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

James Starlight jmsstarlight at gmail.com
Mon Jun 13 03:03:17 PDT 2016

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 !


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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