Command to measure the Atomic to Map fit quality
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 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> 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
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/command... >
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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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<mailto: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<mailto: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/command... > 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<mailto: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 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
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 <https://urldefense.com/v3/__https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqs...> [2]: https://doi.org/10.1038/s41592-020-0731-1 <https://urldefense.com/v3/__https://doi.org/10.1038/s41592-020-0731-1__;!!Nm...> [3]: https://phenix-online.org/ <https://urldefense.com/v3/__https://phenix-online.org/__;!!Nmw4Hv0!19bbuzDTc...> [4]: https://doi.org/10.1107/S2059798318009324 <https://urldefense.com/v3/__https://doi.org/10.1107/S2059798318009324__;!!Nm...>
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/command...
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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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 <mailto: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 <https://urldefense.com/v3/__https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqs...> [2]: https://doi.org/10.1038/s41592-020-0731-1 <https://urldefense.com/v3/__https://doi.org/10.1038/s41592-020-0731-1__;!!Nm...> [3]: https://phenix-online.org/ <https://urldefense.com/v3/__https://phenix-online.org/__;!!Nmw4Hv0!19bbuzDTc...> [4]: https://doi.org/10.1107/S2059798318009324 <https://urldefense.com/v3/__https://doi.org/10.1107/S2059798318009324__;!!Nm...>
On 6 Nov 2024, at 06:18, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto: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 <mailto: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/command... >
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 <mailto: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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_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>
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När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifter...>
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These two are very handy. Thanks very much, Tom! Roden On Thu, Nov 7, 2024 at 6:13 AM Tom Goddard <goddard@sonic.net> wrote:
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 <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/comm...>
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 <https://urldefense.com/v3/__https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqs...> [2]: https://doi.org/10.1038/s41592-020-0731-1 <https://urldefense.com/v3/__https://doi.org/10.1038/s41592-020-0731-1__;!!Nm...> [3]: https://phenix-online.org/ <https://urldefense.com/v3/__https://phenix-online.org/__;!!Nmw4Hv0!19bbuzDTc...> [4]: https://doi.org/10.1107/S2059798318009324 <https://urldefense.com/v3/__https://doi.org/10.1107/S2059798318009324__;!!Nm...>
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/command...
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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När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifter...>
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------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>
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participants (4)
-
Elaine Meng -
Guillaume Gaullier -
Roden Deng Luo -
Tom Goddard