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    For the record: the answer is in the documentation, see<br>
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<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space_refine.html">https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space_refine.html</a><br>
    <br>
    -&gt; Usage examples, #4.<br>
    <br>
    Pavel<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 10/5/16 14:27, Billy Poon wrote:<br>
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cite="mid:CAHmYUcb6GjikQ5UjUzWGN4rWWyaUJHv=7uhZnbBfcX+UzquMQA@mail.gmail.com"
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      <div dir="ltr">Hi Oliver,
        <div><br>
        </div>
        <div>Actually, I think it's just "label"</div>
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                                    <div>--</div>
                                    <div><span
                                        style="font-size:12.8000001907349px">Billy
                                        K. Poon</span><br>
                                    </div>
                                  </div>
                                  <div>Research Scientist, Molecular
                                    Biophysics and Integrated Bioimaging</div>
                                  <div>Lawrence Berkeley National
                                    Laboratory</div>
                                  <div>1 Cyclotron Road, M/S 33R0345</div>
                                  <div>Berkeley, CA 94720</div>
                                  <div>Tel: (510) 486-5709</div>
                                  <div>Fax: (510) 486-5909</div>
                                  <div>Web: <a moz-do-not-send="true"
                                      href="https://phenix-online.org"
                                      target="_blank">https://phenix-online.org</a></div>
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        <div class="gmail_quote">On Wed, Oct 5, 2016 at 2:21 PM, Billy
          Poon <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@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 Oliver,
              <div><br>
              </div>
              <div>Oops, the keyword for the command-line would be
                "map_coefficients_label". I think you have to wrap the
                label in quotes. Let us know if that doesn't work.</div>
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                                            <div>--</div>
                                            <div><span
                                                style="font-size:12.8000001907349px">Billy
                                                K. Poon</span><br>
                                            </div>
                                          </div>
                                          <div>Research Scientist,
                                            Molecular Biophysics and
                                            Integrated Bioimaging</div>
                                          <div>Lawrence Berkeley
                                            National Laboratory</div>
                                          <div>1 Cyclotron Road, M/S
                                            33R0345</div>
                                          <div>Berkeley, CA 94720</div>
                                          <div>Tel: <a
                                              moz-do-not-send="true"
                                              href="tel:%28510%29%20486-5709"
                                              value="+15104865709"
                                              target="_blank">(510)
                                              486-5709</a></div>
                                          <div>Fax: <a
                                              moz-do-not-send="true"
                                              href="tel:%28510%29%20486-5909"
                                              value="+15104865909"
                                              target="_blank">(510)
                                              486-5909</a></div>
                                          <div>Web: <a
                                              moz-do-not-send="true"
                                              href="https://phenix-online.org"
                                              target="_blank">https://phenix-online.org</a></div>
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                <div class="h5">
                  <div class="gmail_quote">On Wed, Oct 5, 2016 at 2:16
                    PM, Oliver Clarke <span dir="ltr">&lt;<a
                        moz-do-not-send="true"
                        href="mailto:olibclarke@gmail.com"
                        target="_blank">olibclarke@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 style="word-wrap:break-word">Hi Billy, I
                        should clarify that I typically use
                        real_space_refine on the command line - I have
                        not checked it in the GUI. 
                        <div><br>
                        </div>
                        <div>On the command line, it provides a list of
                          the available arrays, but no way to input a
                          selected array (and the output of
                          phenix.real_space_refine --help doesn’t
                          provide any promising looking options).
                          <div><br>
                          </div>
                          <div>Cheers</div>
                          <div>Oli
                            <div>
                              <div class="m_-3422254048928163458h5"><br>
                                <div>
                                  <div>
                                    <blockquote type="cite">
                                      <div>On Oct 5, 2016, at 5:12 PM,
                                        Billy Poon &lt;<a
                                          moz-do-not-send="true"
                                          href="mailto:bkpoon@lbl.gov"
                                          target="_blank">bkpoon@lbl.gov</a>&gt;
                                        wrote:</div>
                                      <br
class="m_-3422254048928163458m_7206865451393818348Apple-interchange-newline">
                                      <div>
                                        <div dir="ltr">Hi Oliver,
                                          <div><br>
                                          </div>
                                          <div>When you provide a MTZ
                                            file with map coefficients
                                            to the
                                            phenix.real_space_refine
                                            GUI, the widget labeled "Map
                                            coefficients label" should
                                            refresh and provide a list
                                            of available arrays. It
                                            should behave the same way
                                            as the "Data labels" and
                                            "Phase labels" widgets in
                                            the phenix.refine GUI. If
                                            the "Map coefficients label"
                                            widget is not displaying the
                                            arrays in your MTZ file, can
                                            you provide your file so
                                            that I can take a closer
                                            look? Thanks!</div>
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                                                          <div>
                                                          <div>--</div>
                                                          <div><span
                                                          style="font-size:12.8000001907349px">Billy
                                                          K. Poon</span><br>
                                                          </div>
                                                          </div>
                                                          <div>Research
                                                          Scientist,
                                                          Molecular
                                                          Biophysics and
                                                          Integrated
                                                          Bioimaging</div>
                                                          <div>Lawrence
                                                          Berkeley
                                                          National
                                                          Laboratory</div>
                                                          <div>1
                                                          Cyclotron
                                                          Road, M/S
                                                          33R0345</div>
                                                          <div>Berkeley,
                                                          CA 94720</div>
                                                          <div>Tel: <a
moz-do-not-send="true" href="tel:%28510%29%20486-5709"
                                                          value="+15104865709"
target="_blank">(510) 486-5709</a></div>
                                                          <div>Fax: <a
moz-do-not-send="true" href="tel:%28510%29%20486-5909"
                                                          value="+15104865909"
target="_blank">(510) 486-5909</a></div>
                                                          <div>Web: <a
                                                          moz-do-not-send="true"
href="https://phenix-online.org/" target="_blank">https://phenix-online.org</a></div>
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                                          <br>
                                          <div class="gmail_quote">On
                                            Wed, Oct 5, 2016 at 2:02 PM,
                                            Oliver Clarke <span
                                              dir="ltr">&lt;<a
                                                moz-do-not-send="true"
                                                href="mailto:olibclarke@gmail.com"
                                                target="_blank">olibclarke@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">Hi,<br>
                                              <br>
                                              I find phenix.real_space
                                              refine very effective for
                                              initial refinement of a
                                              model against a density
                                              modified map after
                                              molecular replacement
                                              (with morphing and
                                              reference restraints etc
                                              enabled).<br>
                                              <br>
                                              However, when I do this it
                                              seems like if there is
                                              more than one array of map
                                              coefficients in the file
                                              there is no way to select
                                              which columns to use,
                                              unlike for phenix.refine -
                                              would it be possible to
                                              add such an option?
                                              Currently I just use cad
                                              in ccp4 to make a file
                                              with the desired columns,
                                              but it would be a smoother
                                              process if the desired
                                              column labels could be
                                              specified directly at run
                                              time.<br>
                                              <br>
                                              Cheers<br>
                                              Oli<br>
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