[Chimera-users] Analysis of NMR-like ensembles in CHIMERA

James Starlight jmsstarlight at gmail.com
Tue Jun 14 06:41:49 PDT 2016


Thanks so much Elaine!

To simplify the problem -
I have 2 cases both of which are the same process: binding established
between A and B caputred by means of i) docking ii) MD simulation.

 Let's assumes that contact map is the most important criterioum for
my case - because one of the *docking* ensemble was driven by means of
experiemtal restraits so the contacts between pairs of the residues of
A and B can be considered here as the reference which I want to
reproduce in the second MD ensemble in unbiassed fassion.

Is it possible to calculate contact maps for both ensembles separately
using MD movie and than calculate some statistical variance or RMSD of
established contact pairs between A and B within each of the ensembles
and after all to compare both outputs to understand what are the
cotacts from the MD ensembles has most statistical significance?

Gleb

2016-06-13 18:42 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi Gleb,
> For #1, there isn’t anything to automatically copy chain IDs like you describe.  However, if you text-edit the PDB files to put a TER between the chains, then the Change Chain IDs tool will allow you to change the ID of each part separately.
>
> For #3, I can’t think of anything very automatic to do the comparison. You could maybe do something with Chimera command scripts and “distance” and “angle” command measurements between the two proteins (possibly also with “define” to calculate centroids, planes, and axes which could then be used in the “distance” and “angle” measurements).  Another idea is to open each ensemble as a trajectory and then use the MD Movie tool’s plotting of distances, angles, etc. (MD Movie menu: Analysis… Plot…).  There is a “Dump Values” button on the plot window to write the measurements to file.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>
>
> I hope this helps,
> Elaine
>
>> On Jun 13, 2016, at 3:03 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>
>> Thanks so much Elaine!
>>
>> Regarding #2 it's OK!
>> Regarding #1 - I have tried to set new chains via Tools menu but
>> unfortunatelly in the model where chains has not been asigned the
>> whole sequence is defined as Principal chain without partitition on
>> sub-segments. BTW in case If another model of the same protein is
>> loaded in the same session as the second ensemble where the chains are
>> assigned correctly is it possible to copy chains ID from it to the
>> first model (Ensemble) using Match-align plugin for intance?
>>
>> And finally the question #3
>> For my particular case - each ensembles represent several snapshots of
>> the docking poses between 2 proteins - one produced by protein-protein
>> docking and the another one - as the result of clustetring of several
>> independet long MD trajectories (taking one representative snapshot
>> from each of the trajectory - corresponded to the established
>> macromolecular complex). Having those two ensembles  I need to
>> compareit in terms of the distribution of the docking poses within
>> each to find some shared trends in each of them e.g RMSD of the
>> distances between common residues-pairs found in contact map analysis
>> or something else. What are most trivial suggestions might be in that
>> particular case?
>>
>>
>>
>> Thanks for help !
>>
>> Gleb
>>
>> 2016-06-10 2:08 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
>>> Hi Gleb,
>>> Unfortunately, the short answer is “not really” to both parts.
>>>
>>> For #1 you’d need to do it semi-manually with Tools… Structure Editing…. Change Chain IDs (or command “changechains”).
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>
>>>
>>> For #2 if you just had individual models (not ensembles), you could spread them out with Tools… Utilities… Tile Structures (or command “tile”).  Unfortunately if you try this on the ensembles, the invidual members of the ensembles will be spread out.  As far as I know, there is no way just to tile the 2 groupings.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensembletile/ensembletile.html>
>>>
>>> A similar approach is if you had opened the two ensembles as models #1,2 you could translate them apart, e.g. command:
>>>
>>> move x 50 model #2
>>>
>>> … and then set independent rotation, e.g. command:
>>>
>>> set independent
>>>
>>> The basic problem remains that each individual member (not ensembles collectively) will then rotate about its own individual center, and the ensemble members will diverge from one another as you rotate with the mouse, rather than keeping together as a tight unit.
>>>
>>> Sorry for the limitations,
>>> 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 Jun 9, 2016, at 7:06 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>>
>>>> Dear Chimera Users!
>>>>
>>>> I have loaded 2 NMR ensembles each of which is consisted of several
>>>> models as 2 different object and now would like to do:
>>>>
>>>> 1 - becasue actually two esembles made from the conformers of the same
>>>> protein (one from experiment (NMR) and another one from MD simulation)
>>>> with totally equal sequence - I would like to copy from the first
>>>> ensemble the chain information to the second one where such
>>>> information is absent but the order of residues and atoms are the
>>>> same.
>>>>
>>>> 2- Is it possible to set visualization mode as split view to see on
>>>> the screen both ensembles in the adjacent positions with the
>>>> posibility to easily browes separate models within each of them (like
>>>> pymol style)?
>>>>
>>>> Thanks for help !
>>>>
>>>> Gleb
>>>
>



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