<div dir="ltr">On Sun, Aug 24, 2014 at 9:34 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">why not? You can arbitrarily choose one model and map as a reference
and overlay the rest over it. Phenix tools such as "Structure
comparison" or lower level ones such as phenix.superpose_maps and
phenix.superpose_pdbs should help here. Nat spent time on this so I
hope he offers more advice on this once he sees this email.<br></div></blockquote><div><br></div><div>There isn't much to add to this, other than a more thorough description of what the programs do, which as usual, is not (yet) mentioned in our documentation:</div>
<div><br></div><div>- phenix.superpose_maps: given two models and two MTZ files containing map coefficients, superposes the models (using user-provided selections if desired), moves them into a P1 box (where all sites > [0,0,0]), then transforms the selected maps to follow. Only works on one pair of map coefficients at a time, but allows any type of complex array to be used.</div>
<div><br></div><div>- structure comparison: given M models containing N copies of chain X, and M corresponding MTZ files, extracts all copies of chain X, superposes in a P1 box, transforms the maps to follow. Works with any arbitrary number of models or chains, but limited to the most common map types (2mFo-DFc, mFo-DFc, anomalous).</div>
<div><br></div><div>We can make these methods more flexible if necessary - this is probably another set of code that's overdue for refactoring and consolidation anyway.</div><div><br></div><div>-Nat</div>
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