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Hi Elke,<br>
<br>
you can make ADP restraints stronger by making X-ray target weight
smaller, for example, set wxu_scale weight to something smaller than
the default (1.0). You may need to try a few values to see which one
works best.<br>
<br>
Alternatively, you can make ADP restraints weight, wu, larger than
the default (1.0), which is equivalent.<br>
<br>
Let me know if you have any questions or need help with this!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/25/14, 7:18 AM, Elke De Zitter
wrote:<br>
</div>
<blockquote
cite="mid:9AFB61C71F0E254985F30311D88342F4B61708@ICTS-S-MBX7.luna.kuleuven.be"
type="cite">
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;"><font face="Arial" size="2">Dear Pavel</font>
<div><font face="Arial" size="2"><br>
</font></div>
<div><font face="Arial" size="2">Thank you for the quick
response. After reading this paper and some of its
references, I suppose that Phenix.refine automatically
restraint the anisotropic B-factor calculation. However, I
want to restraint it more because certain atoms have very
long small ellipsoids and atoms in some tyrosine rings are
moving in different directions. Is there a way to play with
the restraints manually?</font></div>
<div><font face="Arial" size="2"><br>
</font></div>
<div><font face="Arial" size="2">Kind regards</font></div>
<div><font face="Arial" size="2">Elke</font><br>
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Elke De Zitter</p>
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PhD student, KU Leuven</p>
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Biochemistry, Molecular and Structural Biology</p>
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<div id="divRpF4014" style="direction: ltr;"><font
color="#000000" face="Tahoma" size="2"><b>Van:</b> Pavel
Afonine [<a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>]<br>
<b>Verzonden:</b> dinsdag 24 juni 2014 14:31<br>
<b>Aan:</b> Elke De Zitter; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Onderwerp:</b> Re: [phenixbb] Anisotropic B-factor
restraints<br>
</font><br>
</div>
<div>Hi Elke,<br>
<br>
phenix.refine uses similarity restraints on anisotropic ADPs
as described here:<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf"
target="_blank">http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/24/14, 5:03 AM, Elke De
Zitter wrote:<br>
</div>
<blockquote type="cite">
<style type="text/css" id="owaParaStyle"></style>
<div style="direction:ltr; font-family:Tahoma;
color:#000000; font-size:10pt">Dear All
<div><br>
</div>
<div>I'm refining a protein structure with a resolution
of 1.25 A, using Phenix GUI version 1.9. I am refining
the B-factors for the protein atoms anisotropic and
those for the water molecules isotropic. How can I
restrain the anisotropic B-factors so that bonded
atoms have similar ellipsoids (like the SIMU and DELU
commands in Shelx making the atoms moving similarly in
direction and amount)?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Elke<br>
<div><br>
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background-color:rgb(255,255,255)">
Elke De Zitter</p>
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padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
PhD student, KU Leuven</p>
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padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Biochemistry, Molecular and Structural
Biology</p>
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font-family:Arial,Helvetica,sans-serif;
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background-color:rgb(255,255,255)">
Celestijnenlaan 200f - bus 2404, 3001 Leuven</p>
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Room 00.84, +32 16 3 26530</p>
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