[Chimera-users] Running a job in chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 12 11:04:36 PST 2008

Dear Tuhin,
The script to perform the actions (your #1 or #2) could be written in  
python or in Chimera commands.  Just opening the python file (*.py) or  
Chimera command file (*.com) in Chimera will execute it.  The trickier  
part would be how to automatically loop through your multiple  
structures.  You could write a long Chimera command script that  
includes the names of the structures, or you could use a python script  
that loops through a list of filenames.  The methods can be combined;  
for example, the python script could merely loop through the names and  
open the structures, then open a separate Chimera command script.  You  
could also use a shell script to loop through filenames, but I guess  
that would be slower because it would involve starting a new Chimera  
for each input (#1) or set of inputs (#2). If that is easier for you,  
however, it is reasonable.

Please see this previous posting for examples/discussion of Chimera  
scripts for processing multiple structures, calling a script from  
another script, and using aliases:

See also Chimera nogui mode:

I believe all the actions you want to perform can be done with Chimera  
commands, for example

open /location/location/frame20.pdb
delete solvent & protein z>5
write format pdb relative 0 0 /location/location/frame20zone5.pdb
close 0


open /location/mystruct1.pdb
open /location/mystruct2.pdb
open /location/mystruct3.pdb
matchmaker #0 #1
matchmaker #0 #2

These are just possibilities out of several ways to perform the  
tasks.  For example, the top example assumes your structure is a  
protein, and in the bottom example, you could use "match" instead of  
"matchmaker" to superimpose structures.

I hope this helps,
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

On Nov 11, 2008, at 1:41 AM, tuhin at iitk.ac.in wrote:

> Dear All,
> I have run several simulations. But, I need to analyse a selective  
> number
> of structures from each simulation saved at a given time step "t".  
> Thus,
> for a 20ns simulation, starting t=0 and incrementing it by 50ps,  
> I'll have
> ~400 individual structures. Each structure is within a waterbox, which
> contains approx. 20,000 water molecules. Once I get the structures,  
> I need
> to do the following using CHIMERA:
> 1. Open each structure and save water molecules within a cutoff  
> distance of
>   5.0 Angstrom from the protein. Thus, I'll end-up having a shell  
> (<=5.0A)
>   of water molecules around the protein. The saved structure will be  
> in
>   .pdb format and include the protein with 5.0A water shell.
>      I know how to do it in CHIMERA using the commandline option/ 
> pulldown
>   menu, but, how to do it for 400 structures. Is there a way to run it
>   in a "Batch Job" ?
> 2. I also need to superimpose Ca-Ca atoms of 400 structures. But, I  
> feel
>   there is a limit to the no. of structures that CHIMERA could handle,
>   thus, at max. I would be superimposing 20-30 structures at a time.  
> How
>   could I automatize the same through a script sothat I could run it  
> in
>   batches?
> Thanks in advance. Any suggestion(s) is welcomed.
> Warm regards,
> Tuhin

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