Displaying maps with threshold defined by mapstats
Dear ChimeraX-Team and all, I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value. Is this possible in chimerax? Any help would be greatly appreciated. Thank you. Best, Lorenz
Hello Lorenz, The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal. So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons. If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows: 1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume I hope this helps, Guillaume From: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu Subject: [chimerax-users] Displaying maps with threshold defined by mapstats Dear ChimeraX-Team and all, I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value. Is this possible in chimerax? Any help would be greatly appreciated. Thank you. Best, Lorenz 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
Hey Lorenz! Maybe something like this works? runscript /Users/artem.kushner/Desktop/threshold90.py ```python from chimerax.map import Volume from chimerax.core.commands import run def thresh_90_all(): for model in session.models: if isinstance(model, Volume): max_val = model.data.matrix().max() threshold_90 = 0.9 * max_val run(session, f"volume #{model.id_string} level {threshold_90}") print(f"Map '{model.name <http://model.name/>}': max={max_val:.2f}, 0.9 threshold is {threshold_90:.3f}") thresh_90_all() ``` On Tue, Aug 26, 2025 at 5:25 PM Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX-Team and all,
I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.
Is this possible in chimerax? Any help would be greatly appreciated. Thank you.
Best, Lorenz _______________________________________________ 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/
Hello Lorenz, I was going to say you can report the max with "measure mapstats" and then set the threshold to 90% of that with something like volume #1 level 50.47 ...however, Guillame's answer is much better as how to actually compare maps in a meaningful way (thanks Guillame!). 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 Aug 26, 2025, at 8:48 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello Lorenz,
The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level
But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal.
So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons.
If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows:
1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume
I hope this helps,
GuillaumeFrom: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu Subject: [chimerax-users] Displaying maps with threshold defined by mapstats Dear ChimeraX-Team and all,
I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.
Is this possible in chimerax? Any help would be greatly appreciated. Thank you.
Best, Lorenz
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.
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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 _______________________________________________ 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/
Just to add one point to Guillame's comprehensive answer - for setting the thrshold based on volume, you can use the "fastenclosevolume" option - so something like volume #1-5 fastenclosevolume 40000 ought to (roughly) set the levels of maps 1-5 such that they each enclose the same volume
On Aug 26, 2025, at 11:48 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Lorenz,
The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level
But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal.
So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons.
If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows:
1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume
I hope this helps,
Guillaume From: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu Subject: [chimerax-users] Displaying maps with threshold defined by mapstats
Dear ChimeraX-Team and all,
I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.
Is this possible in chimerax? Any help would be greatly appreciated. Thank you.
Best, Lorenz
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 _______________________________________________ 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/
You might prefer the "encloseVolume" option which is just like the fastEncloseVolume option but will give a more accurate threshold. The "fast" versions is faster and uses the volume histogram shown in the Volume Viewer panel to determine the correct threshold while the version without fast uses the actual volume values without the histogram binning and by computing contour surfaces and using bisection and is not too slow, taking about 15 seconds on 500 x 500 x 500 grid pont map EMDB 51004 at enclosing 1e6 cubic Angstroms. Tom
On Aug 26, 2025, at 9:24 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Just to add one point to Guillame's comprehensive answer - for setting the thrshold based on volume, you can use the "fastenclosevolume" option - so something like volume #1-5 fastenclosevolume 40000 ought to (roughly) set the levels of maps 1-5 such that they each enclose the same volume
On Aug 26, 2025, at 11:48 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Lorenz,
The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level
But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal.
So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons.
If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows:
1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume
I hope this helps,
Guillaume From: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu Subject: [chimerax-users] Displaying maps with threshold defined by mapstats
Dear ChimeraX-Team and all,
I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.
Is this possible in chimerax? Any help would be greatly appreciated. Thank you.
Best, Lorenz
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 _______________________________________________ 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/
_______________________________________________ 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/
Dear Tom, Oliver, Guillaume, Artie and Elaine, This are all great (!) suggestions and they all are applicable to my problem. Thank you so much. Best, Lorenz From: Tom Goddard <goddard@sonic.net> Date: Tuesday, 26. August 2025 at 19:27 To: Oliver Clarke <olibclarke@gmail.com> Cc: Guillaume Gaullier <guillaume.gaullier@kemi.uu.se>, chimerax-users-owner@cgl.ucsf.edu <chimerax-users-owner@cgl.ucsf.edu>, Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at> Subject: Re: [chimerax-users] Displaying maps with threshold defined by mapstats You might prefer the "encloseVolume" option which is just like the fastEncloseVolume option but will give a more accurate threshold. The "fast" versions is faster and uses the volume histogram shown in the Volume Viewer panel to determine the correct threshold while the version without fast uses the actual volume values without the histogram binning and by computing contour surfaces and using bisection and is not too slow, taking about 15 seconds on 500 x 500 x 500 grid pont map EMDB 51004 at enclosing 1e6 cubic Angstroms. Tom On Aug 26, 2025, at 9:24 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Just to add one point to Guillame's comprehensive answer - for setting the thrshold based on volume, you can use the "fastenclosevolume" option - so something like volume #1-5 fastenclosevolume 40000 ought to (roughly) set the levels of maps 1-5 such that they each enclose the same volume On Aug 26, 2025, at 11:48 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello Lorenz, The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal. So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons. If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows: 1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume I hope this helps, Guillaume From: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu Subject: [chimerax-users] Displaying maps with threshold defined by mapstats Dear ChimeraX-Team and all, I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value. Is this possible in chimerax? Any help would be greatly appreciated. Thank you. Best, Lorenz 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 _______________________________________________ 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/ _______________________________________________ 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/
I used the normalization by volume enclosed before with the vseries command, but didn’t know it was also available with the volume command. Very good to know, thanks Oli and Tom! Cheers, Guillaume
On 27 Aug 2025, at 10:41, Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at <mailto:lorenz.grundmann@imp.ac.at>> wrote:
Dear Tom, Oliver, Guillaume, Artie and Elaine,
This are all great (!) suggestions and they all are applicable to my problem. Thank you so much.
Best, Lorenz
From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Date: Tuesday, 26. August 2025 at 19:27 To: Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Cc: Guillaume Gaullier <guillaume.gaullier@kemi.uu.se <mailto:guillaume.gaullier@kemi.uu.se>>, chimerax-users-owner@cgl.ucsf.edu <mailto:chimerax-users-owner@cgl.ucsf.edu> <chimerax-users-owner@cgl.ucsf.edu <mailto:chimerax-users-owner@cgl.ucsf.edu>>, Grundmann,Lorenz Emanuel <lorenz.grundmann@imp.ac.at <mailto:lorenz.grundmann@imp.ac.at>> Subject: Re: [chimerax-users] Displaying maps with threshold defined by mapstats
You might prefer the "encloseVolume" option which is just like the fastEncloseVolume option but will give a more accurate threshold. The "fast" versions is faster and uses the volume histogram shown in the Volume Viewer panel to determine the correct threshold while the version without fast uses the actual volume values without the histogram binning and by computing contour surfaces and using bisection and is not too slow, taking about 15 seconds on 500 x 500 x 500 grid pont map EMDB 51004 at enclosing 1e6 cubic Angstroms.
Tom
On Aug 26, 2025, at 9:24 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Just to add one point to Guillame's comprehensive answer - for setting the thrshold based on volume, you can use the "fastenclosevolume" option - so something like volume #1-5 fastenclosevolume 40000 ought to (roughly) set the levels of maps 1-5 such that they each enclose the same volume
On Aug 26, 2025, at 11:48 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello Lorenz,
The command 'volume sdLevel' or 'volume rmsLevel' will adjust the contour level by standard deviations from the mean value or by rms deviations from zero, respectively: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#level
But, if you use the command 'measure mapstats' to get summary statistics of map values ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ), you will notice that different maps have very different distributions of voxel values. This is because: 1) cryoEM maps are not on an absolute scale (the voxel values totally depend on the pixel values in the original micrographs, which will be different from dataset to dataset); and 2) box sizes are arbitrary, which affects the mean and median voxel values because you never have the same ratio of voxels containing background versus voxels containing signal.
So, setting contour levels like this might not work exactly as you want. Always check visually! I have had no problem choosing contour levels visually as best as I can, and reporting the absolute contour level for each map when writing about such comparisons.
If you are comparing similar structures at similar resolutions, say for example an apo structure versus the same with a bound ligand, then one way to obtain comparable contour levels could be as follows:
1) choose a "reference" map, set its contour level interactively to something adequate for the features you are looking at, and note the absolute level (from the volume viewer) in case you need to set it again later after other changes 2) use the 'measure volume' command on this map at this contour level to measure the volume enclosed by this isosurface, note the volume reported in the Log; https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#volume 3) now on your other map, adjust the contour level visually until it roughly matches the reference map, measure the volume, and adjust the contour level finely (fine adjustments are easier with the 'volume level' command than manually with the slider) until the measured volume matches the one you had for the reference map in step 2 4) note the absolute contour level of this other map from the volume viewer: it is likely not identical to the one of the reference map, despite both maps now at a contour enclosing the same volume
I hope this helps,
Guillaume From: Grundmann,Lorenz Emanuel via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Sent: Tuesday, August 26, 2025 10:28:16 AM To: chimerax-users-owner@cgl.ucsf.edu <mailto:chimerax-users-owner@cgl.ucsf.edu> Subject: [chimerax-users] Displaying maps with threshold defined by mapstats
Dear ChimeraX-Team and all,
I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value.
Is this possible in chimerax? Any help would be greatly appreciated. Thank you.
Best, Lorenz
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/
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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/
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.
participants (6)
-
Artie Kushner -
Elaine Meng -
Grundmann,Lorenz Emanuel -
Guillaume Gaullier -
Oliver Clarke -
Tom Goddard