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

[cathy lawson]

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> 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:-0.555Maximum density:1.20Average density:-0.008Standard deviation:0.049Recommended contour level:0.25 (author)
> 
> 
> 
> 
> 
> 
> 
> By comparison, the map parameters for EMDB 2278 are:
> Minimum density:-9.453Maximum density:15.384Average density:0.048Standard deviation:1.252Recommended contour level:1.35 (emdb)
> 
> 
> 
> 
> 
> 
> 
> And the map parameters for EMDB 6324 are:
> Minimum density:-0.092Maximum density:0.139Average density:0.001Standard deviation:0.005Recommended contour level:0.016 (emdb)
> 
> 
> 
> 
> 
> 
> 
> 
> Thanks,
> Ben Barad
> 
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20150721/cab0e918/attachment.html>