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    Hi,<br>
    <br>
    I agree: having different occupancies for covalently linked atoms
    doesn't make much sense! If ligand is partially occupied then simply
    refine its overall occupancy.<br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 2/7/16 14:44, Christian Roth wrote:<br>
    </div>
    <blockquote
cite="mid:CA+hUm_NW94zQO8SZn1yC0C1jB8nDz-vbiNNtdWjOjtOQ6Mo+SQ@mail.gmail.com"
      type="cite">
      <div dir="ltr">
        <div>Dear Chris,</div>
        <div><br>
        </div>
        <div>personally I wouldn't go for different occupancies in one
          ligand and set everything to 1 or everything to a values of
          your choice (constraint groups necessary). I would also check
          the electron density and the RSRZ for your ligands. The
          B-factors look quite high. Concerning the outliers, that is
          due to slight variations in the boundaries. Your outliers are
          probably exactly on a boundary. I wouldn't worry too much
          about that. They are fine.</div>
        <div><br>
        </div>
        <div>Cheers</div>
        <div><br>
        </div>
        <div>Christian</div>
        <div><br>
        </div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Sat, Feb 6, 2016 at 12:19 PM, Chris
          Fage <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:cdfage@gmail.com" target="_blank">cdfage@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 dir="ltr">Hello,
              <div><br>
              </div>
              <div>The non-unity occupancies were scattered among
                different glucose (and BICINE) molecules, as shown
                below. But, again, I think the occupancy refinement
                doesn't contribute much to the final model/maps.</div>
              <div><br>
              </div>
              <div>Another concern of mind is that phenix.refine reports
                no Ramachandran outliers in the results, but the plot
                in�Coot lists 5. I'm tempted to trust Coot here and
                attempt to fix these boundary cases.�<span></span></div>
              <div><br>
              </div>
              <div>Best,</div>
              <div>Chris</div>
              <div><br>
              </div>
              <div>
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              </div>
            </div>
            <div class="HOEnZb">
              <div class="h5">
                <div class="gmail_extra"><br>
                  <div class="gmail_quote">On Fri, Feb 5, 2016 at 7:34
                    PM, Christian Roth <span dir="ltr">&lt;<a
                        moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a></a>&gt;</span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0 0 0
                      .8ex;border-left:1px #ccc solid;padding-left:1ex">
                      <p dir="ltr">Hi Chris, what would concern me is
                        that one glucose have atoms with different
                        occupancies or all of them. That is chemically
                        unlikely. You should define sensible constraint
                        groups, I think.</p>
                      <p dir="ltr">Cheers Christian</p>
                      <div class="gmail_quote">
                        <div>
                          <div>On 5 Feb 2016 18:09, "Chris Fage" &lt;<a
                              moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:cdfage@gmail.com">cdfage@gmail.com</a></a>&gt;
                            wrote:<br type="attribution">
                          </div>
                        </div>
                        <blockquote class="gmail_quote" style="margin:0
                          0 0 .8ex;border-left:1px #ccc
                          solid;padding-left:1ex">
                          <div>
                            <div>
                              <div dir="ltr">Hi Pavel,
                                <div><br>
                                </div>
                                <div>The B-factors of these atoms are
                                  quite high (most are 100+), so maybe
                                  the occupancy is compensating as you
                                  said. After refinement, the maps don't
                                  look much different. Perhaps it's not
                                  worth bothering with occupancy
                                  refinement, then?</div>
                                <div><br>
                                </div>
                                <div>I think you got my question. I was
                                  asking if it is unusual that only 5/93
                                  occupancies were refined to values
                                  other than 0 or 1.</div>
                                <div><br>
                                </div>
                                <div>Best,</div>
                                <div>Chris</div>
                              </div>
                              <div class="gmail_extra"><br>
                                <div class="gmail_quote">On Fri, Feb 5,
                                  2016 at 6:38 PM, Pavel Afonine <span
                                    dir="ltr">&lt;<a
                                      moz-do-not-send="true"><a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></a>&gt;</span>
                                  wrote:<br>
                                  <blockquote class="gmail_quote"
                                    style="margin:0 0 0
                                    .8ex;border-left:1px #ccc
                                    solid;padding-left:1ex">Hi Chris,<span><br>
                                      <br>
                                      <blockquote class="gmail_quote"
                                        style="margin:0 0 0
                                        .8ex;border-left:1px #ccc
                                        solid;padding-left:1ex">
                                        I've built several glucose
                                        molecules from my cryosolution
                                        into regions of weaker electron
                                        density. Attempting to refine
                                        the occupancies of the
                                        corresponding atoms, I set the
                                        value of each to 0.25 in the pdb
                                        file. However, after running
                                        phenix.refine, most of the atoms
                                        still have occupancies of 1.00:<br>
                                      </blockquote>
                                      <br>
                                    </span>
                                    perhaps they are fully occupied but
                                    highly mobile which explains weak
                                    density? Or B-factor refines to
                                    larger value so that occupancy tries
                                    to compensate? How maps look like
                                    after refinement?<span><br>
                                      <br>
                                      <blockquote class="gmail_quote"
                                        style="margin:0 0 0
                                        .8ex;border-left:1px #ccc
                                        solid;padding-left:1ex">
                                        14 atoms with occ = 0.00<br>
                                        5 atoms with 0.00 &lt; occ &lt;
                                        1.00<br>
                                        74 atoms with occ = 1.00<br>
                                        <br>
                                        Is this unusual?<br>
                                      </blockquote>
                                      <br>
                                    </span>
                                    Do you mean is it unusual to have 5
                                    atoms in your structure with
                                    occupancies between 0 and 1? Hm.. I
                                    don't know, may be not! I think I'm
                                    not understanding what's the real
                                    question here..<span><font
                                        color="#888888"><br>
                                        <br>
                                        Pavel<br>
                                        <br>
                                      </font></span></blockquote>
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