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

James Starlight jmsstarlight at gmail.com
Mon May 30 08:54:30 PDT 2016

Thank you for the information, Elaine!

As I found it's possbile to narrow frame range to 2 frames, defining
first and last frames for calculations of the contacts from the MD
movie plugin. Does it meas that it will compare contacts from those 2
given snapshots and not for only 1 selected snapshot?
Also how is better operate with the selection of the statistical
thresholds on the stage of the visualization of the contact
calculations via cytoscape networks?



2016-05-25 20:29 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
> 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).
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rins>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rin-contacts>
> I hope this helps,
> Elaine
> -----
> 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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