Default only an averaged matrix over the whole trajectory is output. Also a count of the number of different atomic contacts between residues over the whole trajectory can be made. The output can be processed with xpm2ps to make a PostScript (tm) plot. 

Best wishes,
  Marc Baaden

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden[at]smplinux.de      -      http://www.marc-baaden.de
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