Sam
Can you send me all the files directly so I can reproduce the error?
Nigel
On Thu, Jun 24, 2010 at 8:42 AM, Sam Stampfer
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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