(Arun: this is a resent e-mail. My first e-mail was deleted along with spam messages. Thomas Holder asked me to resend it.)
Hi Arun, I am able to run your script (run ELM_ellipsoid.py) in PyMOL without reported errors or warnings, and it displays an ellipsoid centered on the hardwired position in the script. It looks like you need to edit the script to supply the center of mass of your structure, the lengths of the semi-axes and the orientation of the ellipsoid via three Eulerian angles. Please be more explicit about what is the "intended" result. Do you really want the geodesic surfaces in Diffusion_Geometry.png? The result in ROTDIFF_Ellipsoid looks better. You can tweak the parameter settings in makeEllipsoid() to make the triangles smaller so that the surface is smoother. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________________ From: Gupta, Arun via PyMOL-users [pymol-users@lists.sourceforge.net] Sent: Wednesday, April 21, 2021 2:51 PM To: pymol-users@lists.sourceforge.net Subject: [EXTERNAL] [PyMOL] " Global Diffusion Models" Dear Pymol users I am interested in generating the representative figures of Global diffusion geometrical models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB of my interest after the Model-free analysis" ( As shown in attached pic). And ROTDIF software provides the desired output pymol script to generate the predicted shape model information. However, it seems that I am missing some further inputs or Pymol commands for the correct initialization of the script (attached pic). As, I am not getting the intended results with the script. Can anyone please suggest the correct modifications to the attached script.... Thanks!!! Arun _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
