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      You will need to make sure that the group of the AME is "peptide"
      (or "L-peptide").&nbsp; If you tell Coot that it's a non-polymer, it
      will believe you.<br>
      <br>
      I guess this should be added to the FAQ.&nbsp; Thanks.<br>
      <br>
      Paul.<br>
      <br>
      On 20/09/13 23:22, Ursula Schulze-Gahmen wrote:<br>
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cite="mid:CA+erM+07P+cp4JuM3G8mFSVUwZMf6skvp2CxUdhgesEuKEK+oA@mail.gmail.com"
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          <div>Thanks Nigel,<br>
            <br>
          </div>
          All I need now is a cif file for acetyl-methionine.&nbsp; How do I
          get to this? And should the cif file be for the free amino
          acid or for the residue in the peptide chain?<br>
          <br>
        </div>
        Ursula<br>
      </div>
      <div class="gmail_extra"><br>
        <br>
        <div class="gmail_quote">On Fri, Sep 20, 2013 at 1:15 PM, Nigel
          Moriarty <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@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">To have the refinement link the residues you
              should use the parameter intra_chain=True and check the
              bonds in the .geo file.
              <div>
                <br>
              </div>
              <div>Paul Emsley will likely answer that Coot question.</div>
              <div><br>
              </div>
              <div>Nigel</div>
            </div>
            <div class="gmail_extra"><br>
              <br>
              <div class="gmail_quote">
                <div>
                  <div class="h5">On Fri, Sep 20, 2013 at 12:06 PM,
                    Ursula Schulze-Gahmen <span dir="ltr">&lt;<a
                        moz-do-not-send="true"
                        href="mailto:uschulze-gahmen@lbl.gov"
                        target="_blank">uschulze-gahmen@lbl.gov</a>&gt;</span>
                    wrote:<br>
                  </div>
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                <blockquote class="gmail_quote" style="margin:0 0 0
                  .8ex;border-left:1px #ccc solid;padding-left:1ex">
                  <div>
                    <div class="h5">I am trying to include a N-terminal
                      acetylated methionine in my model.<br>
                      I replaced my methionine with a AME residue from
                      the pdb data bank and<br>
                      included a link command to connect the C from AME
                      with the N of the<br>
                      second residue. The AME is defined as HETATM. When
                      I try to regularize<br>
                      this structure in Coot it doesn't recognize that
                      the 1. and 2. residue<br>
                      should stay connected. What or how do I need to
                      define this residue or<br>
                      the connection so that I can model in Coot and
                      refine in Phenix?<br>
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                  <span><font color="#888888">
                      <div>
                        <div class="h5"><br>
                          Ursula<br>
                          --<br>
                          Ursula Schulze-Gahmen, Ph.D.<br>
                          Assistant Researcher<br>
                          UC Berkeley, QB3<br>
                          356 Stanley Hall #3220<br>
                          Berkeley, CA 94720-3220<br>
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                        </font></span></font></span></blockquote>
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              <span class="HOEnZb"><font color="#888888"><br>
                  <br clear="all">
                  <div><br>
                  </div>
                  -- <br>
                  Nigel W. Moriarty<br>
                  Building 64R0246B, Physical Biosciences Division<br>
                  Lawrence Berkeley National Laboratory<br>
                  Berkeley, CA 94720-8235<br>
                  Phone : <a moz-do-not-send="true"
                    href="tel:510-486-5709" value="+15104865709"
                    target="_blank">510-486-5709</a>&nbsp; &nbsp;&nbsp; Email :
                  <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
                  Fax&nbsp;&nbsp; : <a moz-do-not-send="true"
                    href="tel:510-486-5909" value="+15104865909"
                    target="_blank">510-486-5909</a>&nbsp; &nbsp; &nbsp;&nbsp; Web&nbsp; : <a
                    moz-do-not-send="true" href="http://CCI.LBL.gov"
                    target="_blank">CCI.LBL.gov</a>
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        <br>
        <br clear="all">
        <br>
        -- <br>
        Ursula Schulze-Gahmen, Ph.D.<br>
        Assistant Researcher<br>
        UC Berkeley, QB3<br>
        356 Stanley Hall #3220<br>
        Berkeley, CA 94720-3220<br>
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