Does anyone know what file phenix uses to do NAG restraints when the molecule being refined has NAG groups?  My groups are called &quot;NAG&quot;.  I found data_NAG.cif and NAG-B-D.cif in the phenix folder but can&#39;t tell whether it&#39;s using either of those to refine my NAGs (they don&#39;t show up in the log file).<br>
Thanks,<br>-Sam<br><br><div class="gmail_quote">On Thu, Jun 24, 2010 at 11:42 AM, Sam Stampfer <span dir="ltr">&lt;<a href="mailto:Samuel.Stampfer@tufts.edu">Samuel.Stampfer@tufts.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>I&#39;m in the process of preparing 4 structures for submission to rcsb, and the validation server has pointed out numerous issues with the N-acetyl-glucosamine moieties on my structures.  While I have fixed the torsion angles accordingly (using CARP from <a href="http://www.glycosciences.de/tools/carp/" target="_blank">http://www.glycosciences.de/tools/carp/</a> as a validation checker) and they stay fixed after phenix refinement, phenix keeps generating 2-2.2 Angstrom clashes between ND2 on asparagine with C2 on the NAG (the linkage is ND2-C1 and the usual distances are at least 2.28 Angstroms).  Occasionally, the ND2 to C2 distance is as low as 1.8 Angstroms.  This is happening in all my structures and happens independently of the setting of wxc_scale (even for wxc_scale=0.05!)  My NAG groups fit the density well, both pre- and post- refinement.<br>

<br>Any suggestions?  Will rcsb care?  These clashes are present in 12 out of 39 NAG moieties.<br><br>Thanks!<br><font color="#888888"><br>-Sam<br>
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