[Chimera-users] modify structure

Francesco Pietra chiendarret at gmail.com
Sun Sep 26 08:46:19 PDT 2010

Thanks to Tim and Elaine. Tried successfully. However, I went to the
Dunbrack web site noticing that in Dunbracks algorithm

"Residues with names that do not match the standard 20 amino acid
names are also treated as glycines"

That is too bad for me as my peptide family is characterized by having
a modified amino acid. Do you know of a software that accomplices the
job with non-standard amino acids in the peptide? I used a molecular
mechanics general program that may not the best solution and which
does not read the (standard) pdb format of Chimera. It has its own pdb
format which is read by VMD, not by Chimera. I also have a simulated
annealing software that, however, is for vacuum.



On Mon, Sep 20, 2010 at 5:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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.html>
> 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 at 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.

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