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@.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@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@uab.es
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