[chimerax-users] ChimeraX stalls when trying to display surfaces from a (strange) group of atoms

[Christophe Leterrier]

Hi,

I'm trying to use ChimeraX to visualize Single-Molecule Localization
Microscopy (SMLM) data. In short, the output of an SMLM acquisition and
processing is a list of fluorophores XYZ coordinates with associated
uncertainty, that can be used to reconstruct a 3D image.

I have made a script that make a pdb file from these localization so that I
can directly display the resulting structure as if it was a protein with a
number of random atoms (the only difference is that angstroms in ChimeraX
are really nanometers in my data). The rendered pqr file is here (I use a
pqr pdb format to specify the radius to the localization uncertainty, hence
the variable diameter of each sphere):
http://www.neurocytolab.org/up/Example_File.pqr
The rendering with the "Spheres" view of atoms works well, see a screenshot
here:
http://www.neurocytolab.org/up/Render.png

However, when I try to get the enveloppe of the resulting object using the
"Surfaces" display (click on Surfaces>Show), ChimeraX hangs (I'm on OSX and
get the dreaded infinite rainbow beachball).

Is there a chance that I can get ChimeraX to render the enveloppe object
this way, or is it really too far from what it's supposed to do? I can
imagine that I'm trying to use ChimeraX for something completely different
than its intended use, but it definitely has a lot of potential for this.

Thank you,

--
Christophe Leterrier
NeuroCyto lab
INP CNRS UMR 7051
Aix Marseille University, France
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