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@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@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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