[Chimera-users] Running a job in chimera

[Eric Pettersen]

Just to add a few tidbits to Elaine's reply:

> 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?

You might consider doing this by opening one structure in model #0 as  
your reference structure then opening your 400 structures, one at a  
time, in model #1 and matching them on the reference, pruning the  
unwanted waters, and then writing them out, closing each one as you  
finish with it.

As for the script you use, you could use any programming language you  
know in order to generate a Chimera command script that performs the  
functions I outlined.  If you don't know any programming languages,  
you might as well try writing a Python script since it's pretty easy  
to learn Python and Chimera can execute it directly.  The most  
important single thing to know is that you can run any regular Chimera  
command via Chimera's runCommand() function.  Here's a tiny script  
that opens files model001.pdb through model400.pdb into model #1,  
colors them red, and then closes them.  You can probably figure out  
how to flesh out the script to do what you want:

from chimera import runCommand
for i in range(400):
	runCommand("open 1 model%03d.pdb" % (i+1))
	runCommand("color red")
	runCommand("close 1")

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Nov 12, 2008, at 11:04 AM, Elaine Meng wrote:

>
> 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:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003218.html
>>
>
> See also Chimera nogui mode:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui>
>
> 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
>
> or
>
> 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
> -----
> 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
>
> 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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