[Chimera-users] Poor performance with 30 molecules

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 3 10:07:34 PDT 2008

On Oct 3, 2008, at 1:31 AM, Benoit Zuber wrote:
> I was wondering, if after fitting say 50 Calpha chains I wanted to  
> replace them by the full molecular model (for showing in a talk for  
> example), would there be an easy way to do that?

Hi Ben,
This probably does not qualify as easy, but I would just open the  
full copies and transform them to match their respective alpha-carbon  
traces, then close the alpha-carbon trace models.   Definitely save a  
session file before doing this part!  Something like:

matrixcopy #0 #50
(apply transformation matrix of CA model 0 to full model 50, which  
assumes their untransformed CA coords are identical)


match #50 at ca #0 at ca
(fit CA atoms of model 50 to those of model 0, which assumes the  
models have the same number of CA atoms in the same order)

then possibly

close 0

You could make a Chimera command file to do all 50.  Alternatively,  
for the programming expert, there must be a sneaky way to substitute  
the full coordinates of each structure for the CA-trace coordinates  
within the python session file, but this is beyond my skill set, and  
session-editing can be a risky sport.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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