intensity scaling of multiple cryo EM reconstructions
Dear Chimera Community: We have several electron scattering intensity cubes from cryo EM. We would like to scale the intensity (not the size) of the particle so that we can fairly compare the intensity values in different cubes. We understand that some biophysical principle is required. Does Chimera contain tools related to such principles and the scaling calculations they imply? Thank you very much in advance for your help! Best regards, Peter
Hi Peter, You would need some experimental means of calibrating the intensity scales of two EM maps. I’m not familiar with how this is done. I think one approach is to have something in both samples that is the same and calibrate the intensity scale so that part of the structure is the same in both EM maps. You could get the scale factor that minimize the root-mean-square point-wise difference using the Chimera “vop subtract” command with the minrms option: vop subtract #2 #3 minRMS true which reports in the reply log the scale factor Minimum RMS scale factor for #3 above level 0.036305 subtracted from #2 is 1.2464 Chimera can also measure enclosed area (Tools / Volume Data / Measure Volume and Area or Measure and Color Blobs) and you can try to get the enclosed area to be the same. And you could also try to calibrate two equivalent peaks getting the intensity at the maximum intensity of a feature by adjusting contour level so that feature is just shown. Tom
On Apr 3, 2018, at 11:31 AM, Peter Doerschuk <pd83@cornell.edu> wrote:
Dear Chimera Community: We have several electron scattering intensity cubes from cryo EM. We would like to scale the intensity (not the size) of the particle so that we can fairly compare the intensity values in different cubes. We understand that some biophysical principle is required. Does Chimera contain tools related to such principles and the scaling calculations they imply? Thank you very much in advance for your help! Best regards, Peter
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Forgot to mention the most basic thing. To scale the map intensity values use “vop scale” vop scale #2 factor 1.25 Tom
On Apr 3, 2018, at 12:38 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Peter,
You would need some experimental means of calibrating the intensity scales of two EM maps. I’m not familiar with how this is done. I think one approach is to have something in both samples that is the same and calibrate the intensity scale so that part of the structure is the same in both EM maps. You could get the scale factor that minimize the root-mean-square point-wise difference using the Chimera “vop subtract” command with the minrms option:
vop subtract #2 #3 minRMS true
which reports in the reply log the scale factor
Minimum RMS scale factor for #3 above level 0.036305 subtracted from #2 is 1.2464
Chimera can also measure enclosed area (Tools / Volume Data / Measure Volume and Area or Measure and Color Blobs) and you can try to get the enclosed area to be the same. And you could also try to calibrate two equivalent peaks getting the intensity at the maximum intensity of a feature by adjusting contour level so that feature is just shown.
Tom
On Apr 3, 2018, at 11:31 AM, Peter Doerschuk <pd83@cornell.edu> wrote:
Dear Chimera Community: We have several electron scattering intensity cubes from cryo EM. We would like to scale the intensity (not the size) of the particle so that we can fairly compare the intensity values in different cubes. We understand that some biophysical principle is required. Does Chimera contain tools related to such principles and the scaling calculations they imply? Thank you very much in advance for your help! Best regards, Peter
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Tom: Thank you very much for your very quick response! Best regards, Peter On Tue, 3 Apr 2018, Tom Goddard wrote:
Forgot to mention the most basic thing. To scale the map intensity values use “vop scale”
vop scale #2 factor 1.25
Tom
On Apr 3, 2018, at 12:38 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Peter,
You would need some experimental means of calibrating the intensity scales of two EM maps. I’m not familiar with how this is done. I think one approach is to have something in both samples that is the same and calibrate the intensity scale so that part of the structure is the same in both EM maps. You could get the scale factor that minimize the root-mean-square point-wise difference using the Chimera “vop subtract” command with the minrms option:
vop subtract #2 #3 minRMS true
which reports in the reply log the scale factor
Minimum RMS scale factor for #3 above level 0.036305 subtracted from #2 is 1.2464
Chimera can also measure enclosed area (Tools / Volume Data / Measure Volume and Area or Measure and Color Blobs) and you can try to get the enclosed area to be the same. And you could also try to calibrate two equivalent peaks getting the intensity at the maximum intensity of a feature by adjusting contour level so that feature is just shown.
Tom
On Apr 3, 2018, at 11:31 AM, Peter Doerschuk <pd83@cornell.edu> wrote:
Dear Chimera Community: We have several electron scattering intensity cubes from cryo EM. We would like to scale the intensity (not the size) of the particle so that we can fairly compare the intensity values in different cubes. We understand that some biophysical principle is required. Does Chimera contain tools related to such principles and the scaling calculations they imply? Thank you very much in advance for your help! Best regards, Peter
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Peter Doerschuk -
Tom Goddard