Re: [PyMOL] Thermal ellipsoids with principal axes

[Thomas H. <th...@th...>]

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
<tna...@os...> 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
> >>
> >>
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