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

[Elaine Meng]

Hi Tanmoy,
What is the question, specifically?  Whether any of this is possible?

Currently, no, or at least not with the regular user interface (commands and menu).  You cannot change the color of Bild objects after they are created. Maybe with python, but somebody else would have to answer about that.  Also, even if you could, there is no way to specify different objects within a single Bild model (opened from a single Bild file) in the command line, i.e. there is no logical equivalent to the atom serial number attribute, or the atom name, residue number, chain ID specifiers that you'd have in an atomic model.  At least with the shapes, you can specify them by their unique model numbers.

I can't tell whether you really want 10,000 shapes at the same time or whether you just end up with that by trying to recolor 2 shapes (or some other small number).

(A) First I'll pretend you only want a few shapes, or at least some number or models that doesn't make your computer hang.  When you make the shape in the new color, just  use the "modelId" option to specify the existing model number so that it will overwrite the previous shape.  This is one of the general options of the command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#options>

(B) Next I'll answer pretending you want 10,000 shapes at the same time:

Given that you are just showing spheres and cylinders, can you instead make fake atoms and bonds or pseudobonds (or equivalently, markers and links)?  In that way, you could open a single file making a single model, but have the mechanisms listed above of specifying each sphere or cylinder uniquely in the command line.

The marker-file format is described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/markers.html#markerfiles>

 There are no links without markers (no bonds without atoms) but if you wanted flat-ended cylinders you could try making the link radius large compared to the radii of the markers delineating the ends of the cylinders, or set the bond attribute to display regardless of whether their end atoms are displayed.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Feb 26, 2021, at 4:30 PM, Tanmoy Sanyal <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