[ccp4bb]: list of residues buried in an interface

["Fred. Vellieux" <vellieux@ibs.fr>]

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Dear subscribers (to the bb),

Thanks to all who replied.

The operation I wish to perform is not entirely "automagic" yet.

I tried first what would give me the least amount of work
(i.e. the protein-protein interaction server
http://www.biochem.ucl.ac.uk/bsm/PP/server/).

I was unsuccessful there (output table giving figures of 0, nan's etc)
even though I was using Netscape from several Unix stations (several
attempts).

Then on to dimplot: I think I am exceeding some atom limit probably,
since I get an error message from hbplus.

The next I tried (successfully) was contact. I know already that the
interface, in my case, is across a crystallographic 2-fold so that
I entered the following commands:

contact XYZIN monomer.pdb > contact.out << EOI
? MODE AUTO
? SYMM -X,-Y,Z
? EOI

Then I edit the output file (contact.out) using my favourite text
editor, in order to remove the "header" and "tail" which contain
some "useless" information (i.e. useless for the purpose of preparing
a table...).

Then a simple grep operation to remove all lines not containing the
required symmetry operator (this is in case there are many many lines
in the output file, otherwise any editor will do):

grep -e -X contact.out > contact.table

Note that "grep -e" is required here because I am only keeping lines
with the -X,  -Y,  Z operator; to specify "-X" is sufficient in that
case but "-X" would be misinterpreted as a grep option were it not
for the "-e" that precedes it. Hope that's clear. The resulting table
agrees very well with the high tech alternative (pencil and paper in
front of the graphics station).

Anyway, thanks to Stephen Graham <stepheng@mail.usyd.edu.au> for having
suggested to use "contact MODE AUTO". Also to Miroslav Papiz who just
suggested CONTACT.

Fred.

-- 
s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
        Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
        41 rue Jules Horowitz
        38027 Grenoble Cedex 01
        France
Tel:    (+33) (0) 438789605
Fax:    (+33) (0) 438785494
e-mail: vellieux@ibs.fr
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 Don't even think of asking me: "I would              Het leven is genieten
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