<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Pavel</div>According to your mail from yesterday I wonder how can I treat Ramachandran outliers in very large molecules (close to 9000 residues). Despite <div>R=0.22 and Rfree=0.29 there is still a lot of changes to do. It was molecular replacement project with 28 subunits 14 and 14 and with about 50% identity and some small insertions deletions. map is 3.4 A and after permissive CC1/2 decision - about 3.05 . A lot of clashes, a lot of Ramachandran</div><div>outliers ( about 6% after COOT Ramachandran improvement and about 9% after refinement.</div><div>What I need is not elimination of manual intervention, but minimisation of it : - \</div><div>FF<br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Dr Felix Frolow <br>Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology<br>Tel Aviv University 69978, Israel<br><br>Acta Crystallographica F, co-editor<br><br>e-mail: <a href="mailto:mbfrolow@post.tau.ac.il">mbfrolow@post.tau.ac.il</a><br>Tel: ++972-3640-8723<br>Fax: ++972-3640-9407<br>Cellular: 0547 459 608</span>
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<br><div><div>On Jul 22, 2013, at 20:21 , Pavel Afonine <<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div class="moz-cite-prefix">Hi Joel,<br>
<br>
from <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/version_docs/dev-1439/CHANGES">http://www.phenix-online.org/version_docs/dev-1439/CHANGES</a> :<br>
<br>
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- Local RSR: residue-by-residue, replaces old fix_rotamers option<br>
- fits both main chain and sidechain<br>
- only applies to residues with rotamer outlier, poor CC, or
clashes<br>
- new residue fit serves as torsion restrains for subsequent
macro-cycle<br>
- currently not performed when explicit hydrogens present<br>
<br>
To turn this off simply exclude real-space refinement from
refinement strategy.<br>
<br>
Note, RSR above means Real-Space-Refinement, and not
Reciprocal-Space-Refinement.<br>
<br>
Pavel<br>
<br>
<br>
On 7/22/13 9:33 AM, Joseph Noel wrote:<br>
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Dear Pavel,
<div>To clarify, in the latest nightly build, 1435, do you have to
click on real space refinement to carry out side chain rotamer
fitting? If you just refine xyz I assume side chain rotamer
fitting is not enabled, correct?</div>
<div>Joe Noel<br>
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<br>
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