[chimerax-users] [EXTERNAL] Colour residues by local resolution estimation map

[Oliver Clarke]

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 at 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 at cgl.ucsf.edu> on behalf of Oliver Clarke <olibclarke at gmail.com>
> Sent: Wednesday, May 19, 2021 9:58 AM
> To: Ioannis Skalidis
> Cc: chimerax-users at 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 at gmail.com <mailto:johnskalidis at 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
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>> 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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