<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
Hi Taylor,<br>
<br>
you are correct, in group B factor refinement overall B factors of
adjacent residues are restrained to be similar (or not too
different). I will fix the documentation, thanks for pointing this
out.<br>
<br>
There isn't much validation done to B factors, so dropping
restraints can indeed lower R-factors but it isn't necessarily clear
whether refined B factors are going to be meaningful. I guess you
can try both and see what produces more meaningful B factors.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/25/19 16:34, Taylor Stevens
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:92459E6D-3F2C-4D07-AA46-4799F4F9D501@caltech.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hello,
<div class=""><br class="">
</div>
<div class="">I am currently refining a low-ish resolution
structure (through the phenix.refine GUI) with phenix version
1.14 and had some questions about the use of restraints in group
ADP refinement. In the phenix.refine documentation (<a
href="https://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-atomic-displacement-parameters-adp-or-b-factors"
class="" moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-atomic-displacement-parameters-adp-or-b-factors</a>)
it is stated that “Group isotropic ADP or TLS refinement do not
use any restraints”, however, this does not seem to be the case.
If I look in the log file I can see the following lines of text
which I believe indicate that the restraints are being applied:</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|-group b-factor refinement (macro cycle = 0;
iterations = 0)————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">| r_work = 0.3331 r_free = 0.3717 target = 5.823062
restraints weight = None |</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|——————————————————————————————————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|-group b-factor refinement (macro cycle = 1;
iterations = 22)————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">| r_work = 0.3331 r_free = 0.3717 target = 5.823062
restraints weight = 821.871|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|——————————————————————————————————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|-group b-factor refinement (macro cycle = 2;
iterations = 22)————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">| r_work = 0.3331 r_free = 0.3717 target = 5.823062
restraints weight = 821.871|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|——————————————————————————————————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|-group b-factor refinement (macro cycle = 3;
iterations = 22)————————|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">| r_work = 0.3331 r_free = 0.3717 target = 5.823062
restraints weight = 821.871|</div>
<div style="margin: 0px; font-stretch: normal; line-height:
normal; font-family: Courier; color: rgba(0, 0, 0, 0.85098);"
class="">|——————————————————————————————————————|</div>
</div>
<div class=""><br class="">
</div>
<div class="">If I manually set the wu parameter to 0 under
“Refinement target weights" nothing changes, however, if I
navigate to "All parameters > ADP settings > Group
B-Factors" in the GUI there is a “Use restraints” box that is
checked by default. If I uncheck this box, there are no longer
any restraints being applied according to the log file, and in
the case of the structure I am refining, there is a substantial
drop in the rfree/rwork. Is this an issue with the program or
documentation? Or am I misunderstanding how the program is
supposed to work? Is it generally a good idea to use group ADP
refinement without restraints?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Taylor</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</body>
</html>