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

[Tom Goddard]

Hi Christophe,

  Using a solvent excluded molecular surface with the surface command with larger probe size as Eric suggested is going to produce a very weird looking surface. These solvent excluded surfaces are made by rolling a ball over the "atoms" so you get a scalloped appearance.  It makes more sense for your data to use a Gaussian surface produced with the molmap command, for example,

	molmap #1 10 balls true

Attached are images of the Gaussian surface (pink) and the solvent excluded surface (blue).  Here are docs on molmap

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html>

  Tom



> On Nov 27, 2019, at 2:14 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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
>> 
>> 
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