<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Elke,<br>
<br>
could you please send me data and model files, and indicate residues
that you think have incorrect B-factors?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/26/14, 6:31 AM, Elke De Zitter
wrote:<br>
</div>
<blockquote
cite="mid:9AFB61C71F0E254985F30311D88342F4B6294B@ICTS-S-MBX7.luna.kuleuven.be"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<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">I played with wxu_scale and wu
several times. When wu = 0, this unrestrained refinement
results in totally unrealistic ADP's. However, if I use wu =
1, wu = 5 or wu = 20, I always get the same results. Is this
normal? On the bottom of this e-mail, you can find the
target weight settings (for wu = 20).</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></div>
<div><font face="Arial" size="2"><br>
</font></div>
<div>
<div>target_weights {</div>
<div> optimize_xyz_weight = False</div>
<div> optimize_adp_weight = False</div>
<div> wxc_scale = 0.5</div>
<div> wxu_scale = 1</div>
<div> wc = 1</div>
<div> wu = 20</div>
<div> fix_wxc = None</div>
<div> fix_wxu = None</div>
<div> shake_sites = True</div>
<div> shake_adp = 10</div>
<div> regularize_ncycles = 50</div>
<div> verbose = 1</div>
<div> wnc_scale = 0.5</div>
<div> wnu_scale = 1</div>
<div> rmsd_cutoff_for_gradient_filtering = 3</div>
<div> force_optimize_weights = False</div>
<div> weight_selection_criteria {</div>
<div> bonds_rmsd = None</div>
<div> angles_rmsd = None</div>
<div> r_free_minus_r_work = None</div>
<div> r_free_range_width = None</div>
<div> mean_diff_b_iso_bonded_fraction = None</div>
<div> min_diff_b_iso_bonded = None</div>
</div>
<div>
<div><font face="Arial" size="2"><br>
</font>
<div>
<div>
<div>
<p style="margin-right:0px; margin-left:0px;
padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px; background-color:rgb(255,255,255)">
Elke De Zitter</p>
<p style="font-size: 12px; font-family: Arial,
Helvetica, sans-serif; margin-right: 0px;
margin-left: 0px; padding: 0px; border: 0px;
background-color: rgb(255, 255, 255);">
PhD student, KU Leuven</p>
<p style="font-size: 12px; font-family: Arial,
Helvetica, sans-serif; margin-right: 0px;
margin-left: 0px; padding: 0px; border: 0px;
background-color: rgb(255, 255, 255);">
Biochemistry, Molecular and Structural Biology</p>
<p style="font-size: 12px; font-family: Arial,
Helvetica, sans-serif; margin-right: 0px;
margin-left: 0px; padding: 0px; border: 0px;
background-color: rgb(255, 255, 255);">
Celestijnenlaan 200f - bus 2404, 3001 Leuven</p>
<p style="font-size: 12px; font-family: Arial,
Helvetica, sans-serif; margin-right: 0px;
margin-left: 0px; padding: 0px; border: 0px;
background-color: rgb(255, 255, 255);">
Room 00.84, +32 16 3 26530</p>
</div>
</div>
</div>
</div>
<div style="font-family: Times New Roman; color: #000000;
font-size: 16px">
<hr tabindex="-1">
<div id="divRpF642615" 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> woensdag 25 juni 2014 18:22<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>
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 type="cite">
<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>
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<p style="margin-right:0px; margin-left:0px;
padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Elke De Zitter</p>
<p style="margin-right:0px; margin-left:0px;
padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
PhD student, KU Leuven</p>
<p style="margin-right:0px; margin-left:0px;
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>
<p style="margin-right:0px; margin-left:0px;
padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Celestijnenlaan 200f - bus 2404, 3001 Leuven</p>
<p style="margin-right:0px; margin-left:0px;
padding:0px; border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Room 00.84, +32 16 3 26530</p>
</div>
</div>
</div>
</div>
<div style="font-family:Times New Roman;
color:#000000; font-size:16px">
<hr tabindex="-1">
<div id="divRpF4014" style="direction:ltr"><font
color="#000000" face="Tahoma" size="2"><b>Van:</b>
Pavel Afonine [<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>]<br>
<b>Verzonden:</b> dinsdag 24 juni 2014 14:31<br>
<b>Aan:</b> Elke De Zitter; <a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:phenixbb@phenix-online.org"
target="_blank">
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>
<div style="font-family:Tahoma;
font-size:13px">
<div style="font-family:Tahoma;
font-size:13px">
<div style="font-family:Tahoma;
font-size:13px">
<p style="margin-right:0px;
margin-left:0px; padding:0px;
border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Elke De Zitter</p>
<p style="margin-right:0px;
margin-left:0px; padding:0px;
border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
PhD student, KU Leuven</p>
<p style="margin-right:0px;
margin-left:0px; 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>
<p style="margin-right:0px;
margin-left:0px; padding:0px;
border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Celestijnenlaan 200f - bus 2404,
3001 Leuven</p>
<p style="margin-right:0px;
margin-left:0px; padding:0px;
border:0px;
font-family:Arial,Helvetica,sans-serif;
font-size:12px;
background-color:rgb(255,255,255)">
Room 00.84, +32 16 3 26530</p>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"
target="_blank"></fieldset>
<br>
<pre>_______________________________________________
phenixbb mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</body>
</html>