[phenixbb] NAG clashes: C2 with ND2

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jun 25 08:31:11 PDT 2010


Can you send me all the files directly so I can reproduce the error?


On Thu, Jun 24, 2010 at 8:42 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

More information about the phenixbb mailing list