[chimerax-users] Accessing shapes created through a .BLD script

[Greg Couch]

There are several issues here.  Bild spheres and cylinders use a fixed 
subdivision into triangles.   Unlike atoms and bonds, which alter the 
amount of subdivisions based on how big they are drawn. So if all you 
have are atoms and bonds, a fake molecule would be much faster, if they 
are tiny on the screen, or much better visual quality, if they are 
larger on the screen.  But, ignoring the subdivision issue, 10000 bild 
shapes should roughly the same speed as a molecule with 10000 elements. 
and possibly a little faster.

So back to coloring bild objects, with some Python code, you can change 
the color of individual bild shapes.  Consider this "unofficial", but 
this works if the bild model is the first one opened:

> RED = [255, 0, 0, 255]
>
> def recolor_shape(model, index, color):
>     s = m.child_drawings()[0]
>     sh = s._shapes[index]
>
>     vertices = set()
>     tris = s.triangles
>     for t in sh.triangle_range:
>         vertices.update(tris[t])
>
>     vc = s.vertex_colors
>     for v in vertices:
>         vc[v] = color
>     s.vertex_colors = vc
>
>
> m = session.models[0]
> recolor_shape(m, 1, RED)

     HTH,

     Greg


On 2/26/2021 6:14 PM, Tom Goddard wrote:
> Hi Tanmoy,
>
>   The BLD models do not support changing colors of individual spheres 
> and cylinders.  And to get decent performance for 10000 shapes you 
> need to use a fake molecule.  You can use a marker set which can have 
> spheres and cylinders connecting spheres.  Each marker is an atom and 
> each cylinder is a bond.  Each marker has an id number which is its 
> residue number, so you can color marker 57 with "color :57 gold". 
>  Markers can be read from an XML file or made from Python.
>
> https://www.rbvi.ucsf.edu/chimerax/docs/user/markers.html 
> <https://www.rbvi.ucsf.edu/chimerax/docs/user/markers.html>
>
>   Tom
>
>> On Feb 26, 2021, at 4:30 PM, Tanmoy Sanyal <tanmoy.7989 at gmail.com 
>> <mailto:tanmoy.7989 at gmail.com>> wrote:
>>
>> Hi,
>> I have a bunch of shapes (spheres and cylinders) created through a 
>> .bld script. I'd like to load this script once, and then be able to 
>> change the colors of said shapes in successive operations. It is 
>> possible to set the colors directly in the .bld script, but I need to 
>> make an animation out of this. E.g: if my .bld script contains lines 
>> that draws shapes like so:
>> .sphere 0 0 -1 5.0
>> .cylinder 0 0 0 1 1 1 1.0
>>
>> I want to be able to later have a bunch of scripts called 1.cxc, 
>> 2.cxc, 3.cxc, .... each of which change the color of the sphere and 
>> cylinder. This way, I can load these scripts in the per-frame mode, 
>> to create an animation out of the color changes.
>>
>> Alternatively, I tried doing this with just the shape command and 
>> without a .bld script, but I have over ~10000 shapes; the shape 
>> command interprets each as a different model, and my computer hangs.
>>
>> -----
>> Thanks,
>> Tanmoy
>>
>> Tanmoy Sanyal
>> Postdoctoral scholar, Sali lab <https://salilab.org/>,
>> Department of Bioengineering and Therapeutic Sciences 
>> <https://bts.ucsf.edu/>,
>> University of California San Francisco
>> Phone:- (+1) 805-637-0375
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