Hi Takanori, This is brilliant. Works like a charm. Thanks a lot for sharing the script.
Your scaling factor 32 on "ellipsoid_quality" is a lot higher than PyMOL's native ellipsoids, which use a factor of 12 as far as I can tell. "ellipsoid_probability" per atom would also be easy, like this: from pymol.editor import iterate_to_list color_indices = iterate_to_list(selection, "color") prob_per_atom = iterate_to_list(selection, "s.ellipsoid_probability") Cheers, Thomas On Thu, May 1, 2025 at 8:04 AM Takanori Nakane <tnakane.prot...@osaka-u.ac.jp> wrote: > > Hi, > > > At the moment my code does not support object's TTT matrix > > and per-atom colors. Once I fix these limitations, > > I will put my script to my GitHub or PyMOL wiki. > > I made my script public at > https://gist.github.com/biochem-fan/0a5b690670e90af8946adddc1c40fa6b. > > Unfortunately I could not find enough time to support the > TTT matrix but I hope this is already useful. > > WARNING: I tried my best to make sure my ellipsoids match > PyMOL's native ellipsoids but can never guarantee this is > bug free. Please double check before you use my script > for serious purposes (e.g. publication). > > Best regards, > > Takanori Nakane > > On 3/28/25 13:11, Takanori Nakane wrote: > > Hi, > > > > I ended up implementing this myself, drawing three ellipses > > by CGO over PyMOL's native ellipsoids. > > My current style is like the one in > > https://www.chem.gla.ac.uk/~louis/software/ortep/index.html. > > > > At the moment my code does not support object's TTT matrix > > and per-atom colors. Once I fix these limitations, > > I will put my script to my GitHub or PyMOL wiki. > > > > I also want to implement the "cutting out one octant" feature > > like ORTEP but that would require completely hiding > > PyMOL's native ellipsoids and drawing everything from scratch. > > > > Best regards, > > > > Takanori Nakane > > > > On 3/25/25 22:30, Takanori Nakane wrote: > >> Dear PyMOL users, > >> > >> I am preparing figures for small molecular crystallography. > >> I know I can plot thermal ellipsoids in PyMOL but can I add > >> principal axes on the surface (or cut out one octant)? > >> > >> I would like to draw something like ORTEP: > >> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif. > >> > >> Do I have to code CGO objects? > >> > >> Best regards, > >> > >> Takanori Nakane > >> > >> > >> _______________________________________________ > >> 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 > > > _______________________________________________ > 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 _______________________________________________ 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
