Dear Andy, Yes, there is a much easier way: use the Rotamers tool (under Tools... Structure Editing). You can specify residue type and rotamer library, and that will give you a "bouquet" of rotamers at that position. You can calculate H-bonds and clashes for the rotamers (or even how well they fit into a density map!) to help you choose the best one, and then have it replace the original sidechain. This tool could be used to generate different rotamers for the same amino acid type or to mutate to a different amino acid type. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...
The "Structure Analysis and Comparison" tutorial includes use of Rotamers: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> There is also a command-line implementation, "swapaa": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 30, 2009, at 2:57 PM, Andrew P. Hinck wrote:
Dear all,
I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions.
Andy Hinck