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@gmail.com <mailto:tanmoy.7989@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users