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

Eric Pettersen pett at cgl.ucsf.edu
Tue May 31 16:44:25 PDT 2016

> On May 30, 2016, at 8:54 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 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?

Yes, in that case it will use both snapshots.  However, what you can do is put in a “stride” value large enough that the start value plus the stride is immediately larger than the last frame.  In that case, only the starting frame will be used.

> 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?

I’m not sure what you’re asking here.  Maybe you could rephrase the question?


	Eric Pettersen
	UCSF Computer Graphics Lab

> Thanks!
> Gleb
> 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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