Global Diffusion Tensor Models
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
Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
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@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
Hi Arun,
I tried replacing the PyMol ellipsoid drawing code in the example file with ChimeraX ellipsoid drawing. Here is the Python I came up with. I just copy the 4 parameters at the bottom of the PyMol script (center, axis lengths, color, rotation) to the ChimeraX script and open it in ChimeraX. I am not sure if I got the rotation right because you didn't provide a molecule -- my rotation may be the inverse of what is needed -- I can fix the script if that is the case.
First I tried the "shape ellipsoid" command and that didn't look so good because ChimeraX uses a smooth spiral triangulation intended for making nice surfaces so it does not show the desired latitude and longitude lines.
Tom
On Mar 16, 2021, at 3:43 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
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@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
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participants (3)
-
Elaine Meng -
Gupta, Arun -
Tom Goddard