Re: [PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

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
> <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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>>
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