Hi Josh, I guess you mean actually changing the 3D structure. Yes, you can “swap” amino acids by replacing side chains with the Rotamers tool (menu: Tools.. Structure Editing… Rotamers) or the “swapaa” command. This only does a simple replacement; it does not predict any large/overall changes in the structure. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> There is an example of using Rotamers in the Structure Analysis and Comparison tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 25, 2019, at 2:00 PM, Joshua Plank <jplan002@ucr.edu> wrote:
Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh