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

[Tanmoy Sanyal]

Thanks Elaine and Tom for the very helpful information!
I eventually chose the option of representing these spheres and bonds as
markers and links, and then re-coloring the selected ones every frame. That
turned out to be a simple solution and it's reasonably fast now.



-----
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


On Fri, Feb 26, 2021 at 6:12 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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