Hi Bala, (1) With EnsembleMatch you can superimpose multiple structures. Maybe what is confusing is that when you start EnsembleMatch it asks for one Reference PDB file and one Alternative PDB file. Each of those PDB files, however, can contain multiple different conformations, separated by MODEL/ENDMDL records (for examples, see any NMR ensemble in the PDB, such as 1vm3). In your case, to use EnsembleMatch you could put all of your conformations in one file separated by MODEL/ ENMDL records, and then use that file as both the reference and the alternative. Then you will have all pairwise comparisons for conformations in the file. You can see how this works by opening 1vm3 (for example) and then specifying it as both the reference and the alternative. If you don't want to put your conformations together in one file, however, there are other ways to superimpose them and calculate RMSDs (more information below). (2) With EnsembleMatch you can specify the substructure or which atoms you want to use for the calculation in the "Parts to Match" area. For example, if you wanted to use only alpha-carbons of chain A residues 8-95, you would enter this: :8-95.A@CA EnsembleMatch manual page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html There is also an example at the end of this tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html Here are some other ways to superimpose and calculate RMSD. All of the ways (including EnsembleMatch) are pairwise and give only pairwise RMSD values, but you can superimpose multiple structures by combining pairwise superpositions (match B->A, C->A to superimpose A,B,C). There is currently no method to calculate a multiple (>2) structure RMSD. If you have the conformations as separate PDB files, you could use - the "match" command, and give the specific atoms (substructure) you want to match http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html - the MatchMaker tool, which figures out for you which residues should be paired and then matches their alpha-carbons (assuming you have proteins) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html - the "matchmaker" command, which works the same way as the MatchMaker GUI http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html There are some examples of using "match" and "matchmaker" in the Images tutorial. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ images.html#matching With MatchMaker/matchmaker, there is an option to show the sequence alignment in a separate window. If you show that alignment, you can then highlight part of that alignment, choose Structure... Match from the alignment window, and choose "match active region only" to specify using only the CA atoms in the highlighted area(s). Yet another possibility: If you have too many conformations for EnsembleMatch (>~20) you could open them as a trajectory in MD Movie and then do an RMSD analysis. This doesn't superimpose the conformations, however, just calculates all pairwise RMSDs using the atoms of your choice. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#rmsd 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 Jun 6, 2007, at 5:25 AM, bala wrote:
1) Basically i hav three conformations (only 3 pdb) of the same molecule picked up from three different regions of a simulated trajectory. I hv to calculte rmsd and superimpose structure. I tried the emsemble match but it seems that it can work on only two conformation. Kindly suggest me how i can overcome this.
2) Is it possible to create a substructure (subset) of a molecule and do rmsd calcutn and superimposing only on the substructures for the conformations i have.