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

[Reza Khayat]

In my opinion, both of these images look really cool!!!!


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Tom Goddard <goddard at sonic.net>
Sent: Wednesday, November 27, 2019 6:13 PM
To: ChimeraX Users Help
Cc: Christophe Leterrier
Subject: [EXTERNAL] Re: [chimerax-users] ChimeraX stalls when trying to display surfaces from a (strange) group of atoms

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://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimerax_docs_user_commands_molmap.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=-DLC9Ypqy51avfavOLQfMdfzanzoEkNJZBhitAuytZM&e=>

  Tom

[cid:CDC3F2C6-6614-460E-9C38-303E5A8CBB0F at cgl.ucsf.edu][cid:F857B379-94FB-45D7-97F6-0713B5EE8D80 at cgl.ucsf.edu]

On Nov 27, 2019, at 2:14 PM, Eric Pettersen <pett at cgl.ucsf.edu<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neurocytolab.org_up_Example-5FFile.pqr&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=vPnNzyJaX_dbdoerQrjGRREdfg2sDZV1wrKsn1GzhOY&e=>
The rendering with the "Spheres" view of atoms works well, see a screenshot here:
http://www.neurocytolab.org/up/Render.png<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neurocytolab.org_up_Render.png&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=CCR-uiiLzR5x6Dv27XtB8qxpLDFI2yDApoPPETG6lzE&e=>

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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