<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">On Fri, Sep 20, 2013 at 12:06 PM, Ursula Schulze-Gahmen <span dir="ltr"><<a href="mailto:uschulze-gahmen@lbl.gov" target="_blank">uschulze-gahmen@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<span class="HOEnZb"><font color="#888888"><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></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>
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