[chimerax-users] Global Diffusion Tensor Models

[Elaine Meng]

Hi Arun,
ChimeraX can't use a Pymol script, which is probably not a surprise.  ChimeraX does have a "shape" command that can draw spheres and ellipsoids, among other shapes.  However, you would need to figure out how to specify the centers, dimensions, and orientations of your ellipsoids in the way needed by this command.  Probably the radius and center specifications are easy, whereas specifying the orientation of the ellipsoid is potentially more tricky.

shape command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 16, 2021, at 1:21 PM, Gupta, Arun <Arun.Gupta at warwick.ac.uk> wrote:
> 
> Dear ChimeraX team,
>  
> I am interested in generating Global diffusion tensor geometry models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB or structure of my interest. (As shown in attached pic). I am using diffusion tensor prediction module provided in ROTDIF software (http://gandalf.umd.edu/FushmanLab/pdsw.html) to generate an ellipsoid  diffusion tensor of a protein molecule of my interest. 
> 
> Is it possible that I can use ROTDIF generated output (Which is in Pymol output format, please find attached ) to open in ChimeraX with my protein PDB, to render such representative figure ?
> 
> Thanks!!! 
> 
> Arun