[Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory

Elaine Meng meng at cgl.ucsf.edu
Wed May 25 11:29:35 PDT 2016

Hi Gleb,
If you are using the approach where you first start Cytoscape, use it to start Chimera, and then use the MD Movie tool to show the network, the residue interaction network (RIN) contacts-parameters dialog has options to limit the calculation to the selection. Even though you would still be using MD Movie with the trajectory, in the first RIN dialog you could specify only using a single specific frame (snapshot).


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 24, 2016, at 9:51 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera Users!
> Also what I am interesting to ask regarding Network view of contact
> maps done via Cytoscape + Chimera:
> In principal I have no problems with such analysis of the MD
> trajectory however having some unsertainly in the statistical
> theresholds which should be set by user in the histogram upon the
> analysis of the contact maps.
> 2) Now I would like to do the same but now for trajectories but for
> the selected snapshots from the trajectory and compare them vizually.
> In chimera it is possible just to calculate contact for the pairs of
> residues defined in the selection (find clashes/contacts) for each of
> the pdb.
> Is it possible to do the same including  Cytoscape to obtain networks
> for each of the pdb under analysis?
> Thanks!
> Gleb

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