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    Hi All,<br>
    <br>
    FWIW, this scenario is described in <br>
    <br>
    "13 typical occupancy refinement scenarios and available options in
    phenix.refine" article here<br>
    <br>
    <a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/">http://phenix-online.org/newsletter/</a><br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 1/15/16 12:30, Helena Taberman
      wrote:<br>
    </div>
    <blockquote cite="mid:128D914F-94DF-494F-829A-4BF561BF3604@uef.fi"
      type="cite">
      <meta http-equiv="Content-Type" content="text/html;
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      <div><br>
      </div>
      <div>Thank you for your help indeed! Renaming them would have
        never crossed my mind!</div>
      <div><br>
      </div>
      <div>Best regards,</div>
      <div><br>
      </div>
      <div>Helena</div>
      <div><br>
        On 15.1.2016, at 22.27, Oleg Sobolev &lt;<a
          moz-do-not-send="true" href="mailto:osobolev@lbl.gov"><a class="moz-txt-link-abbreviated" href="mailto:osobolev@lbl.gov">osobolev@lbl.gov</a></a>&gt;
        wrote:<br>
        <br>
      </div>
      <blockquote type="cite">
        <div>
          <div dir="ltr">Hi Helena,
            <div><br>
            </div>
            <div>I just spotted that residue 249 is close to 252. To
              resolve this, you will have to rename conformations of
              residue 249 (exchange A and B altlocs), assing all partial
              occupancies to 0.5 to make things simple and add it to
              selections:</div>
            <div><br>
            </div>
            <div>
              <div>selection = chain A and (resseq 252 or resseq 249)
                and altloc A</div>
              <div>selection = chain A and (resseq 252 or resseq 249)
                and altloc B or chain S and resseq 1702 and altloc B</div>
            </div>
            <div><br>
            </div>
            <div>Renaming is necessary because conformaion B of residue
              249 is close to conformation B of residue 252.</div>
            <div><br>
            </div>
            <div>Best regards,</div>
            <div>Oleg Sobolev.</div>
          </div>
          <div class="gmail_extra"><br>
            <div class="gmail_quote">On Fri, Jan 15, 2016 at 12:13 PM,
              Oleg Sobolev <span dir="ltr">
                &lt;<a moz-do-not-send="true"
                  href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.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 dir="ltr">Hi Helena,
                  <div><br>
                  </div>
                  <div>The problem was in altlocs, occupancies and
                    selections.<br>
                  </div>
                  <div><br>
                  </div>
                  <div>First, simple case of 249 residue. I don't see
                    why residue 249 is relevant to 252 or to water 1702
                    because it is rather far from them. Therefore it
                    should be treated separately. Residue 249 simply has
                    2 alternative conformations of side chain (including
                    CA atom). We set occupancy of A and B conformations
                    to 0.5 (that is in your file). Also we need to set
                    occupancy to 1 for N, C and O atoms in this residue
                    to prevent their occupancy from refinement (in your
                    file they are also present with 0.5 occupancy).</div>
                  <div><br>
                  </div>
                  <div>The second case: coupled conformations of 252 and
                    water 1702.</div>
                  <div>For partially occupied water molecules you also
                    need to define appropriate altloc. In your case it
                    is present only when the residue 252 in B
                    conformation, therefore water molecule also should
                    have B altloc and partial occupancy (the same as B
                    conformation of residue 252, 0.49). The residue 252
                    is split to alternative conformations completely,
                    and this is OK. Next, to let phenix.refine know that
                    these conformations are coupled, you need the
                    following parameter file:</div>
                  <div>
                    <div>refinement {</div>
                    <div>� refine {</div>
                    <div>� � occupancies {</div>
                    <div>� � � constrained_group {</div>
                    <div>� � � � selection = chain A and resseq 252 and
                      altloc A</div>
                    <div>� � � � selection = chain A and resseq 252 and
                      altloc B or \</div>
                    <div>� � � � � chain S and resseq 1702 and altloc B</div>
                    <div>� �}</div>
                    <div>� }</div>
                    <div>�}</div>
                    <div>}</div>
                  </div>
                  <div>or enter these selections in appropriate place in
                    GUI (in one constraint occupancy group).</div>
                  <div><br>
                  </div>
                  <div>Here each selection will get the same occupancy
                    for all atoms in it, therefore we have both 252
                    residue and water residue and use altloc B. We don't
                    have water with altloc A (but you may consider it)
                    therefore the first selection contains only residue
                    252. These two selections present in one constrained
                    group ensures that occupancies of these selections
                    will add up to 1.</div>
                  <div><br>
                  </div>
                  <div>You can do all the model manipulations in Coot.�<br>
                  </div>
                  <div><br>
                  </div>
                  <div><br>
                  </div>
                  <div>I'll send you corrected pdb file shortly
                    off-list.</div>
                  <div><br>
                  </div>
                  <div>The useful reading on topic would be</div>
                  <div><br>
                  </div>
                  <div>"13 typical occupancy refinement scenarios and
                    available options in phenix.refine" by Pavel Afonine
                    in the latest Computational Crystallography
                    Newsletter:<br>
                  </div>
                  <div><br>
                  </div>
                  <div><a moz-do-not-send="true"
                      href="http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12"
                      target="_blank">http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12</a><br>
                  </div>
                  <div><br>
                  </div>
                  <div>Case #7 is almost your case, the only difference
                    is one of your residues is water and it has only one
                    conformation.</div>
                  <div><br>
                  </div>
                  <div>Best regards,</div>
                  <div>Oleg Sobolev.</div>
                </div>
                <div class="HOEnZb">
                  <div class="h5">
                    <div class="gmail_extra"><br>
                      <div class="gmail_quote">On Wed, Jan 13, 2016 at
                        11:59 PM, Helena Taberman <span dir="ltr">
                          &lt;<a moz-do-not-send="true"
                            href="mailto:helena.taberman@uef.fi"
                            target="_blank">helena.taberman@uef.fi</a>&gt;</span>
                        wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0
                          0 0 .8ex;border-left:1px #ccc
                          solid;padding-left:1ex">
                          <div style="word-wrap:break-word"><br>
                            <div>
                              <div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Hi,</div>
                              <div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><br>
                              </div>
                              <div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Thanks
                                for your advice. It�s still not working.
                                I use the phenix gui version and if I
                                set, for example,<br>
                                <br>
                              </div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">chain
                                A and resid 249</div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">chain
                                A and resid 252</div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">chain
                                S and resid 1702</div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word"><br>
                              </div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">as
                                a constrained group at the occupancy
                                refinement selections (the two residues
                                have 2 conformations both and the water
                                is there just if the conformation of
                                residue 252 is B) the refinement just
                                makes the residues a constrained group
                                alone making even their main chain occ.
                                something like 0.49 as for the both of
                                the side chains too. And it also kicks
                                them a bit out of their densities. So
                                how to continue? What am I doing wrong?</div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word"><br>
                              </div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">Best
                                regards,</div>
                              <div
                                style="text-align:start;text-indent:0px;word-wrap:break-word">Helena</div>
                            </div>
                            <div>
                              <div><br>
                                <div>
                                  <blockquote type="cite">
                                    <div>Folmer Fredslund &lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:folmerf@gmail.com"
                                        target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:folmerf@gmail.com">folmerf@gmail.com</a></a>&gt;
                                      kirjoitti 11.1.2016 kello 15.20:</div>
                                    <br>
                                    <div>
                                      <div dir="ltr">
                                        <div>
                                          <div>
                                            <div>Hi Helena,<br>
                                              <br>
                                            </div>
                                            I believer this is the
                                            relevant bit from the
                                            manual:<br>
                                            <a moz-do-not-send="true"
href="https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement"
                                              target="_blank">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a>
                                            (in the examples)<br>
                                            <br>
                                            <ol>
                                              <li value="4">
                                                <p>Complex occupancy
                                                  refinement strategy
                                                  (combination of
                                                  various available
                                                  occupancy refinement
                                                  types):</p>
                                                <pre>% phenix.refine data.hkl model.pdb strategy=occupancies occ.params
</pre>
                                              </li>
                                            </ol>
                                            <p>The amount of atom
                                              selections makes it
                                              inconvenient to type them
                                              all from the command line.
                                              This is why the parameter
                                              file
                                              <tt>occ.params</tt> is
                                              used and it contains
                                              following lines:</p>
                                            <pre>refinement {
  refine {
    occupancies {
      individual = element BR or water
      individual = element Zn
      constrained_group {
        selection = chain A and resseq 1
      }
      constrained_group {
        selection = chain A and resseq 2
        selection = chain A and resseq 3
      }
      constrained_group {
        selection = chain X and resname MAN
        selection = chain X and resseq 42
        selection = chain X and resseq 121
      }
      remove_selection = chain B and resseq 1 and name O
      remove_selection = chain B and resseq 3 and name O
    }
  }
}
</pre>
                                            <br>
                                            <br>
                                          </div>
                                          Hope this helps,<br>
                                        </div>
                                        Folmer<br>
                                      </div>
                                      <div class="gmail_extra"><br>
                                        <div class="gmail_quote">2016-01-11
                                          13:14 GMT+01:00 Christian Roth
                                          <span dir="ltr">
                                            &lt;<a
                                              moz-do-not-send="true"
                                              href="mailto:christianroth034@gmail.com"
                                              target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a></a>&gt;</span>:<br>
                                          <blockquote
                                            class="gmail_quote"
                                            style="margin:0 0 0
                                            .8ex;border-left:1px #ccc
                                            solid;padding-left:1ex">
                                            <p dir="ltr">Hi Helena, <br>
                                              Indeed you have to group
                                              the relevant aa and the
                                              respective water together
                                              in a constrained group to
                                              avoid your problem and get
                                              the occupancies add up to
                                              1. This us described in
                                              the manual under occupancy
                                              refinement. I can't access
                                              the manual at the moment
                                              to give you a more
                                              detailed answer.</p>
                                            <p dir="ltr">Cheers</p>
                                            <p dir="ltr">Christian</p>
                                            <div class="gmail_quote">
                                              <div>
                                                <div>On 11 Jan 2016
                                                  11:56, "Helena
                                                  Taberman" &lt;<a
                                                    moz-do-not-send="true"
href="mailto:helena.taberman@uef.fi" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:helena.taberman@uef.fi">helena.taberman@uef.fi</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
                                                      style="word-wrap:break-word">Hi,
                                                      <div><br>
                                                      </div>
                                                      <div>I�m trying to
                                                        refine a
                                                        structure
                                                        determined to
                                                        1.6 �
                                                        resolution.
                                                        There�s several
                                                        residues with
                                                        additional
                                                        conformations
                                                        and waters with
                                                        partial
                                                        occupancies
                                                        stating that
                                                        they would be
                                                        there when the
                                                        conformation of
                                                        the residues
                                                        allows it. When
                                                        I try to refine
                                                        these
                                                        conformations
                                                        and partially
                                                        occupied waters
                                                        together the
                                                        refinement kicks
                                                        the second
                                                        conformations
                                                        and water
                                                        molecules out of
                                                        their densities,
                                                        since they are
                                                        obviously too
                                                        close to the
                                                        other additional
                                                        conformations of
                                                        the residues or
                                                        the following
                                                        residues. What
                                                        could I do?
                                                        Should I somehow
                                                        group them
                                                        together or
                                                        what?</div>
                                                      <div><br>
                                                      </div>
                                                      <div>Best regards,</div>
                                                      <div>Helena</div>
                                                      <div><br>
                                                      </div>
                                                      <div>
                                                        <div
style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">Helena
                                                          Taberman,
                                                          Ph.D.<br>
                                                          <br>
                                                          University of
                                                          Eastern
                                                          Finland<br>
                                                          Department of
                                                          Chemistry<br>
                                                          Joensuu Campus<br>
                                                          P.O. Box 111<br>
                                                          FI-80101
                                                          Joensuu,
                                                          FINLAND<br>
                                                          <br>
                                                          Mobile: <a
                                                          moz-do-not-send="true"
href="tel:%2B358%2050%20337%202488" value="+358503372488"
                                                          target="_blank">
                                                          +358 50 337
                                                          2488</a><br>
                                                          <br>
                                                        </div>
                                                      </div>
                                                      <br>
                                                    </div>
                                                    <br>
                                                  </div>
                                                </div>
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                                        <br>
                                        <br clear="all">
                                        <br>
                                        -- <br>
                                        <div>Folmer Fredslund<br>
                                        </div>
                                      </div>
                                    </div>
                                  </blockquote>
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