From owner-chemistry@ccl.net Mon Mar 20 17:21:01 2006
From: "Warren DeLano warren**delsci.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: How to select residues
Message-Id: <-31247-060320171204-22283-snU6ELEK669uhUAxnSVTrg(-)server.ccl.net>
X-Original-From: "Warren DeLano" <warren%%delsci.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Mon, 20 Mar 2006 14:15:05 -0800
MIME-Version: 1.0


Sent to CCL by: "Warren DeLano" [warren/a\delsci.com]
Nicholas,

> If I am wrong, please correct me. If not, do you know any 
> free software allowing such residue selection and saving ?

PyMOL has a rich atom selection language for such tasks:

load protA.pdb
select my_sele, byres (protA within 10 of resi 54) 
save subset.pdb, my_sele

etc.

http://delsci.com/rel/099

As "free", PyMOL is entirely free if you compile it from the open-source
code, and our convenient precompiled binaries are free to evaluate, free
for full-time students, and free when used on prexisting public data.  

Payment for other uses is via the honor system.  

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:warren#delsci.com      
 

> -----Original Message-----
> From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] 
> Sent: Monday, March 20, 2006 1:45 PM
> To: Warren DeLano
> Subject: CCL: How to select residues
> 
> 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 ?
> 
> Best regards,
> 
> Nicolas
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =- To recover the email address of the author of the 
> message, please change the strange characters on the top line 
> to the # sign. You can also look up the X-Original-From: line 
> in the mail header.> Conferences: 
> http://server.ccl.net/chemistry/announcements/conferences/
> 
> Search Messages: http://www.ccl.net/htdig  (login: ccl, 
> Password: search)> 
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
> 
> 
> 
> 
> 
> 
> 
>