[Chimera-users] Running a job in chimera

tuhin at iitk.ac.in tuhin at iitk.ac.in
Tue Nov 11 01:41:43 PST 2008

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

Thanks in advance. Any suggestion(s) is welcomed.

Warm regards,

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