[Chimera-users] selecting a unique ligand structure from multiple copy

[Elaine Meng]

Hi JD,
It is a little hard to answer without looking at one of the same  
structures you are working with, but typically if there are multiple  
copies of a ligand, they differ in one or more of the following:

- residue number
- chain ID
- alternate location ID

If you label the residues of interest with the "rlabel" command, it  
will show their names, numbers, and chains. If residue number is  
sufficient to identify the specific copy, you can just use :N where N  
is the number.  I know 4hhb is an example where the number is the same  
but the chain IDs are different - the four hemes are residues 1.a 1.b  
1.c 1.d and each is named HEM.  Those could be specified individually  
with :1.a or :hem.a (for example).

If the atoms are instead all in the same residue but exist as sets of  
alternate locations, you can specify them individually with something  
like :hem.b at .a
(alternate location A atoms in HEM in chain B).  You can look at the  
text of the PDB file to see if there is something in the alternate  
location column (format is described here:  
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
pdbintro.html#coords )
... or, if the structure is open in Chimera, the way I usually tell if  
there are alternate locations anywhere in the structure is to use a  
command something like

sel @.a

If you're still having trouble, let me know of a specific example and I  
will try to answer more specifically!
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


On May 3, 2007, at 1:18 AM, Jean-Didier Marechal wrote:

> Hi everyone,
>
> I am working with different protein structures that have at least two
> copies of the ligand in their binding site. How could I select only one
> of them? (I'd like a selection specification that does not require the
> atom numbers if possible).
>
> Cheers
> JD
>
>
> -- 
> Dr. Jean-Didier Maréchal
> Professor Assistant
> Physical-Chemistry Unit
> Department of Chemistry
> University Autonomous of Barcelona
> 08193 Bellaterra, Spain
> Tel: (+34).93.581.49.36
> Fax: (+34).93.581.29.20
> e-mail: jeandidier.marechal at uab.es
>
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