[phenixbb] Generating electron density from protein coordinate (PDB)

Kit Sang Chu kschu at ucdavis.edu
Wed Mar 18 19:52:21 PDT 2020

Dear phenix users,

Although phenix in general is used to convert electron density into protein
coordinates (PDB), I am interested in retrieving electron density of an
optimized PDB, hopefully at a resolution of ~1-2A.  Since there could be
manipulation of the coordinate file upstream, some crystal structure
information could be lost.

I notice that phenix generates structure factor from coordinates (assuming
P1 symmetry) by phenix.fmodel. However, the conversion from structure
factor to electron density requires a normalization constant (sum of atomic
form factors). I am still trying to identify the correct function to use to
output a non-binary output format. phenix.maps might work but I am unsure
about the map_type.

If anyone is willing to provide some suggestions, that would be very

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