[Chimera-users] Re-order models in function of their rmsd regarding a given structure

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 27 11:27:57 PST 2012

Hi JD,
Not sure I understand the question: details would depend on whether you are comparing and then re-ordering non-trajectory models and/or frames within a trajectory.  

Either way, the general approach would be to measure the RMSDs first (with MD Movie's RMSD analysis, or command "matchmaker" or "match" or "rmsd," depending on the situation and what you want) and then based on that information, display the structures in the appropriate order (with "modeldisplay" for models, or "coordset" for frames within a trajectory).  

If you meant the sorting by RMSD to be automatic instead of manual, it would require Python.  You could assign structures an RMSD attribute with "setattr" or "defattr" commands, but the sorting part would need to be Python.

Finally, if you had morphs A->B and B->C but then decided to reorder display as A,C,B and show morphing, you would have to use the "morph" command (or Morph Conformations tool) again to create the A->C part (or a single new morph A->C->B) to be able to play that part with "coordset" commands.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 27, 2012, at 9:50 AM, Jean Didier Pie Marechal wrote:

> Hi everyone,
> I have a set of protein and would like to morph between them in the smoothy manner. I'd like then, to re-order following the rmsd regarding a given structure. What would be the command-line, script that could do this relatively easily?
> All the best.
> JD

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