Dear Minming, Dr. Ferrin forwarded your question to me. We recently added calculation of structure similarity measures to Chimera. This capability is not in versions 1.4/1.4.1, but only in 1.5 (recent daily builds, which are also available from our download page). In such recent builds, the "Match -> Align" tool (under Tools... Structure Comparison in the menu) calculates two measures that have been described in previous publications, the SDM and the Q- score. The SDM has been used to construct phylogenetic trees before. I don't know if the Q-score has been used that way. Documentation for Match->Align and details of these measures: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchali...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchali...
However, there are some issues that may affect whether you decide to use Chimera to calculate these values for your structures: (1) You would need to run Match->Align for each pair. There is no option to do all pairwise comparisons on multiple structures. You would need to script looping through all pairs (with python or shell scripting). (2) There is no Chimera command for Match->Align. Thus Match->Align would also need to be run via python. I don't have scripting expertise, so someone else would have to provide more details if you decide to try this. (3) Before you run Match->Align, the structures need to be superimposed. We purposefully made Match->Align independent of the superposition method. There are several possible ways to superimpose structures in Chimera, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> but probably the easiest in your case would be MatchMaker, which is also available as a Chimera command (matchmaker or mmaker, see that URL and links within). Usually the mmaker defaults work pretty well, for example Chimera commands: open 2mnr open 4enl mmaker #0 #1 (Then you could try running Match->Align interactively. The SDM, Q- score, etc. are reported in the Reply Log, opened with Favorites... Reply Log in the menu.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending Chimera questions to chimera-users@cgl.ucsf.edu (I CC'd that list here after removing the details from your original mail)
-------- Original Message -------- Subject: A question about your software(UCSF Chimera) Date: Tue, 23 Mar 2010 21:55:06 -0400
Dear Dr. Ferrin,
I am very interested in using your software UCSF Chimera, which have some commands that can do the job of aligning and measuring a distance between two protein structures.
I am a PhD student at Purdue University working on the evolution of protein structure with Professor Peter Waddell. I was hoping to use your structure alignment software to obtain a pairwise structure distance matrix. This matrix will then be used in phylogenetic analyses, comparing the trees and “treeness” of that structural distance compared to that produced by other published methods. [...] Could you please tell me if your structural alignment software can easily produce a complete pairwise distance matrix for a list of ~50 structures? I did not see a way to do this. If not, is there any easy way to modify it to do this? [...]
Best Regards and Sincerely, Minming Li