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    <p><font face="Arial">Hi Dorothee</font></p>
    <p><font face="Arial">to answer your questions</font></p>
    <p><font face="Arial">The resolution is about 2.0 Ang and the
        average B around 55. The Bfactor from the ligand was set to the
        default of 20 by Coot when placing the ligands.</font></p>
    <p><font face="Arial">It seems that setting the B-value to the
        average B of the structure nearly solves the problem (most of
        the ligand fine, just parts with unusuallly high values).
        Setting it to a bit higher values 70 for a start and the ligand
        refines fine. <br>
      </font></p>
    <font face="Arial">I noticed that in the first macrocycle with and
      initial factor of 20, the B's are nearly unchanged (20 +- 2) Red
      diff density appears as expected. In the second cycle The
      minimizer let the B-factors "explode" to about 200 and that
      basically is the overkill and it never recovers.<br>
      <br>
      HTH<br>
      <br>
      Cheers<br>
      <br>
      Christian<br>
       </font><br>
    <div class="moz-cite-prefix">Am 31.10.2016 um 15:59 schrieb Dorothee
      Liebschner:<br>
    </div>
    <blockquote
cite="mid:CAAA+ObmpLqo7-6YVLC0aBGb+oZmZ4ek3G6ZaVr-+LeG0RKcbJw@mail.gmail.com"
      type="cite">
      <div dir="ltr">Hi Christian,
        <div><br>
        </div>
        <div>Could you answer the following questions:</div>
        <div><br>
        </div>
        <div>- what is the resolution of the data set?</div>
        <div>- what is average B of the protein?</div>
        <div>- what are the starting B values for the ligand?</div>
        <div>- did you try lowering starting B for the ligand and repeat
          the refinement? Is this behavior reproducible with different
          refinement options?</div>
        <div><br>
        </div>
        <div>Best wishes,</div>
        <div><br>
        </div>
        <div>Dorothee</div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Sun, Oct 30, 2016 at 11:06 AM,
          Christian Roth <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div bgcolor="#FFFFFF" text="#000000">
              <p><font face="Arial">Hi Phenix Team,</font></p>
              <p><font face="Arial">regarding that ligand issue in this
                  thread, we observed the same with a ligand in one of
                  our structures now. After refinement the ligand is
                  surrounded by pos diff density and the B-Factors are
                  around 200 (way above any useful range in that case).</font></p>
              <p><font face="Arial">The cif was generated using elbow
                  and phenix runs with options Real space refinement,
                  TLS on, individual B, and optimizing weights. Nothing
                  crazy.</font></p>
              <p><font face="Arial">Could you find a solution for the
                  previous case and give us some tips?</font></p>
              <p><font face="Arial"><br>
                  Cheers</font></p>
              <span class="HOEnZb"><font color="#888888">
                  <p><font face="Arial"><br>
                      Christian</font></p>
                </font></span>
              <div>
                <div class="h5">
                  <p><font face="Arial"><br>
                    </font></p>
                  <p><font face="Arial"><br>
                    </font></p>
                  <br>
                  <div class="m_-3740913058495017715moz-cite-prefix">Am
                    06.09.2016 um 01:44 schrieb Pavel Afonine:<br>
                  </div>
                </div>
              </div>
              <blockquote type="cite">
                <div>
                  <div class="h5"> Hi Tongqin,<br>
                    <br>
                    I second Dorothee's point that we need more
                    information to resolve this problem. If you still
                    have this problem please send me inputs files (data,
                    model, .eff from last refinement, as well as ligand
                    .CIF files if any) and I will look into this once I
                    have files.<br>
                    <br>
                    Pavel<br>
                    <br>
                    <div class="m_-3740913058495017715moz-cite-prefix">On
                      8/31/16 09:29, Dorothee Liebschner wrote:<br>
                    </div>
                    <blockquote type="cite">
                      <div dir="ltr">Hi Tongqin,
                        <div><br>
                        </div>
                        <div>It is a bit difficult to diagnose with the
                          information you provided. Could you please
                          answer the following questions?<br>
                          <div><br>
                          </div>
                          <div>- Did you also try to reset the B-factors
                            to similar values than neighboring atoms?</div>
                          <div>F.ex. the average B-factor in the model
                            could be 50 A**2, but in the ligand region,
                            it could be lower, let's say 20 A**2. Then
                            the starting value using average B is quite
                            far from the likely B-factor of the ligand.</div>
                          <div><br>
                          </div>
                          <div>- What refinement strategy do you apply?
                            How many macro-cycles? Do you use any
                            non-default parameters for B-factor
                            refinement?</div>
                        </div>
                        <div><br>
                        </div>
                        <div>- Which Phenix version are you using?</div>
                        <div><br>
                        </div>
                        <div>Best wishes,</div>
                        <div><br>
                        </div>
                        <div>Dorothee</div>
                      </div>
                      <div class="gmail_extra"><br>
                        <div class="gmail_quote">On Wed, Aug 31, 2016 at
                          7:12 AM, Zhou, Tongqing (NIH/VRC) [E] <span
                            dir="ltr">&lt;<a moz-do-not-send="true"
                              href="mailto:tzhou@mail.nih.gov"
                              target="_blank">tzhou@mail.nih.gov</a>&gt;</span>
                          wrote:<br>
                          <blockquote class="gmail_quote"
                            style="margin:0 0 0 .8ex;border-left:1px
                            #ccc solid;padding-left:1ex">
                            <div link="#0563C1" vlink="#954F72"
                              lang="EN-US">
                              <div>
                                <p class="MsoNormal">Dear All,</p>
                                <p class="MsoNormal"> </p>
                                <p class="MsoNormal">I am refining a
                                  structure with diffraction to 2.2A
                                  resolution and 95 % overall
                                  completeness. Now the Rs are at 18%
                                  and 23%, respectively. But the program
                                  failed to refine B factors for several
                                  ligands, atoms had high B factors
                                  while showing positive Fo-Fc map
                                  around them. Occupancy was set to 1
                                  and I also tried to reset B to mean B
                                  of the whole PDB. Any of you seeing
                                  this phenomenon? Thanks!</p>
                                <p class="MsoNormal"> </p>
                                <p class="MsoNormal">Shown below is
                                  HEPES that has high B factor and
                                  positive density around it after
                                  refinement:<br>
                                </p>
                              </div>
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