From owner-chemistry.,at,.ccl.net Tue Mar 21 11:11:00 2006
From: "Florian Haberl Florian.Haberl[#]chemie.uni-erlangen.de" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: How to select residues
Message-Id: <-31261-060321100741-539-BSd8U1Mt5/y4jspX7c3bew:-:server.ccl.net>
X-Original-From: Florian Haberl <Florian.Haberl*chemie.uni-erlangen.de>
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Date: Tue, 21 Mar 2006 15:13:46 +0100
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Sent to CCL by: Florian Haberl [Florian.Haberl[A]chemie.uni-erlangen.de]
hi,

On Monday 20 March 2006 22:19, Nicolas Ferre nicolas.ferre*univ-provence.fr 
wrote:
> Sent to CCL by: "Nicolas  Ferre" [nicolas.ferre]^[univ-provence.fr]
> Dear CCL'ers,
>
> I'd like to select and save a small part of a pdb file. Actually I want to
> select all the residues inside a given sphere centered on an amino-acid. I
> know I can use RasMol's "select within (expression)" but it results in
> selecting some atoms, not whole amino-acids. Obviously I can look at the
> selection using "show selected" and copy/paste every amino-acid label, but
> this is a rather tedious task. Alternatively I can use Molden, but as far
> as I known, it only shows the corresponding amino-acids without giving the
> possibility to save them in a file. If I am wrong, please correct me. If
> not, do you know any free software allowing such residue selection and
> saving ?

Also swisspdb viewer ( http://www.expasy.org/spdbv/text/download.htm )   can 
do this:

Select - neighbors of selected aa:
Within distance

If you want to do this with multiple files (for example: You want all aa 
around a ligand),  you can use something like perlmol 
(to be found on: http://www.perlmol.org/ )

and than the module: midas pattern

There`s also a solution for python i think its`s called mdtools 
(http://www.ks.uiuc.edu/Development/MDTools/ )
and some other molecular toolkits around.


Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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