On Jun 14, 2007, at 10:15 PM, Shunsuke Meshitsuka wrote:
I have used chimera as a viewer of proteins. I have a question how to overlay the 20 structures of NMR pdb data by chimera. When there are 20 structures of structurename01.pdb, structurename02.pdb,,,structurename20.pdb, chimera structurename**.pdb makes a random location and random orientation of each protein. Please let me know the method.
Hi Shunsuke, First I should mention there are two ways to read in the data: (1) with all the different structures in one PDB file separated by MODEL and ENDMDL records, like the NMR structures in the PDB. If opened as model 0 in Chimera, the structures can be specified as #0.1, #0.2, #0.3 ... (2) with each structure a separate PDB file, as you described. The structures can be specified as #0, #1, #2 ... Then, there are many possible ways to match the structures in Chimera: (A) use the "match" command and tell it which atoms to fit http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html ...also covered in "Images" tutorial (go to the Matching Structures part) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html (B) use MatchMaker (under Tools... Structure Comparison), which makes a sequence alignment and then fits the CA atom pairs of the aligned residues http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html ...also covered in "Alignments" tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html (C) use the "matchmaker" command, which works the same way as MatchMaker http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html (D) use EnsembleMatch (under Tools... Structure Comparison) - only works when the structures are together in one PDB file http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblematch/ ensemblematch.html ...also covered near the end of the "Ensembles and Model Panel" tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html See also these recent messages to chimera-users: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001566.html http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001609.html That should get you started! Best, 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