[phenixbb] cryo-EM density modification

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Mon Nov 18 17:45:30 PST 2019

Hi Phenix cryo-EM users,

For those of you trying out density modification for cryo-EM
(phenix.resolve_cryo_em), the automatic estimation of resolution in the
current version uses unmasked resolution instead of masked, in some cases
resulting in running density modification at too low a resolution.

Consequently it is best with this version if you specify your nominal
resolution.  To run it you can type:

phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \
   seq_file=seq.dat resolution=3.5

or something like that.  It requires the current nightly build to run.

You might also want to wait just a short while and a version that has this
and a few other bugs fixed, a GUI, full documentation, and an example
dataset will be out (hopefully this week).

The full description of the method is at

Let me know of any problems or suggestions!

All the best,
Tom T

Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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