[3dem] Sample density in CryoEM

[Ingvar Lagerstedt]

Hi,
I am looking at correlating the volume of a 3D EM reconstruction with the
theoretical volume of the sample.  To do that I need the density of
sample.  There are several published values for proteins, see for instance
http://www.ncbi.nlm.nih.gov/pubmed/10930825, but values for nucleic acids
are harder to find.  There is also the question what, if any, the thermal
contraction is when snap-freezing a sample.  It may be that any thermal
contraction is to small to be noticable, e.g. water ice contract about
1.8% from 273 K to 95 K, and I expect the uncertainty in the volume
calculation to be larger than that.

By calculating the volume at a series of contour level, I can choose the
level that is closest to the theoretical volume.  It may be necessary to
mask out the background noise before calculating.

Any pointers on this type of calculation appreciated.

Regards,
Ingvar

-- 
Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
Ingvar at ebi.ac.uk