<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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="">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 clear="all" class=""><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,&nbsp;Molecular Biophysics and Integrated Bioimaging</div><div class="">Lawrence Berkeley National Laboratory<br class="">Berkeley, CA 94720-8235<br class="">Phone : 510-486-5709&nbsp; &nbsp;&nbsp; <a href="mailto:NWMoriarty@LBL.gov" class="">Email : NWMoriarty@LBL.gov</a><br class="">Fax&nbsp;&nbsp; : 510-486-5909&nbsp; &nbsp; &nbsp;&nbsp; Web&nbsp; : <a href="http://cci.lbl.gov/" target="_blank" class="">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="">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">
  
    
  
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    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">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="">
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          <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="">--&nbsp;<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="">+39 02 9437 5167</a><br class="">
                fax <a href="tel:+39%2002%209437%205990" value="+390294375990" target="_blank" class="">+39 02 9437 5990</a></div>
              <div style="text-align:-webkit-auto;word-wrap:break-word" class="">web&nbsp;<a href="http://is.gd/IEOXtalUnit" target="_blank" class="">http://is.gd/IEOXtalUnit</a></div>
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