[phenixbb] calculating map from pdb

Pavel Afonine pafonine at lbl.gov
Thu Jan 29 07:48:10 PST 2015

Hi Scott,

> I was wondering how to quickly back-compute an electron density map 
> from a PDB using phenix from the command line. I'm assuming it's not 
> hard, but I can't find documentation that would lead me to it.

first you get your PDB file:

phenix.fetch_pdb 1akg --mtz

then compute 2mFo-DFc and residual mFo-DFc maps:

phenix.maps 1akg.pdb 1akg.mtz

If you want model calculated map

phenix.fmodel 1akg.pdb high_resolution=1

this will give your Fourier map of 1A resolution.

We don't have a user-exposed tool to calculate exact electron density 
map from a PDB file.


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