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Hi Sam,<br>
<br>
phenix.refine outputs .geo file that lists all the geometry restraints
used in refinement for all atoms. You can find the atoms you are
interested in and see what are the restraints targets (ideal values for
bonds, angles, etc...), then compare those with the CIF file to make
sure which one is used. I'm almost sure that will answer your question.<br>
<br>
Pavel.<br>
<br>
<br>
On 6/25/10 11:50 AM, Sam Stampfer wrote:
<blockquote
cite="mid:AANLkTilAqCgN_AqdmKZE8WIvoNNIEPLqHyT_Kr3PCxHU@mail.gmail.com"
type="cite">Does anyone know what file phenix uses to do NAG
restraints when the molecule being refined has NAG groups? My groups
are called "NAG". I found data_NAG.cif and NAG-B-D.cif in the phenix
folder but can't tell whether it's using either of those to refine my
NAGs (they don'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"><<a moz-do-not-send="true"
href="mailto:Samuel.Stampfer@tufts.edu">Samuel.Stampfer@tufts.edu</a>></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'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 moz-do-not-send="true"
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>
</font></blockquote>
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<br>
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