On Aug 1, 2008, at 7:35 AM, Srinath Thiruneelakantan wrote:

Hi, I am microbiologist and wanted to know the strucutre of a protein of M. tuberculosis, whose crystal structure has not been solved, but its homologue in Bacillus has been. So by Swiss-modeller generated a MODEL and downloaded it in PDB format. Now I wanted to superimpose the generated model with of bacillus and with PDB of truncated protein of E. coli. As I am not of bioinformatic bakground, please suggest me how to get the FINAL output in PDB format so can have a comarison of domains between these three proteins. Thank you, Srinath

Hi Srinath, Just open all of the PDB files in Chimera (for example, with File... Open). You can change the display if you want, for example with Presets... Interactive 1 (ribbons). Then you can use the MatchMaker tool (under Tools... Structure Comparison) to superimpose the proteins. Choose the "reference" structure on the left and one or more structures to match onto it on the right. It usually does not matter which one you use as the "reference" - try using the first one listed. In most cases, the default settings work well, so it is very easy: turn off "Show alignment(s)..." if you don't want to see the sequence alignments, but otherwise just click "Apply" to match the structures. It will take a few seconds to compute the alignments and then match the structures. Then you can compare the structures in Chimera, or write out PDB as mentioned below. If that does not give a good enough superposition, then you can try changing parameters. For details see the MatchMaker manual page (simply clicking "Help" on the dialog will open your local copy): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html These tutorials have examples of superimposing and comparing structures: "Superpositions and Alignments" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html "Structure Analysis and Comparison" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html Additional discussions about superimposing structures: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html#superimposing http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ images.html#matching After the proteins are superimposed, you can write out the structures as one or more PDB files with "File... Save PDB" in the Chimera menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb 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