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

[Penczek, Pawel A]

I loath to bring up the obvious, but outside of possible non-linear transformations
in real space, the relative values in real space are affected by usually poorly defined
power spectrum adjustment in reciprocal space.  This is rarely described or done
in a proper manner.  EMDP has no standard for this adjustment.

More on the subject in my Meth Enz 2010 review on EM image restoration.

In X-rays the situation is different as the final outcome is an atomic model,
which does not require any normalization.

Regards,
Pawel

On Jul 21, 2015, at 9:15 PM, cathy lawson <cathy.lawson at rutgers.edu<mailto:cathy.lawson at rutgers.edu>> wrote:

Hi Ben,

EMDB map density values are generally passed without modification from the depositor's uploaded map (a rare exception is when values need to be inverted to make map object density positive). The variation you observe reflects the wide diversity of tools used by the 3DEM community.

The situation is similar to X-ray crystallography several decades ago, before the normalizing maps to statistical parameters became common practice.

HTH,

Cathy Lawson




On Jul 21, 2015, at 21:13, 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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