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Hi Phoebe,<br>
<br>
I'm always interested to have a look at unusual cases... Often this
builds knowledge and helps to improve methodology. Would you mind
sending me files (data and model) so that I can investigate what's
going on?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/12/15 8:18 AM, Phoebe A. Rice
wrote:<br>
</div>
<blockquote
cite="mid:089821C8F2223D4DBFC0B8B4B224C6733796F24F@xm-mbx-08-prod.ad.uchicago.edu"
type="cite">
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">I've been refining a 3.4A structure
(now using dev-1951) and find that anything besides TLS (with
multiple groups at least) makes Rs go up. A lot. And I am
asking it to optimize weights.<br>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<p>++++++++++++++++++++++++++++++++++++++++++</p>
<p>Phoebe A. Rice<br>
Dept. of Biochemistry & Molecular Biology<br>
The University of Chicago</p>
<a moz-do-not-send="true" href="mailto:PRice@uchicago.edu">PRice@uchicago.edu</a><br>
</div>
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font-size: 16px">
<hr tabindex="-1">
<div id="divRpF49546" style="direction: ltr;"><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] on behalf of Pavel
Afonine [<a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>]<br>
<b>Sent:</b> Thursday, March 12, 2015 12:35 AM<br>
<b>To:</b> 李翔; PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] Group B factor refinement
not working for low resolution data<br>
</font><br>
</div>
<div>Hello Xiang,<br>
<br>
short answer: try refining with all defaults plus weight
optimization. If that does not go well please send me data
and model files and I will do my best to make it work.<br>
<br>
Longer answer: the way B-factor restraints are implemented
in phenix.refine (that you can learn about in corresponding
paper) allows refining individual Bs at any resolution. So
this is why this is the first choice to try. If that does
not work it's best to a) let us know and b) try group B
refinement.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/11/15 7:30 PM, 李翔 wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I am working on my ~6A data with molecular
replacement method. The MR works out and after rigid
body and xyz refinement the result is OK. However,
when I tried the ADP refinement with Group B factor
option in PHENIX GUI, the R factor significantly
increased as well as the B-factor. Any expert can help
me to take a look and give some suggestions please?</div>
<div><br>
</div>
<div>Thank you very much for your help!</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Xiang</div>
<div>
<div><br>
</div>
-- <br>
<div class="gmail_signature">Li Xiang <br>
Department of chemistry,<br>
University of Michigan<br>
Email:<a moz-do-not-send="true"
href="mailto:lixiang1642@gmail.com"
target="_blank">lixiang1642@gmail.com</a></div>
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