[phenixbb] pdb_redo

Nathaniel Echols nechols at lbl.gov
Tue Aug 12 04:49:50 PDT 2014

> From: "Lenin Domínguez" <acheron24 at gmail.com>
> Subject: Re: [phenixbb] pdb_redo
> I was wondering about PDB_REDO too. Your command line is priceless, Nat.
> I have one further question: Using phenix.fetch_pdb --maps  shouldn't I be
> able tro reproduce a figure from a paper showing the electron density of a
> ligand?

Well, yes, usually.  But:


The one caveat is that there are a few legitimate manipulations that could
make the figure look slightly different from how it appears in e.g. Coot:

1. Use of a finer FFT grid (d_min/5 or smaller, versus d_min/4 or d_min/3
which are the defaults for Phenix and Coot respectively)
2. Maximum entropy treatment (removes Fourier artifacts, extends
coefficients to high resolution without actually adding information)
3. Map sharpening

(2) and (3) should really be explicitly mentioned, however.  And I have yet
to see a case where these would make the difference between a ligand being
detectable or not by eye.  (Maximum entropy can sometimes improve the
performance of LigandFit but the density is still pretty obvious to a

The maps from PDB_REDO shouldn't be hugely different from the maps that
come out of phenix.maps, so looking at those results would be another

 I have tried using phenix.fetch_pdb, PDB_REDO (conservative and aggresive
> refinement) as well as the data straight from EDS.
> Any thoughts?

Send me the PDB ID (and ligand name) off-list and I'll take a look.

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