Re: [PyMOL] Thermal ellipsoids with principal axes

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

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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