[Chimera-users] Chimera - Question

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 13 12:02:54 PDT 2007

Hi Peter,
Chimera does not do any threading (evaluating sequence compatibility  
with a 3D structure) or comparative modeling with energy evaluation.   
I am not sure what you mean by consensus structure, but there is  
nothing in Chimera currently that creates a new structure based on a  
set of input structures.

In the future, we would like Chimera to interface with the separate  
program MODELLER for comparative modeling, but this has not been  

You can certainly align multiple input structures and get a  
corresponding sequence alignment, and you can add your sequence that  
doesn't have a structure to the sequence alignment and see where  
parts of it map onto the structures.  If you want more details on any  
of these, let me know.

I hope this helps,
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 Mar 13, 2007, at 11:45 AM, Peter Murphy wrote:

> Hi,
>     I have a quick question about your program. Normally (on a day  
> to day basis) I use fairly basic features of chimera (coloring,  
> etc) to produce pictures of crystal structure images (for  
> presentations, papers, etc). Rarely do I have to use the more  
> advanced features of chimera (Solvent accessible surface area,  
> distance calculations, etc) so I don`t have a good idea of the  
> limits of your program. Thus, I figured I would check to see if  
> what I wanted to do is out of the scope of your program. I have a  
> few crystal structures which I want to align (I now understand how  
> to do this based on your online tutorial (thanks)), but what I  
> really want to do is feed a third structure into the consensus  
> structure (or if there is no consensus structure, just feed a known  
> sequence into a known crystal structure to see if the sequence  
> could form that structure.
> Is there anyway to do this in your program..
> Thanks for any help you may be able to provide,
> -- 
> Peter Murphy, B.Sc., M.Sc Candidate
> Atlantic Research Center
> Dalhousie University
> Halifax, Nova Scotia,
> Canada
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