Also there are two ChimeraX commands "measure correlation" and "measure mapvalues" that can give scores for how a map fits in another map or atoms fit in a map.

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html

   Tom

On Nov 6, 2024, at 1:06 AM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Guillaume, 

Great input! Will give them a try. Many thanks. 

Best,

Roden

On Wed, Nov 6, 2024 at 11:24 AM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:

Hello,

In addition to Ellen’s suggestions, you can use the qscore add-on [1] from the ChimeraX ToolShed to calculate Q-scores [2]. This is easy to use and will give you a plot of Q-score by residue for each chain. Clicking the dots will center the view on the corresponding residues for visual inspection.

Alternatively, the phenix suite [3] has a program called phenix.model_map_cc that will give you model-to-map correlation coefficients as defined in [4], although not in an interactive way like the first option.

I hope this helps,

Guillaume

[1]: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore

[2]: https://doi.org/10.1038/s41592-020-0731-1

[3]: https://phenix-online.org/

[4]: https://doi.org/10.1107/S2059798318009324

On 6 Nov 2024, at 06:18, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Great. Thanks for the input, Elaine.

Best,
Roden

On Tue, Nov 5, 2024 at 8:34 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Roden,
I think you can run "fitmap" but without moving the atoms by using options "shift false" and "rotate false" ... that will report the fitmap result.  However, most of the metrics are for map-map fitting - what you get for atoms-map fitting may just  be the average value of the map at atom positions.  It might also say how many atoms are inside the map contour surface.

Or, you can use the "resolution" option to make a map from the atoms and then get the map-map metrics like correlation.

See "fitmap" and options:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html__;!!Nmw4Hv0!zYEZZRuTVPijpdHBQsZBUd4zCPRPtGkhNBlwEQz5nMWVtmuSCk5-ZJrW_NOmdJI18n7t3Ov8J-csZDRPxanI$ >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 5, 2024, at 8:58 AM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi ChimeraX Team,

I wonder if there is a command that can measure the fit quality of an atomic structure to a volume map. I imagine the metric could be the sum of the density of all atoms or a correlation. Something like: fit_quality #ModelID in #VolumeID (similar to: rmsd #1 to #2).

Thanks,
Roden

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