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

[Eric Pettersen]

Hi Christophe,
	Because your isolated atoms are spaced much further apart than for an actual molecule, computing a surface with the default parameters (probe radius 1.4Å and grid spacing of 0.5Å takes a very long time and produces a surface that looks like your isolated spheres anyway because the small probe radius doesn’t join any of your “atoms” together.  Try this command:

	surf probe 20 grid 5

You can play around with the actual probe and grid values, just don’t use anything near their default values!

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 27, 2019, at 3:13 AM, Christophe Leterrier <christophe.leterrier at univ-amu.fr> wrote:
> 
> 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 <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 <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
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20191127/f0fdef80/attachment-0001.html>