Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir
Dear Ahir, We're glad you like Chimera! Your question is reasonable but there isn't a simple answer. First I'll explain how the superimposed structures are interpreted by Chimera, and then talk about the sequence alignment part. How the structures are handled in Chimera depends on the format of the PDB file created by the superposition server: (a) Some servers separate the structures with MODEL and ENDMDL lines, and this makes each one a separate model with separate listing in the Chimera Model Panel. This is more convenient than the other possibilities. (b) Some servers put the structures into one model but give them separate chain IDs, for example making one structure chain A and the other chain B. You can still separately control them in Chimera, but not as easily as separate models. (c) Some servers create incorrect PDB that have duplicate atom and residue numbers without using MODEL/ENDMDL or different chain IDs. These will display in Chimera, but it is very difficult to do anything else because you cannot uniquely specify the atoms or residues. I list several superposition servers and discuss their outputs in this page: <http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html> If the server does not output a sequence alignment, it is not possible to back-calculate from the superposition that exact sequence alignment. Why? Because different sequence alignments (with different numbers of paired residues) can give essentially the same superposition, and we do not know the details of the fitting procedure used by the server: whether alpha-carbons or all backbone atoms were fitted, iteration cutoffs that could weight certain positions in the alignment more heavily than others, etc. That said, however, you can use the "Match->Align" tool in Chimera (under Tools... Structure Comparison) to create a sequence alignment consistent with your structural superposition. It uses CA-CA distances and a user-specified cutoff for how far apart the residues can be in space, yet end up in the same column of the output sequence alignment. <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchalign/...
If the server does give a sequence alignment but not in a standard format, you could manually edit it (not pleasant, but often required in bioinformatics!). Previously the Mammoth server allowed downloading the sequence alignment in a convenient format, but I see it has moved to a different URL and behaves differently now. You could try contacting the authors and see if they are willing to include the sequence alignment in the outputs. Finally, you may want to try Chimera's superposition tool: "MatchMaker" (under Tools... Structure Comparison) or command "matchmaker": <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/...
These Chimera tools are also used in the "Superpositions and Alignments" tutorial: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/alignments...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 4, 2009, at 2:55 AM, Ahir Utsav Pushpanath wrote:
Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it.
1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition.
2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there)
3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this?
Apologies if this is a very straightforward scenario.
Thanks Ahir _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Ahir Utsav Pushpanath -
Elaine Meng