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

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 9 17:08:27 PDT 2016


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




More information about the Chimera-users mailing list