[phenixbb] NAG clashes: C2 with ND2

Pavel Afonine PAfonine at lbl.gov
Fri Jun 25 13:43:45 PDT 2010

Hi Sam,

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.


On 6/25/10 11:50 AM, Sam Stampfer wrote:
> 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 <mailto: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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