Thanks! -----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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Hi Sumitro, The problem is that there is no intrinsic ordering of atoms after an intersection operation. Do you keep the order that was on the left side of the intersection or the order that was on the right side? Since the orders can differ, Chimera simply carries out the intersection operation in the fastest way possible with no regard to atom ordering. Nonetheless, it seems natural to try to preserve the ordering on the left side of the intersection. I will open a request in our Trac database for this feature, with you on the recipient list so you'll know when it gets implemented. In the interim, the only option you have is to be more explicit in the atom specifier. This command gets the match you want: match #0:1-6.c@ca:7.c@ca.a:8-9.c@ca #1:1.c@ca:2.c@ca.a:3.c@ca:4.c@ca.a: 5-9.c@ca With the two structures you mentioned, the RMSD from the above is 0.087 angstroms. --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 31, 2009, at 2:12 AM, Sumitro Harjanto wrote:

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

No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.427 / Virus Database: 270.14.108/2565 - Release Date: 12/14/09 19:40:00 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users