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