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_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=

---

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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

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