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

Pavel Afonine pafonine at lbl.gov
Thu Mar 19 07:14:42 PDT 2020

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!

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