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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>
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cite="mid:089821C8F2223D4DBFC0B8B4B224C6733796F24F@xm-mbx-08-prod.ad.uchicago.edu"
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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>
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              <p>++++++++++++++++++++++++++++++++++++++++++</p>
              <p>Phoebe A. Rice<br>
                Dept. of Biochemistry &amp; Molecular Biology<br>
                The University of Chicago</p>
              <a moz-do-not-send="true" href="mailto:PRice@uchicago.edu">PRice@uchicago.edu</a><br>
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          <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>
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          <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>
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              <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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