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 2017-11-27 12:03 GMT+01:00 James Starlight <jmsstarlight@gmail.com>:
Thank you so much for the suggestions, Elaine!
Indeed, I have turned off the both flags but the intra-models contacts are still recognized.
it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA.
James
2017-11-27 9:23 GMT+01:00 <sdimicco@unisa.it>:
Grazie mille
Il 2017-11-23 04:47 James Starlight ha scritto:
Thank you for the suggestions, Elaine !
I have already tried "Find Clashes/Contacts" plugin. In generally, it works good, however its application on more complex oligomeric patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit complicated. Briefly, if I select only one monomer and than try to find its contacts with the rest of the atoms ( I have changed the contact threshold to -1.2 for the MARTINI) - it works fine. However, If I selected all of the atoms (even excluding inter-residue and inter-molecular contacts) and changing the search criterium "against themselves" - it found alot of contacts within the monomers. Does anybody use any tricks for the MARTINI models to fascilitate the contact searching?
James
2017-11-22 17:52 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Dear James / Gleb, This question seems too broad, perhaps. I don't know that much about MARTINI, so I'm guessing instead of atoms you just have a bunch of points that each represent multiple atoms. In that case you could probably use any analysis that does not directly use exact atomic locations, atomic radii, or atomic point charges. Analyses that DO use those things include surface-area calculations, Find Clashes/Contacts, FindHBond.
Maybe you should just first think about what Chimera analysis you want to use, then just try it on your GC model and see if it works rather than trying to get some exhaustive list of what might work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera users!
I would like to make some analysis of the protein-protein binding established in coarse-grained MARTINI simulations. Briefly Chimera has recognized a coarse-grained pdb file of 16 martini models of GPCRs. What Chimera tools (e.g. contact maps, clustering of interphaces) should work with CG models? What tricks should be used to make this analysis easier? Because I am working with several proteins in one system, I would like to work with its CG models without the conversion to all atomistic representations.
I thank you so much for the help! James
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