Hi Francesco, Tim is totally right -- I just wanted to add that besides the "swapaa" command, there is also a graphical interface, the "Rotamers" tool, if you want to pick the sidechain conformation interactively. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...> 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 Sep 19, 2010, at 1:04 PM, Tim Travers wrote:
Hello Francesco,
If you want to mutate a residue, you can try the swapaa command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html
For instance: swapaa val #0:12.a lib Dunbrack preserve true
where val is the target mutation, #0 gives the model number of the peptide in Chimera, 12.a says to make the mutation on residue position 12 of chain a, lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries to keep the rotamer of the mutation close to the original one.
Hope this helps, Tim
On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret@gmail.com> wrote: Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions.