In my opinion, both of these images look really cool!!!!
On Nov 27, 2019, at 2:14 PM, Eric Pettersen <pett@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 PettersenUCSF Computer Graphics Lab
On Nov 27, 2019, at 3:13 AM, Christophe Leterrier <christophe.leterrier@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):The rendering with the "Spheres" view of atoms works well, see a screenshot here:
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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