[Chimera-users] modify structure

Elaine Meng meng at cgl.ucsf.edu
Sun Sep 26 09:10:37 PDT 2010

Hi Francesco,
Rotamer data comes from statistical analyses of structures in the  
PDB.  Compared to standard amino acids, there is much less data for  
nonstandard amino acids, and I don't know of any program that provides  
or uses such data ("rotamer" information for nonstandard amino acids).

As far as I know you would just have to build them manually, using  
Chimera or any of several other programs, and then do further  
molecular mechanics/dynamics calculations.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 26, 2010, at 8:46 AM, Francesco Pietra wrote:

> 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.
> thanks
> francesco
> 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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