<div dir="ltr"><div>Hi Pavel,</div><div>I sent you a separate email with all the files. Thank you very much for your help!</div><div>Best,</div><div>Yangqi<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at 8:31 PM Pavel Afonine &lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
  
    
  
  <div>
    Hi Yangqi,<br>
    <br>
    it depends what you call &quot;worse&quot; and also keep in mind that
    clashscore is not the only metric of success. Some metrics get get
    worse and some better, and changes in some may be just fine and some
    may indicate problems.<br>
    It&#39;s hard to comment meaningfully based upon rather scarce amount of
    information you provide. <br>
    I can have a look if you share (off list!) map, models (input and
    output) and the log file from refinement.<br>
    <br>
    Pavel<br>
    <br>
    <div>On 1/21/20 17:19, Yangqi Gu wrote:<br>
    </div>
    <blockquote type="cite">
      
      <div dir="ltr">Thank you Tom and Oleg. I tried refinement as you
        suggested. I did local refinement after I did the rigid body.
        However, the first couple of cycles, the clashscore and
        everything (statistics) seems improved, but then getting worse
        after more cycles. I did both 5 and 10 cycles, the final outputs
        are all worse than what I started with, which means only after
        rigid body fitting. Is this normal? 
        <div>Best,</div>
        <div>Yangqi</div>
      </div>
      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at 5:32
          PM Oleg Sobolev &lt;<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>&gt; wrote:<br>
        </div>
        <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
          <div dir="ltr">Hi Yangqi,
            <div><br>
            </div>
            <div>Yes, phenix.simple_ncs_from_pdb is the tool to search
              for NCS in models. Documentation:</div>
            <div><a href="https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html" target="_blank">https://www.phenix-online.org/documentation/reference/simple_ncs_from_pdb.html</a><br>
            </div>
            <div><br>
            </div>
            <div>Also, it is available in GUI: &quot;Select atoms&quot; -&gt;
              &quot;NCS&quot; -&gt; &quot;Find NCS&quot; but with less options available.
              For matrices you&#39;ll have to run command-line.</div>
            <div><br>
            </div>
            <div>Best regards,</div>
            <div>Oleg Sobolev.</div>
          </div>
          <br>
          <div class="gmail_quote">
            <div dir="ltr" class="gmail_attr">On Tue, Jan 21, 2020 at
              1:17 PM BuddySphinx &lt;<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>&gt; wrote:<br>
            </div>
            <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
              <div lang="EN-US">
                <div>
                  <p class="MsoNormal">Also, another question. Could I
                    find ncs from my pdb model? I tried with map, but it
                    failed to find the correct symmetry. Can I use
                    phenix.simple.ncs to generate the ncs operator file?</p>
                  <p class="MsoNormal">Best,</p>
                  <p class="MsoNormal">Yangqi</p>
                  <p class="MsoNormal"> </p>
                  <p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a>
                    for Windows 10</p>
                  <p class="MsoNormal"> </p>
                  <div style="border-color:rgb(225,225,225) currentcolor currentcolor;border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in">
                    <p class="MsoNormal" style="border:medium none;padding:0in"><b>From:
                      </b><a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Tom
                        Terwilliger</a><br>
                      <b>Sent: </b>Tuesday, January 21, 2020 9:18 AM<br>
                      <b>To: </b><a href="mailto:yangqi.gu@yale.edu" target="_blank">Yangqi Gu</a>;
                      <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Thomas
                        Charles Terwilliger</a><br>
                      <b>Cc: </b><a href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX
                        user mailing list</a><br>
                      <b>Subject: </b>Re: [phenixbb] How critical is
                      ncs operator for real space refinement</p>
                  </div>
                  <p class="MsoNormal"> </p>
                  <div>
                    <div>
                      <p class="MsoNormal">Hi Yangqi,</p>
                    </div>
                    <div>
                      <p class="MsoNormal"> </p>
                      <div>
                        <p class="MsoNormal">You don&#39;t actually need the
                          NCS relationships in order to refine with NCS
                          restraints because the default is to use
                          torsion-angle restraints which only use local
                          relationships, not overall NCS matrices.</p>
                      </div>
                      <div>
                        <p class="MsoNormal"> </p>
                      </div>
                      <div>
                        <p class="MsoNormal">So you can go ahead and use
                          your rigid-body-refined starting model with
                          torsion-angle restraints in
                          phenix.real_space_refine.  That will not
                          impose perfect helical restraints, but I am
                          guessing that your map already has
                          near-perfect helical symmetry so that should
                          not matter very much.</p>
                      </div>
                      <div>
                        <p class="MsoNormal"> </p>
                      </div>
                      <div>
                        <p class="MsoNormal">Also you might first run
                          with just one monomer which will be much
                          quicker and give you almost the same answer.</p>
                      </div>
                      <div>
                        <p class="MsoNormal"> </p>
                      </div>
                      <div>
                        <p class="MsoNormal">Let us know if that does
                          not do it!</p>
                      </div>
                      <div>
                        <p class="MsoNormal"> </p>
                      </div>
                      <div>
                        <p class="MsoNormal">All the best,</p>
                      </div>
                      <div>
                        <p class="MsoNormal">Tom T</p>
                      </div>
                      <div>
                        <p class="MsoNormal"> </p>
                      </div>
                    </div>
                    <p class="MsoNormal"> </p>
                    <div>
                      <div>
                        <p class="MsoNormal">On Mon, Jan 20, 2020 at
                          9:33 PM Yangqi Gu &lt;<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>&gt;
                          wrote:</p>
                      </div>
                      <blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
                        <div>
                          <p class="MsoNormal">Dear PHENIX developers,</p>
                          <div>
                            <p class="MsoNormal">I have a question about
                              NCS operator. Since I have a cryo-EM map
                              and I want to refine my filament
                              coordinates within the map. I generated
                              the coordinate map manually in Chimera by
                              building multiple chains with rigid body
                              refinement. Since I did not generate the
                              NCS operator file (I tried by doing map
                              symmetry, it did not give me the right
                              helical symmetry), I did not refine with
                              ncs restraints. I am wondering in this
                              case, how critical it is to refine a model
                              with helical symmetry applied. Is it a
                              must or can I go with the way I did? Hope
                              to hear from you soon!</p>
                          </div>
                          <div>
                            <p class="MsoNormal">Best,</p>
                          </div>
                          <div>
                            <p class="MsoNormal">Yangqi<br clear="all">
                            </p>
                            <div>
                              <p class="MsoNormal"> </p>
                            </div>
                          </div>
                        </div>
                        <p class="MsoNormal">_______________________________________________<br>
                          phenixbb mailing list<br>
                          <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
                          <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
                          Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></p>
                      </blockquote>
                    </div>
                    <p class="MsoNormal"><br clear="all">
                    </p>
                    <div>
                      <p class="MsoNormal"> </p>
                    </div>
                    <p class="MsoNormal">-- </p>
                    <div>
                      <div>
                        <div>
                          <div>
                            <div>
                              <div>
                                <div>
                                  <div>
                                    <div>
                                      <p class="MsoNormal">Thomas C
                                        Terwilliger</p>
                                      <div>
                                        <p class="MsoNormal">Laboratory
                                          Fellow, Los Alamos National
                                          Laboratory</p>
                                      </div>
                                      <div>
                                        <p class="MsoNormal">Senior
                                          Scientist, New Mexico
                                          Consortium</p>
                                      </div>
                                      <div>
                                        <p class="MsoNormal">100 Entrada
                                          Dr, Los Alamos, NM 87544</p>
                                      </div>
                                      <div>
                                        <p class="MsoNormal">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></p>
                                      </div>
                                      <div>
                                        <p class="MsoNormal">Tel:
                                          505-431-0010</p>
                                      </div>
                                    </div>
                                  </div>
                                </div>
                              </div>
                            </div>
                          </div>
                        </div>
                      </div>
                    </div>
                  </div>
                  <p class="MsoNormal"> </p>
                  <p class="MsoNormal"> </p>
                </div>
              </div>
              _______________________________________________<br>
              phenixbb mailing list<br>
              <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
              <a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
              Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote>
          </div>
        </blockquote>
      </div>
      <br clear="all">
      <div><br>
      </div>
      -- <br>
      <div dir="ltr">
        <div dir="ltr">
          <div>
            <div dir="ltr">
              <div><br>
              </div>
              Yangqi Gu
              <div>Graduate Student</div>
              <div>Malvankar Lab</div>
              <div>Yale University, West Campus</div>
            </div>
          </div>
        </div>
      </div>
      <br>
      <fieldset></fieldset>
      <pre>_______________________________________________
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></pre>
    </blockquote>
    <br>
  </div>

</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><br></div>Yangqi Gu<div>Graduate Student</div><div>Malvankar Lab</div><div>Yale University, West Campus</div></div></div></div></div>