[Chimera-users] Generating random helix

[Elaine Meng]

Hi Sudheer,
Not exactly - but you can build a helix and then fit it in a map.

See "Build Structure" (under Tools... Structure Editing), Add Atoms  
section, "peptide sequence":
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#addatom 
 >

and "Fit in Map" (under Tools... Volume Data):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html 
 >

You have to manually position the helix first, as the fitting will  
just find a nearby local optimum.

I believe some related tools (helixhunter etc.) distributed with EMAN  
are also integrated somehow with Chimera, although I have not used  
these myself:
<http://ncmi.bcm.tmc.edu/~stevel/EMAN/>
<http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/programs.html>

I hope this helps,
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 Sep 24, 2008, at 11:24 AM, <skmolugu at miners.utep.edu> wrote:
>
> Dear Chimera team,
> Is there any option in chimera that builds helix in a map at a  
> position that is assumed  to be a helix.
> thanks,
> sudheer