[Chimera-users] matching peptides with altenate locations

Sumitro Harjanto u0601918 at nus.edu.sg
Wed Dec 16 11:07:02 PST 2009


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 16 December 2009 3:23 AM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] matching peptides with altenate locations

Hi Sumitro,
OK, I have 1akj as model 0 and 2gtz as model 1.  The second command  
you gave will work if you remove the spaces before and after "|":

match #0:1-5.c at ca #1:1-3.c at ca|#1:4-5.c at ca.a

The space is used to separate the two sets of atoms.  The first  
command you gave wouldn't work because only some of the residues in #1  
have alternate locations.

If you want to use all nine residues, here is one possibility:

match #0:1-9.c at ca #1:1-9.c at ca&~@.b

meaning ...and not alternate location B.  If there were more alternate  
locations (C,D,...) you would also need to exclude those.  I hope this  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 14, 2009, at 11:23 AM, Sumitro Harjanto wrote:

> Hi,
> I would like to match two peptides; one with alternate conformations  
> in residue 4 and 5. I have tried:
> match   #0:1-9.c at ca   #1:1-9.c at ca.a
> match   #0:1-5.c at ca   #1:1-3.c at ca   |   #1:4-5.c at ca.a
> but both don't work and give me the "unequal number of atom chosen"  
> error message.
> I tried changing match to sel in the latter case and I can get 10  
> atoms; 5 from each model, which is what I intended.
> How should I deal with this?
> Thanks,
> Sumitro

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