[Chimera-users] Poor performance with 30 molecules

Tom Goddard goddard at cgl.ucsf.edu
Fri Oct 3 10:23:06 PDT 2008


Hi Ben,

  Elaine's solution would be done by making a Chimera command file 
(suffix ".cmd") with lines

open 100 allatoms.pdb ; matrixcipy #0 #100 ; close #0
open 101 allatoms.pdb ; matrixcipy #1 #101 ; close #1
open 102 allatoms.pdb ; matrixcipy #2 #102 ; close #2
....

To save some typing you can make a Python script (file suffix ".py") 
instead like:

from chimera import runCommand
for i in range(50):
    runCommand('open %d allatoms.pdb ; matrixcipy #%d #%d ; close #%d' % 
(100+i, i, 100+i, i))

Opening that file with Chimera File/Open... to replace all your models.

    Tom


Elaine Meng wrote:
> 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)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
>
> or
>
> 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)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>
> 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.
> Best,
> Elaine
> -----
> 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
>                        http://www.cgl.ucsf.edu/home/meng/index.html
>
>
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