Hi elaine, I was experimenting with the "match" command and I found that when alternate locations are involved, sometimes the best alignment is not achieved. For example I had 3FQW as #0 and 3FQX as #1; I was comparing the Chain C (9-mer peptide) of the two models. #0 had alternate location in the 7th residue while #1 had the alternate locations in the 2nd and 4th residue. They were essentially identical in sequence except for the 4th residue. When I matched the 6 residues, which did not have any alternate locations, by the command: match #0:1.c,3.c,5.c,6.c,8.c,9.c@ca #1:1.c,3.c,5.c,6.c,8.c,9.c@ca the RMSD returned is 0.080, which was reasonable judging from the high conservation of the sequences. but when I matched all the residues, and designate the .b alternate location to be excluded by the command: match #0:.c@ca&~@.b #1:.c@ca&~@.b The RMSD returned was 8.730, which was unreasonably high. It was also clear by visual inspection that the alignment was way off the best. I would expect that the RMSD returned by the first and second command to be roughly equal; because the alternate locations of the residues do not alter the C-alpha position by much, it was the side-chain positions that were more extensively varied. Please advise. Thanks! =] Cheers, Sumitro -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: 16 December 2009 3:23 AM To: Sumitro Harjanto Cc: chimera-users@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@ca #1:1-3.c@ca|#1:4-5.c@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@ca #1:1-9.c@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 helps, 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 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@ca #1:1-9.c@ca.a
match #0:1-5.c@ca #1:1-3.c@ca | #1:4-5.c@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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