Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash.
Hi Abhilash, The ChimeraX "volume subtract" command has an option "minrms true" (minimize root mean square) that will find the scale factor for a second map such that when the scaled second map is subtracted from the first map the sum of the root mean square residuals is minimum. The scale factor is reported in the log. https://plato.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract Here's an example. open 43675 from emdb open 43676 from emdb open 8vyq open 8vyr matchmaker #4 to #3 view position #2 sameas #4 volume #1 level 0.5 volume #2 level 0.1 volume #1 region 0,0,0,255,255,115 volume subtract #2,1 minrms true > Minimum RMS scale factor for "emdb 43675 #1" above level 0.5 is 0.14031 Several important points to note. The maps need to be aligned with each other. I do that in the example by opening fit atomic models, moving the second atomic model to align with the first, and then moving the second map to the same position as the moved atomic model. For the subtraction to give a useful scale factor you want to limit it to a region where the two maps mostly overlap. I cropped the first map to such a region in the example. Then I subtracted the first map from the second -- the RMS is minimized within the contour level of the map that is being subtracted (#1 in this example), so you also might want to choose the contour level. The result in the example is that map #1 needs to be multiplied by 0.13696 to minimize the RMS difference. I think this is prone to giving a bad scaling factor if there is significant non-overlapping density for the region within the map contour level. You can judge how well the scaling worked by looking at how much density is left in the difference map. Tom 
On May 30, 2025, at 10:58 AM, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis.
I know I could scale them using vop scale, but I am wondering which of the parameters I should use.
Thanks in advance for your suggestions.
Abhilash.
_______________________________________________ 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/
Thank you very much. That is very helpful. Regards Abhilash. On May 30, 2025, at 11:50 AM, Tom Goddard <goddard@sonic.net> wrote: Hi Abhilash, The ChimeraX "volume subtract" command has an option "minrms true" (minimize root mean square) that will find the scale factor for a second map such that when the scaled second map is subtracted from the first map the sum of the root mean square residuals is minimum. The scale factor is reported in the log. https://plato.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract Here's an example. open 43675 from emdb open 43676 from emdb open 8vyq open 8vyr matchmaker #4 to #3 view position #2 sameas #4 volume #1 level 0.5 volume #2 level 0.1 volume #1 region 0,0,0,255,255,115 volume subtract #2,1 minrms true
Minimum RMS scale factor for "emdb 43675 #1" above level 0.5 is 0.14031
Several important points to note. The maps need to be aligned with each other. I do that in the example by opening fit atomic models, moving the second atomic model to align with the first, and then moving the second map to the same position as the moved atomic model. For the subtraction to give a useful scale factor you want to limit it to a region where the two maps mostly overlap. I cropped the first map to such a region in the example. Then I subtracted the first map from the second -- the RMS is minimized within the contour level of the map that is being subtracted (#1 in this example), so you also might want to choose the contour level. The result in the example is that map #1 needs to be multiplied by 0.13696 to minimize the RMS difference. I think this is prone to giving a bad scaling factor if there is significant non-overlapping density for the region within the map contour level. You can judge how well the scaling worked by looking at how much density is left in the difference map. Tom <minrms.png> On May 30, 2025, at 10:58 AM, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash. _______________________________________________ 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 Abhilash, Comparing cryo-EM maps at different resolutions is not a straightforward task. You should first normalize (match) the power spectra of the maps you want to compare to ensure that any differences you see are not due to differences in map filtering, i.e. amplitude weights. To match the power spectra of two maps, you can use, for example, the e2proc3d.py command from EMAN2: e2proc3d.py map1-resampled.mrc map1-resampled-matched.mrc --matchto map2.mrc For this to work, maps should be at the same box size and pixel size (which you can achieve with 'vop resample' from ChimeraX if not already the case). Consider that you will always be limited by the lowest resolution map, so that should be your "reference". For a more detailed discussion please see Joseph et al 2020: https://doi.org/10.1021/acs.jcim.9b01103 Best wishes, -- Ricardo Diogo Righetto Em sex., 30 de mai. de 2025 às 22:05, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escreveu:
Thank you very much. That is very helpful.
Regards
Abhilash.
On May 30, 2025, at 11:50 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Abhilash,
The ChimeraX "volume subtract" command has an option "minrms true" (minimize root mean square) that will find the scale factor for a second map such that when the scaled second map is subtracted from the first map the sum of the root mean square residuals is minimum. The scale factor is reported in the log.
https://plato.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract
Here's an example.
open 43675 from emdb open 43676 from emdb open 8vyq open 8vyr matchmaker #4 to #3 view position #2 sameas #4 volume #1 level 0.5 volume #2 level 0.1 volume #1 region 0,0,0,255,255,115 volume subtract #2,1 minrms true
Minimum RMS scale factor for "emdb 43675 #1" above level 0.5 is 0.14031
Several important points to note. The maps need to be aligned with each other. I do that in the example by opening fit atomic models, moving the second atomic model to align with the first, and then moving the second map to the same position as the moved atomic model. For the subtraction to give a useful scale factor you want to limit it to a region where the two maps mostly overlap. I cropped the first map to such a region in the example. Then I subtracted the first map from the second -- the RMS is minimized within the contour level of the map that is being subtracted (#1 in this example), so you also might want to choose the contour level. The result in the example is that map #1 needs to be multiplied by 0.13696 to minimize the RMS difference. I think this is prone to giving a bad scaling factor if there is significant non-overlapping density for the region within the map contour level. You can judge how well the scaling worked by looking at how much density is left in the difference map.
Tom
<minrms.png>
On May 30, 2025, at 10:58 AM, Abhilash Padavannil via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis.
I know I could scale them using vop scale, but I am wondering which of the parameters I should use.
Thanks in advance for your suggestions.
Abhilash.
_______________________________________________ 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 Ricardo, Thank you very much, this is very helpful. Regards Abhilash. On Jun 2, 2025, at 2:42 AM, Ricardo Righetto <ricardorighetto@GMAIL.COM> wrote: Dear Abhilash, Comparing cryo-EM maps at different resolutions is not a straightforward task. You should first normalize (match) the power spectra of the maps you want to compare to ensure that any differences you see are not due to differences in map filtering, i.e. amplitude weights. To match the power spectra of two maps, you can use, for example, the e2proc3d.py command from EMAN2: e2proc3d.py map1-resampled.mrc map1-resampled-matched.mrc --matchto map2.mrc For this to work, maps should be at the same box size and pixel size (which you can achieve with 'vop resample' from ChimeraX if not already the case). Consider that you will always be limited by the lowest resolution map, so that should be your "reference". For a more detailed discussion please see Joseph et al 2020: https://doi.org/10.1021/acs.jcim.9b01103 Best wishes, -- Ricardo Diogo Righetto Em sex., 30 de mai. de 2025 às 22:05, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> escreveu: Thank you very much. That is very helpful. Regards Abhilash. On May 30, 2025, at 11:50 AM, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: Hi Abhilash, The ChimeraX "volume subtract" command has an option "minrms true" (minimize root mean square) that will find the scale factor for a second map such that when the scaled second map is subtracted from the first map the sum of the root mean square residuals is minimum. The scale factor is reported in the log. https://plato.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract Here's an example. open 43675 from emdb open 43676 from emdb open 8vyq open 8vyr matchmaker #4 to #3 view position #2 sameas #4 volume #1 level 0.5 volume #2 level 0.1 volume #1 region 0,0,0,255,255,115 volume subtract #2,1 minrms true
Minimum RMS scale factor for "emdb 43675 #1" above level 0.5 is 0.14031
Several important points to note. The maps need to be aligned with each other. I do that in the example by opening fit atomic models, moving the second atomic model to align with the first, and then moving the second map to the same position as the moved atomic model. For the subtraction to give a useful scale factor you want to limit it to a region where the two maps mostly overlap. I cropped the first map to such a region in the example. Then I subtracted the first map from the second -- the RMS is minimized within the contour level of the map that is being subtracted (#1 in this example), so you also might want to choose the contour level. The result in the example is that map #1 needs to be multiplied by 0.13696 to minimize the RMS difference. I think this is prone to giving a bad scaling factor if there is significant non-overlapping density for the region within the map contour level. You can judge how well the scaling worked by looking at how much density is left in the difference map. Tom <minrms.png> On May 30, 2025, at 10:58 AM, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash. _______________________________________________ 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/ _______________________________________________ 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/
participants (3)
-
Abhilash Padavannil -
Ricardo Righetto -
Tom Goddard