ChimeraX stalls when trying to display surfaces from a (strange) group of atoms
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 The rendering with the "Spheres" view of atoms works well, see a screenshot here: 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
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@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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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@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@univ-amu.fr <mailto: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): 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@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@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@cgl.ucsf.edu][cid:F857B379-94FB-45D7-97F6-0713B5EE8D80@cgl.ucsf.edu] On Nov 27, 2019, at 2:14 PM, Eric Pettersen <pett@cgl.ucsf.edu<mailto: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 Pettersen UCSF Computer Graphics Lab On Nov 27, 2019, at 3:13 AM, Christophe Leterrier <christophe.leterrier@univ-amu.fr<mailto: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): 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@cgl.ucsf.edu<mailto:ChimeraX-users@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@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Reminds me of a lava lamp. :-)
On Nov 27, 2019, at 3:19 PM, Reza Khayat <rkhayat@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@cgl.ucsf.edu> on behalf of Tom Goddard <goddard@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_chimer...>
Tom
<image1.png><image2.png>
On Nov 27, 2019, at 2:14 PM, Eric Pettersen <pett@cgl.ucsf.edu <mailto: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 Pettersen UCSF Computer Graphics Lab
On Nov 27, 2019, at 3:13 AM, Christophe Leterrier <christophe.leterrier@univ-amu.fr <mailto: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): http://www.neurocytolab.org/up/Example_File.pqr <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neurocytolab.org_up_...> 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_...>
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@cgl.ucsf.edu <mailto:ChimeraX-users@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_mailm...>
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participants (4)
-
Christophe Leterrier -
Eric Pettersen -
Reza Khayat -
Tom Goddard