Colour residues by local resolution estimation map
Dear all, I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow? Thanks a lot for your help! Cheers, Yiannis -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
Hi Yiannis, I am not sure whether this is possible in ChimeraX yet, but you can do this in Chimera using a combination of `Values at Atom Positions` and `Render by Attribute`. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht... <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht...> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html> Cheers Oli
On May 19, 2021, at 9:22 AM, Ioannis Skalidis <johnskalidis@gmail.com> wrote:
Dear all,
I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow?
Thanks a lot for your help!
Cheers, Yiannis
--
Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology
________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
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Isn't this what Q-scores does? https://www.nature.com/articles/s41592-020-0731-1? Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke@gmail.com> Sent: Wednesday, May 19, 2021 9:58 AM To: Ioannis Skalidis Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Colour residues by local resolution estimation map Hi Yiannis, I am not sure whether this is possible in ChimeraX yet, but you can do this in Chimera using a combination of `Values at Atom Positions` and `Render by Attribute`. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_ContributedSoftware_density_density.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=qUJvH5WM1Uut64mw5EYEiH3-YEyReOn0xpoA7yvhA-U&s=uZil8qWzh3fWtec_Fqpi76PvfP_xEH84sjxKOmU2NcM&e=> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_ContributedSoftware_render_render.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=qUJvH5WM1Uut64mw5EYEiH3-YEyReOn0xpoA7yvhA-U&s=EcDDHlqwuPUuSmFKeR9RKJqK4iCHIwkx5__4ARdhxzc&e=> Cheers Oli On May 19, 2021, at 9:22 AM, Ioannis Skalidis <johnskalidis@gmail.com<mailto:johnskalidis@gmail.com>> wrote: Dear all, I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow? Thanks a lot for your help! Cheers, Yiannis -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/<https://urldefense.proofpoint.com/v2/url?u=https-3A__blogs.urz.uni-2Dhalle.de_kastritislab_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=qUJvH5WM1Uut64mw5EYEiH3-YEyReOn0xpoA7yvhA-U&s=F8u6f46yJPq4JGahIH83mWVmZ3geIKKmfDBflEErTrU&e=> web (HALOmem): https://www.halomem.de/en/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.halomem.de_en_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=qUJvH5WM1Uut64mw5EYEiH3-YEyReOn0xpoA7yvhA-U&s=oZIpdUBecbspvVsRFJJT9xsdY2yIXMivutjsIbCdHdk&e=> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I don't think so, although they should be highly correlated if the model is well fit to the density. The Q-score as I understand it is more akin to a per-atom correlation of a map simulated from the atomic model with the experimental density map, whereas just sampling the local resolution at atom positions does not depend the model in the same way. Oli
On May 19, 2021, at 10:02 AM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Isn't this what Q-scores does?
https://www.nature.com/articles/s41592-020-0731-1 <https://www.nature.com/articles/s41592-020-0731-1>
Best wishes, Reza
Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke@gmail.com> Sent: Wednesday, May 19, 2021 9:58 AM To: Ioannis Skalidis Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Colour residues by local resolution estimation map
Hi Yiannis,
I am not sure whether this is possible in ChimeraX yet, but you can do this in Chimera using a combination of `Values at Atom Positions` and `Render by Attribute`.
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.ht... <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimer...>
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimer...>
Cheers Oli
On May 19, 2021, at 9:22 AM, Ioannis Skalidis <johnskalidis@gmail.com <mailto:johnskalidis@gmail.com>> wrote:
Dear all,
I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow?
Thanks a lot for your help!
Cheers, Yiannis
--
Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology
________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__blogs.urz.uni-2Dhalle.d...> web (HALOmem): https://www.halomem.de/en/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.halomem.de_en_&d=Dw...>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yiannis, I'll see if I can add that today to the ChimeraX daily build. Tom
On May 19, 2021, at 6:22 AM, Ioannis Skalidis <johnskalidis@gmail.com> wrote:
Dear all,
I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow?
Thanks a lot for your help!
Cheers, Yiannis
--
Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology
________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yiannis, I added a "measure mapvalues" command to ChimeraX, in tonight's build (dated May 20) that allows you to interpolate a local resolution map at atom positions and assign the interpolated value to each atom. Then the "color byattribute" command can do the coloring you want. For example, if your local resolution map is #2 and your atomic model is #1 measure mapvalues #2 atoms #1 attribute "resolution" color byattribute "resolution" #1 palette 3,blue:4.5,white:6,red key true The color command will color the atoms and each residue in a ribbon using the average resolution value for that residue's atoms. See the color command documentation for more details https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute Tom
On May 19, 2021, at 10:22 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Yiannis,
I'll see if I can add that today to the ChimeraX daily build.
Tom
On May 19, 2021, at 6:22 AM, Ioannis Skalidis <johnskalidis@gmail.com> wrote:
Dear all,
I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow?
Thanks a lot for your help!
Cheers, Yiannis
--
Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology
________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Good morning! Thanks a lot to everybody for their suggestions and especially to Tom for implementing the feature directly! Cheers, Yiannis On 20.05.21 04:25, Tom Goddard wrote: Hi Yiannis, I added a "measure mapvalues" command to ChimeraX, in tonight's build (dated May 20) that allows you to interpolate a local resolution map at atom positions and assign the interpolated value to each atom. Then the "color byattribute" command can do the coloring you want. For example, if your local resolution map is #2 and your atomic model is #1 measure mapvalues #2 atoms #1 attribute "resolution" color byattribute "resolution" #1 palette 3,blue:4.5,white:6,red key true The color command will color the atoms and each residue in a ribbon using the average resolution value for that residue's atoms. See the color command documentation for more details https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute Tom On May 19, 2021, at 10:22 AM, Tom Goddard <goddard@sonic.net> <goddard@sonic.net> wrote: Hi Yiannis, I'll see if I can add that today to the ChimeraX daily build. Tom On May 19, 2021, at 6:22 AM, Ioannis Skalidis <johnskalidis@gmail.com> <johnskalidis@gmail.com> wrote: Dear all, I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow? Thanks a lot for your help! Cheers, Yiannis -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/ _______________________________________________ ChimeraX-users mailing listChimeraX-users@cgl.ucsf.edu Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing listChimeraX-users@cgl.ucsf.edu Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
participants (4)
-
Ioannis Skalidis -
Oliver Clarke -
Reza Khayat -
Tom Goddard