[Chimera-users] Straighten a helix

[Elaine Meng]

Hi Francesco,
Yes, you can use Adjust Torsions to rotate several different bonds  
along the backbone.  It might be a lot of work, and it would not  
prevent you from creating structures with bad contacts, but you could  
certainly try it if MD alone is not successful in generating the  
desired conformations.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust 
 >
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Apr 19, 2009, at 9:56 AM, Francesco Pietra wrote:

> I would like to straighten a helix in a complex composition of
> helices, i.e., at  least some of them may vdw interact with each other
> if moved. Therefore, I plan to let molecular dynamics (MD) changing
> dihedral angles at the pivot amino acid. I wonder whether chimera
> might aid through "adjust torsion" or other tool. If not else to
> provide alternative conformations for input to MD and see if the
> adjustments converge. Bending of the helix occurs along 5 amino acids,
> the central one probably the pivot.
> Thanks
> francesco pietra
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