Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)
Hi Elisabeth, The useRotamers() documentation says it adds each rotamer using atom alternate location specifiers A,B,C,D,E,.... To show the second Rotamer (altloc B) the Chimera command would be show @.B From Python you can run a Chimera command using from chimera import runCommand runCommand('show @.B') Another idea is to only call useRotamer() with a list containing the one rotamer you want to show, instead of all rotamers. Tom
Hi all,
I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it?
Thanks in advance.
Elisabeth Universitat Autònoma de Barcelona (Spain)
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Hi Elisabeth, If you just want to replace the current sidechain with one rotamer, you could do it with the command "swapaa." To use criterion (a) least clashes, and if a tie (b) most H-bonds, then you would indicate that with the "criteria" option. Example: swapaa ile #0:33.a criteria ch Description of "swapaa" and its options: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> 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 On Feb 11, 2011, at 7:56 AM, Elisabeth Ortega wrote:
Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h- bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth
participants (3)
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Elaine Meng -
Elisabeth Ortega -
Tom Goddard