[phenixbb] NAG clashes: C2 with ND2

[Sam Stampfer]

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).
Thanks,
-Sam

On Thu, Jun 24, 2010 at 11:42 AM, Sam Stampfer <Samuel.Stampfer at tufts.edu>wrote:

> Hi,
>
> 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
> http://www.glycosciences.de/tools/carp/ 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.
>
> Any suggestions?  Will rcsb care?  These clashes are present in 12 out of
> 39 NAG moieties.
>
> Thanks!
>
> -Sam
>
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