<html>
  <head>
    <meta content="text/html; charset=windows-1252"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    Hi Christian,<br>
    <br>
    somehow this escaped my attention... so was this solved in the end?
    If not please send me files and I will find a solution.<br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 10/31/16 10:55, Christian Roth
      wrote:<br>
    </div>
    <blockquote
      cite="mid:1b6c7433-017e-0923-2eeb-329b30d7d818@gmail.com"
      type="cite">
      <meta content="text/html; charset=windows-1252"
        http-equiv="Content-Type">
      <p><font face="Arial">Not more than 5 I'm afraid. I don't know if
          it would find the right B's using 10 cycles and more, but that
          also increases the running time quite considerably even on
          some of our faster machines.</font></p>
      <p><font face="Arial">Best wishes <br>
        </font></p>
      <p><font face="Arial">Christian<br>
        </font></p>
      <br>
      <div class="moz-cite-prefix">Am 31.10.2016 um 16:46 schrieb
        Dorothee Liebschner:<br>
      </div>
      <blockquote
cite="mid:CAAA+Ob=d-Y__9M-xR5A0sBfhmTwwrBqFsXPMmVCmUq2yvjWRbg@mail.gmail.com"
        type="cite">
        <div dir="ltr">Hi Christian,
          <div><br>
          </div>
          <div>OK, it looks you found a way to prevent the positive
            density by using "realistic" starting B values (of the order
            of that of surrounding protein atoms). </div>
          <div>Did you also try to increase the number of macro-cycles?</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 Mon, Oct 31, 2016 at 9:11 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 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<span class="HOEnZb"><font color="#888888"><br>
                      <br>
                      Christian<br>
                       </font></span></font>
                <div>
                  <div class="h5"><br>
                    <div class="m_-889494717917611925moz-cite-prefix">Am
                      31.10.2016 um 15:59 schrieb Dorothee Liebschner:<br>
                    </div>
                    <blockquote 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="m_-889494717917611925HOEnZb"><font
                                  color="#888888">
                                  <p><font face="Arial"><br>
                                      Christian</font></p>
                                </font></span>
                              <div>
                                <div class="m_-889494717917611925h5">
                                  <p><font face="Arial"><br>
                                    </font></p>
                                  <p><font face="Arial"><br>
                                    </font></p>
                                  <br>
                                  <div
                                    class="m_-889494717917611925m_-3740913058495017715moz-cite-prefix">Am
                                    06.09.2016 um 01:44 schrieb Pavel
                                    Afonine:<br>
                                  </div>
                                </div>
                              </div>
                              <blockquote type="cite">
                                <div>
                                  <div class="m_-889494717917611925h5">
                                    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_-889494717917611925m_-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>
                                            </div>
                                          </blockquote>
                                        </div>
                                      </div>
                                    </blockquote>
                                    <br>
                                    <br>
                                    <fieldset
                                      class="m_-889494717917611925m_-3740913058495017715mimeAttachmentHeader"></fieldset>
                                    <br>
                                  </div>
                                </div>
                                <span>
                                  <pre>______________________________<wbr>_________________
phenixbb mailing list
<a moz-do-not-send="true" class="m_-889494717917611925m_-3740913058495017715moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>
<a moz-do-not-send="true" class="m_-889494717917611925m_-3740913058495017715moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailm<wbr>an/listinfo/phenixbb</a>
Unsubscribe: <a moz-do-not-send="true" class="m_-889494717917611925m_-3740913058495017715moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.o<wbr>rg</a></pre>
    </span></blockquote>
    

  </div>


______________________________<wbr>_________________

phenixbb mailing list

<a moz-do-not-send="true" href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>

<a moz-do-not-send="true" href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailm<wbr>an/listinfo/phenixbb</a>

Unsubscribe: <a moz-do-not-send="true" href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.o<wbr>rg</a>
</blockquote></div>
</div>



</blockquote>
</div></div></div></blockquote></div>
</div>



</blockquote>


<fieldset class="mimeAttachmentHeader"></fieldset>
<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>
</body></html>