Hi Simon,
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.
you can use phenix.fmodel to generate a Fourier image of model electron density distribution at specified resolution just like this (typing from memory, check syntax) phenix.fmodel model.pdb high_res=2.3 This will generate the exact map, then Fourier transform it and retain and output Fourier map coefficients up to specified (high_res) resolution. You can also cut it at low-res end: using low_res keyword. You can convert the output of the above command into real map using phenix.mtz2map map_coeffs.mtz Also, you can calculate exact density distribution using phenix.model_map model.pdb These are a few pointers for you to play with and see if you get what you want.. Let us know if you have any questions or need help. Good luck! Pavel