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From: "Lenin Domínguez" <<a href="mailto:acheron24@gmail.com">acheron24@gmail.com</a>><br>Subject: Re: [phenixbb] pdb_redo<br>
<span>I was wondering about PDB_REDO too. Your command line is priceless, Nat.<div><br></div>
<div>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?</div></span></blockquote><div><br></div><div>Well, yes, usually. But:</div>
<div><br></div><div><a href="http://www.ncbi.nlm.nih.gov/pubmed/23385452">http://www.ncbi.nlm.nih.gov/pubmed/23385452</a></div><div><br></div><div>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:</div>
<div><br></div><div>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)</div><div>2. Maximum entropy treatment (removes Fourier artifacts, extends coefficients to high resolution without actually adding information)</div>
<div>3. Map sharpening</div><div><br></div><div>(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.)</div>
<div><br></div><div>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.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div>I have tried using phenix.fetch_pdb, PDB_REDO (conservative and aggresive refinement) as well as the data straight from EDS.</div>
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<div>Any thoughts?</div></span></blockquote><div><br></div><div>Send me the PDB ID (and ligand name) off-list and I'll take a look.</div><div><br></div><div>-Nat</div></div></div></div>