<div dir="ltr">Ursula<div><br></div><div>Use this file, it has peptide in the right place. You do have to &quot;import&quot; it into Coot.</div><div><br></div><div>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">

On Mon, Sep 23, 2013 at 10:13 AM, Ursula Schulze-Gahmen <span dir="ltr">&lt;<a href="mailto:uschulze-gahmen@lbl.gov" target="_blank">uschulze-gahmen@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"><div><div><div>Hi Paul,<br><br></div>I am sorry I did not understand that advice. What is the group definition for a residues or compound?  And I do want AME connected to the polypeptide.<br><br></div>I actually got a decent structure out of Phenix with AME connected to the next residue. AME is composed of heteroatoms at this point. When I read this into coot, it looks alright, but I am not able to manipulate any conformations for the AME because it is not defined. What do I need to define, or is it perhaps a better approach to just define an acetylgroup and link this to the N-terminal normal methionine?<span class="HOEnZb"><font color="#888888"><br>


<br></font></span></div><span class="HOEnZb"><font color="#888888">Ursula<br></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Sep 23, 2013 at 3:27 AM, Paul Emsley <span dir="ltr">&lt;<a href="mailto:pemsley@mrc-lmb.cam.ac.uk" target="_blank">pemsley@mrc-lmb.cam.ac.uk</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <div><br>
      You will need to make sure that the group of the AME is &quot;peptide&quot;
      (or &quot;L-peptide&quot;).  If you tell Coot that it&#39;s a non-polymer, it
      will believe you.<br>
      <br>
      I guess this should be added to the FAQ.  Thanks.<span><font color="#888888"><br>
      <br>
      Paul.</font></span><div><div><br>
      <br>
      On 20/09/13 23:22, Ursula Schulze-Gahmen wrote:<br>
    </div></div></div><div><div>
    <blockquote type="cite">
      <div dir="ltr">
        <div>
          <div>Thanks Nigel,<br>
            <br>
          </div>
          All I need now is a cif file for acetyl-methionine.  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 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>On Fri, Sep 20, 2013 at 12:06 PM,
                    Ursula Schulze-Gahmen <span dir="ltr">&lt;<a href="mailto:uschulze-gahmen@lbl.gov" target="_blank">uschulze-gahmen@lbl.gov</a>&gt;</span>
                    wrote:<br>
                  </div>
                </div>
                <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                  <div>
                    <div>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&#39;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>
                    </div>
                  </div>
                  <span><font color="#888888">
                      <div>
                        <div><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>
                        </div>
                      </div>
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                        </font></span></font></span></blockquote>
              </div>
              <span><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 href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a>     Email :
                  <a href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
                  Fax   : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a>       Web  : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a>
                </font></span></div>
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            <br>
          </blockquote>
        </div>
        <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>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
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    </blockquote>
    <br>
  </div></div></div>

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<br></blockquote></div><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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<br></blockquote></div><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 : 510-486-5709     Email : NWMoriarty@LBL.gov<br>

Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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