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 helpful.

Sincerely,