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

Kit Sang Chu kschu at ucdavis.edu
Thu Mar 19 13:08:52 PDT 2020

Dear Pavel,

Thanks for your prompt reply. I tried phoenix.model_map and it successfully
generates ccp4 and xplor files. However, I fail to understand the xplor
file format for further analysis. Is there any suggested documentation on
xplor (ccp4) format? Visualization on pymol also suggests that my electron
density was truncated by the box boundary. Is there any way to first
centralize the box at the core of the protein, then create a box with a
defined (sub)region of the PDB?


On Thu, Mar 19, 2020 at 7:14 AM Pavel Afonine <pafonine at lbl.gov> wrote:

> 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
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