[3dem] Voxel Values (Scaling and Units) in cryoEM

[Ludtke, Steven J]

Hi Ben.
If CTF correction and reconstruction have been completed accurately, then the absolute density values should be linearly related to the potential, which most people refer to slightly incorrectly as the electron density. That is to say there is an arbitrary linear transform applied to these values. Different packages use different conventions. In EMAN, for example, we typically normalize the data such that the mean solvent density is set to zero and the scaling is adjusted such that an isosurface containing some specified volume corresponds to an isosurface threshold of 1.0. The zero solvent density simplifies solvent flattening and some other common tasks, but is really just a convenience. Other packages use completely different conventions.

Bottom line is, no, you cannot trust that the numbers you find in the maps have any meaning in an absolute sense.
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu<http://ncmi.bcm.edu>)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Baylor College of Medicine
sludtke at bcm.edu<mailto:sludtke at bcm.edu>





On Jul 21, 2015, at 8:13 PM, Benjamin Barad <ben.barad at ucsf.edu<mailto:ben.barad at ucsf.edu>> wrote:

Hi everyone,

I wonder whether someone could comment on why the numeric voxel values of maps in the EMDB (or elsewhere) have such large differences in their range. Do the absolute values have physical meaning, and if so how should I interpret the vast ranges in scale? What units should be ascribed to them?

Even if they are not physically meaningful, why is there such a dramatic range in scaling?

For some examples, the map parameters for EMDB 5623 are as follows:
Minimum density:-0.555
Maximum density:1.20
Average density:-0.008
Standard deviation:0.049
Recommended contour level:0.25 (author)







By comparison, the map parameters for EMDB 2278 are:
Minimum density:-9.453
Maximum density:15.384
Average density:0.048
Standard deviation:1.252
Recommended contour level:1.35 (emdb)







And the map parameters for EMDB 6324 are:
Minimum density:-0.092
Maximum density:0.139
Average density:0.001
Standard deviation:0.005
Recommended contour level:0.016 (emdb)








Thanks,
Ben Barad

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