Hi Jan,
I've whacked together a quick-and-dirty implementation for ChimeraX. To
make use of it:
- make a directory called "chimerax_start" in your home directory. Copy
chromadepth.py there, and also create an empty file called "__init__.py"
there
- start ChimeraX and load a model
- open the shell (Tools/General/Shell)
- assuming that you've only loaded the one model:
from chromadepth import ChromaDepth_Mgr
m = session.models.list()[0]
cdm = ChromaDepth_Mgr(session, m)
cdm.start_auto_coloring()
... and your model will automatically recolor on every scene change.
Gets a bit slow when you have cartoons displayed, but it does the job.
When you're done, call:
cdm.stop_auto_coloring()
Hope this helps!
Tristan
On 2019-03-07 11:38, Jan Gebauer wrote:
> Dear all,
>
> I know it's not quite the topic of this list, but hopefully related
> enough.
>
> I am looking for a free software,able to render PDB structures in
> ChromaDepth colours (Meaning from blue to red based on the distance
> from the viewer - https://en.wikipedia.org/wiki/ChromaDepth). I'd like
> to print some structure for an "open-day" of our faculty.
>
> I found that the incentive version of PyMol supports it, but this is a
> little bit to expensive.
>
> Is there any free software out there? Or potentially a plugin? If not
> is there a function to determine distances of atoms from the viewer in
> Chimera -- I could write my own python script then...
>
> Thanks for all help,
>
> Jan Gebauer
> --
> Dr. Jan Gebauer
> Structural Biologist
> px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de
>
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