[Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models

[Elaine Meng]

Hi James,
I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

There are two main kinds of Chimera scripts, Chimera commands and Python.  Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files.  Python is also needed for actions for which no Chimera command is available.

I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>

In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers.  There is a page on how to loop through multiple different structures, which is different, but may still be helpful:
<https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

There are lot of example Chimera python scripts for miscellaneous tasks here:
<http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> One question regarding Find Clashes/Contacts.
> 
> assuming that I have assigned the unique letters for each of the monomer
> in my CG system. Now I am using this selection ("the individual
> chain" vs "all other systems") to calculate contacts using -2.2 cutoff
> for MARTINI (operating with the backbone atoms only). Is it possible
> to run the same routine in batch mode i) for the individual pdb as
> input as well as ii) for the md trajectory (to calculate occurence of
> the contacts along the trajectory)? I would be very grateful for some
> example script file for batch Chimera!
> 
> James