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

[Eric Pettersen]

Reminds me of a lava lamp. :-)

> On Nov 27, 2019, at 3:19 PM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:
> 
> 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
> 
> <image1.png><image2.png>
> 
>> 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
>>> 
>>> 
>>> _______________________________________________
>>> ChimeraX-users mailing list
>>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>>> Manage subscription:
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pxrA27F1CHjJQ19VHMXYPmRhDzgO8n27LN767xP0MP4&s=OSdC41yEX73xCXgqTAwDUs-Hl9ghFF7kQGa30Yu4qec&e=>
>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 
> _______________________________________________
> 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/20191127/316a8415/attachment.html>