Re: [phenixbb] pdb_redo

From: "Lenin Domínguez" 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: http://www.ncbi.nlm.nih.gov/pubmed/23385452 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 human.) 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 control. 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. -Nat