Hi Thomas,
Thank you very much!
> "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")
Apparently this method is a relatively new addition to PyMOL.
For compatibility, I implemented this using `cmd.iterate` with
`s.ellipsoid_probability`. I didn't know I could read per-atom
properties like this.
> 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.
OK. I kept it as is because 12 looked rather ugly (as mine doesn't use
the sphere impostor shader).
Best regards,
Takanori Nakane
On 5/1/25 16:57, Thomas Holder wrote:
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
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