<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    <p><font face="Arial">You could add the link description to your
        dictionary, import that in coot and it should work.</font></p>
    <p><font face="Arial">The non phenix way would be to create the link
        in jligand, write out the dictionary description and merge it
        with your ligand dictionary. The link statement needs to be in
        the pdb of course.</font></p>
    <p><font face="Arial">There might be also a way in phenix to do
        this, but I'm not aware of it at the moment. Maybe Pavel or
        Nigel can help out here.</font></p>
    <p><font face="Arial">Cheers</font></p>
    <p><font face="Arial">Christian</font></p>
    <br>
    <div class="moz-cite-prefix">Am 26.02.2018 um 10:45 schrieb
      Sebastiano Pasqualato:<br>
    </div>
    <blockquote type="cite"
      cite="mid:CD1EBA21-A7AF-46CB-A93C-3970CFC9124E@gmail.com">
      <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
      Dear Nigel and Pavel,
      <div class="">thank you very much for you feedback and precious
        advice.</div>
      <div class="">It is a compound with a C=C double bond that gets
        attacked by the S of a Cys, hence I think it’s normal that the
        program is not recognising automatically the bond.</div>
      <div class="">I have changed the C=C bond to C-C and recreated the
        CIF file for the compound, than provided phenix the bond
        restrains (bond length and angles) for the C-S bond.</div>
      <div class="">It all seems to work very nicely.</div>
      <div class="">Thanks.</div>
      <div class=""><br class="">
      </div>
      <div class="">Any idea on how to tell Coot the same things? ;-)</div>
      <div class="">(I guess this one should go to the Coot_bb though
        ;-))</div>
      <div class=""><br class="">
      </div>
      <div class="">Thanks again,</div>
      <div class="">ciao,</div>
      <div class="">S<br class="">
        <div><br class="">
          <blockquote type="cite" class="">
            <div class="">On 22 Feb 2018, at 18:35, Nigel Moriarty &lt;<a
                href="mailto:nwmoriarty@lbl.gov" class=""
                moz-do-not-send="true">nwmoriarty@lbl.gov</a>&gt; wrote:</div>
            <br class="Apple-interchange-newline">
            <div class="">
              <div dir="ltr" class="">Sebastiano
                <div class=""><br class="">
                </div>
                <div class="">As Pavel said, send me the inputs if you
                  are having issues.</div>
                <div class=""><br class="">
                </div>
              </div>
              <div class="gmail_extra"><br class="" clear="all">
                <div class="">
                  <div class="gmail_signature"
                    data-smartmail="gmail_signature">
                    <div dir="ltr" class="">
                      <div class="">
                        <div dir="ltr" class="">
                          <div dir="ltr" class="">Cheers
                            <div class=""><br class="">
                            </div>
                            <div class="">Nigel
                              <div class=""><br class="">
                              </div>
                              <div class="">---</div>
                              <div class="">Nigel W. Moriarty<br
                                  class="">
                                Building 33R0349, Molecular Biophysics
                                and Integrated Bioimaging</div>
                              <div class="">Lawrence Berkeley National
                                Laboratory<br class="">
                                Berkeley, CA 94720-8235<br class="">
                                Phone : 510-486-5709     <a
                                  href="mailto:NWMoriarty@LBL.gov"
                                  class="" moz-do-not-send="true">Email
                                  : NWMoriarty@LBL.gov</a><br class="">
                                Fax   : 510-486-5909       Web  : <a
                                  href="http://cci.lbl.gov/"
                                  target="_blank" class=""
                                  moz-do-not-send="true">CCI.LBL.gov</a></div>
                            </div>
                          </div>
                        </div>
                      </div>
                    </div>
                  </div>
                </div>
                <br class="">
                <div class="gmail_quote">On Thu, Feb 22, 2018 at 9:25
                  AM, Pavel Afonine <span dir="ltr" class="">&lt;<a
                      href="mailto:pafonine@lbl.gov" target="_blank"
                      class="" moz-do-not-send="true">pafonine@lbl.gov</a>&gt;</span>
                  wrote:<br class="">
                  <blockquote class="gmail_quote" style="margin:0 0 0
                    .8ex;border-left:1px #ccc solid;padding-left:1ex">
                    <div text="#000000" bgcolor="#FFFFFF" class=""> Hi
                      Sebastiano,<br class="">
                      <br class="">
                      if the ligand in PDB file is placed correctly and
                      distance between atoms that are supposed to have a
                      bond is within reasonable then it should be linked
                      automatically. Otherwise you can use custom bonds
                      as described here (available in GUI and command
                      line):<br class="">
                      <br class="">
                      <a
                        class="m_8786071025687345902moz-txt-link-freetext"
href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles"
                        target="_blank" moz-do-not-send="true">http://phenix-online.org/<wbr
                          class="">documentation/reference/<wbr class="">refinement.html#definition-of-<wbr
                          class="">custom-bonds-and-angles</a><br
                        class="">
                      <br class="">
                      Phenix does not recognize LINK records.<br
                        class="">
                      <br class="">
                      To verify the link, check .geo file that lists all
                      the restraints used in refinement.<br class="">
                      <br class="">
                      Let us know if you more questions or need help!<br
                        class="">
                      <br class="">
                      Pavel
                      <div class="">
                        <div class="h5"><br class="">
                          <br class="">
                          <div
                            class="m_8786071025687345902moz-cite-prefix">On
                            2/22/18 05:13, Sebastiano Pasqualato wrote:<br
                              class="">
                          </div>
                        </div>
                      </div>
                      <blockquote type="cite" class="">
                        <div class="">
                          <div class="h5">
                            <div class=""><br class="">
                            </div>
                            Hi there,
                            <div class="">I have a pretty basic
                              question.</div>
                            <div class="">I am refining a structure in
                              which a drug has been covalently linked to
                              a Cys of the protein.</div>
                            <div class="">I have generated the .cif fie
                              for the ligand, but I don’t know how to
                              tell the program that carbon C04 has to be
                              covalently linked to the SG of the Cys. Is
                              that sufficient to insert a LINK record in
                              the pdb file? What is the correct syntax
                              for that?</div>
                            <div class="">Thanks a lot for the feedback
                              and sorry for the naive question,</div>
                            <div class="">ciao,</div>
                            <div class="">Sebastiano</div>
                            <div class=""><br class="">
                            </div>
                            <div class=""><br class="">
                            </div>
                            <div class="">
                              <div style="letter-spacing: normal;
                                text-align: start; text-indent: 0px;
                                text-transform: none; white-space:
                                normal; word-spacing: 0px; word-wrap:
                                break-word;" class="">
                                <div style="letter-spacing: normal;
                                  text-align: start; text-indent: 0px;
                                  text-transform: none; white-space:
                                  normal; word-spacing: 0px; word-wrap:
                                  break-word;" class="">
                                  <div class="">
                                    <div
                                      style="text-align:-webkit-auto;word-wrap:break-word"
                                      class="">-- <br class="">
                                      <b class="">Sebastiano Pasqualato,
                                        PhD</b><br class="">
                                      Crystallography Unit<br class="">
                                      Department of Experimental
                                      Oncology<br class="">
                                      European Institute of Oncology<br
                                        class="">
                                      IFOM-IEO Campus<br class="">
                                      via Adamello, 16<br class="">
                                      20139 - Milano<br class="">
                                      Italy<br class="">
                                      <br class="">
                                      tel <a
                                        href="tel:+39%2002%209437%205167"
                                        value="+390294375167"
                                        target="_blank" class=""
                                        moz-do-not-send="true">+39 02
                                        9437 5167</a><br class="">
                                      fax <a
                                        href="tel:+39%2002%209437%205990"
                                        value="+390294375990"
                                        target="_blank" class=""
                                        moz-do-not-send="true">+39 02
                                        9437 5990</a></div>
                                    <div
                                      style="text-align:-webkit-auto;word-wrap:break-word"
                                      class="">web <a
                                        href="http://is.gd/IEOXtalUnit"
                                        target="_blank" class=""
                                        moz-do-not-send="true">http://is.gd/IEOXtalUnit</a></div>
                                  </div>
                                </div>
                              </div>
                            </div>
                            <br class="">
                            <br class="">
                            <fieldset
                              class="m_8786071025687345902mimeAttachmentHeader"></fieldset>
                            <br class="">
                          </div>
                        </div>
                        <pre class="">______________________________<wbr class="">_________________
phenixbb mailing list
<a class="m_8786071025687345902moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org" target="_blank" moz-do-not-send="true">phenixbb@phenix-online.org</a>
<a class="m_8786071025687345902moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank" moz-do-not-send="true">http://phenix-online.org/<wbr class="">mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="m_8786071025687345902moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org" target="_blank" moz-do-not-send="true">phenixbb-leave@phenix-online.<wbr class="">org</a></pre>
                      </blockquote>
                      <br class="">
                    </div>
                    <br class="">
                    ______________________________<wbr class="">_________________<br
                      class="">
                    phenixbb mailing list<br class="">
                    <a href="mailto:phenixbb@phenix-online.org" class=""
                      moz-do-not-send="true">phenixbb@phenix-online.org</a><br
                      class="">
                    <a
                      href="http://phenix-online.org/mailman/listinfo/phenixbb"
                      rel="noreferrer" target="_blank" class=""
                      moz-do-not-send="true">http://phenix-online.org/<wbr
                        class="">mailman/listinfo/phenixbb</a><br
                      class="">
                    Unsubscribe: <a
                      href="mailto:phenixbb-leave@phenix-online.org"
                      class="" moz-do-not-send="true">phenixbb-leave@phenix-online.<wbr
                        class="">org</a><br class="">
                  </blockquote>
                </div>
                <br class="">
              </div>
            </div>
          </blockquote>
        </div>
        <br class="">
      </div>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
      <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>
    <br>
  </body>
</html>