Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know. Thanks everyone, Helen Josephine
Hi Helen, Take a look at the Rotamers tool (under Tools... Structure Editing) - I think it does exactly what you want. Besides displaying the rotamers of your chosen residue type and their library probability values, it can evaluate clashes, H-bonds, etc. and allows you to incorporate a chosen rotamer back into the structure. Here is the man page for the Rotamers graphical interface: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/ framerot.html There is also a command implementation, swapaa: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html 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 Nov 15, 2007, at 10:35 AM, hjoseph@brandeis.edu wrote:
Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know.
Thanks everyone, Helen Josephine
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I should mention that the Rotamers functionality is relatively new (not in the June production release). You could wait a couple of days and then get the production release we are preparing now, or get the latest daily build (Nov 14) from http://www.cgl.ucsf.edu/chimera/alpha-downloads.html or get the current (Oct 31) release candidate http://www.cgl.ucsf.edu/chimera/download.html I think a few things have been fixed between Oct 31 and Nov 14, but I don't recall anything specifically affecting Rotamers. Regardless of what you do right now, I'd recommend getting the new production release after it appears later this week. 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 Nov 15, 2007, at 10:35 AM, hjoseph@brandeis.edu wrote:
Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know.
Thanks everyone, Helen Josephine
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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