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