[Chimera-users] building a backbone model from deposited Calpha coordinates

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 6 13:52:30 PDT 2009

Hi Mark,
If a smooth tube is sufficient (like what is used for turns in the  
standard ribbon), I am happy to report that it can be shown for CA- 
only and P-only structures in the very newest daily builds, with no  
extra steps!

If you wanted the flat amide-plane-oriented ribbon for helix and  
strand, however, it would be necessary to build in the remaining  
backbone atoms.  Currently this cannot be done in Chimera.  There are  
probably several programs that can do it, but here is one Web server I  
have found useful in the past:


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2009, at 12:40 PM, Mark Girvin wrote:

> I'm sure that this has been asked before, but with limited web
> bandwidth while traveling, and not finding it in the downloaded help,
> will ask again anyway (pls feel free to ignore) -- what would you
> suggest as the best way to coax a ribbon diagram out of deposited
> Calpha coordinates?
> Thanks either way,   - Mark
> (further apologies if this turns into a double posting - seemed to  
> bounce
> the first try).
> -- 
> Mark Girvin
> Biochemistry Department
> Albert Einstein College of Medicine
> 1300 Morris Park Ave.
> Bronx, NY  10461
> http://www.bioc.aecom.yu.edu/labs/girvlab

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