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<div class="moz-cite-prefix"><br>
You will need to make sure that the group of the AME is "peptide"
(or "L-peptide"). 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. Thanks.<br>
<br>
Paul.<br>
<br>
On 20/09/13 23:22, Ursula Schulze-Gahmen wrote:<br>
</div>
<blockquote
cite="mid:CA+erM+07P+cp4JuM3G8mFSVUwZMf6skvp2CxUdhgesEuKEK+oA@mail.gmail.com"
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"><<a moz-do-not-send="true"
href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></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"><<a
moz-do-not-send="true"
href="mailto:uschulze-gahmen@lbl.gov"
target="_blank">uschulze-gahmen@lbl.gov</a>></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 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>
</div>
</div>
<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>
</div>
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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"
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target="_blank">510-486-5909</a> Web : <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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