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<div class="moz-cite-prefix">Hi Michael,<br>
<br>
the fourth option is too use the most general way of defining
bonds between arbitrary atoms (custom bonds):<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm#anch354">http://www.phenix-online.org/documentation/refinement.htm#anch354</a><br>
(you can use it in GUI too).<br>
<br>
Of course more bonds you have to define less convenient this
option becomes.<br>
<br>
Pavel<br>
<br>
On 8/5/13 3:15 PM, Nigel Moriarty wrote:<br>
</div>
<blockquote
cite="mid:CANkP=2dh_wS9bgRFEPdFtJ_9RxV6Yyf8RhgMfqf947WB_3d84Q@mail.gmail.com"
type="cite">
<div dir="ltr">A non-standard amino acid will be automatically
linked into a chain if:
<div><br>
</div>
<div>1. The atoms are with 3.0 angstom</div>
<div>2. The atom names of the linking atoms are consistent with
the standard names, N, CA, O, C.</div>
<div><br>
</div>
<div>To add a covalent between a the amino acid and the tag, you
have choices. </div>
<div><br>
</div>
<div>A. In recent versions of phenix.refine, you can use the
flag intra_chain=True.</div>
<div>B. You can generate some linking files using
phenix.ligand_linking. This option allows you edit the link
parameters to you liking.</div>
<div>C (and least recommended) Have LINK records in you model
and use phenix.link_edits.</div>
<div><br>
</div>
<div>I'm happy to take a look at the specific residues in
questions.</div>
<div><br>
</div>
<div>Cheers</div>
<div>
<br>
</div>
<div>Nigel</div>
<div><br>
</div>
<div>NB. Any files sent to me will be held in strictest
confidence.<br>
<br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Aug 5, 2013 at 2:36 PM, Michael
Feldkamp <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:michael.d.feldkamp@vanderbilt.edu"
target="_blank">michael.d.feldkamp@vanderbilt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">I have a
peptide that has a fluorescent tag attached to its
N-terminus along with a unnatural amino acid incorporated
into the sequence. I know how to generate .cif files for
the individual ligands using elbow, but I'm at a loss as to
get Phenix to recognize these modifications to the peptide
so that it refines the structure as one molecule with
covalent linkages between the fluorescent tag, peptide and
modified amino acid. Any help would be much appreciated.<br>
Thanks,<br>
Michael<br>
<br>
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</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 : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a moz-do-not-send="true"
href="http://CCI.LBL.gov">CCI.LBL.gov</a>
</div>
<br>
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