[phenixbb] geometry of disulfide and NAG

Li-Zhi Mi mi at idi.harvard.edu
Thu Jan 22 10:12:07 PST 2009

Hi Pavel and Nigel,
   Thanks very much for the help. I will check ".geo" file to make sure
the restraints are used. In addition, I will try other tips mentioned by
   Nigel, as you mentioned, the monomer library only define N2, C7, O7
and C8 in the same plane. But just like Ca, C, O, N, Ca' in peptide bond
need to be in the same plane, all these five atoms (C8, C7, O, N and C2)
should be in the same plane. May I give a temporary name for NAG and
provide corresponding cif file in the refinement? 
On Thu, 2009-01-22 at 08:59 -0800, Nigel W Moriarty wrote:
> Li-Zhi
> In addition to what Pavel said, the monomer library entry for NAG has 
> N2, C7, O7 and C8 in a plane.  C2 is not necessarily in the same plane.
> Nigel
> On 1/22/09 7:06 AM, Li-Zhi Mi wrote:
> > Hi,
> >   I am using phenix to refine a low resolution structure. The problem I
> > had is that the geometry of disulfide and NAG in the refined structure
> > is not right. I did use a very tight geometry restrains. Both wxc_scale
> > and wxu_scale are set to 0.05. In the refined structures, the sulfur of
> > one cys is very close to the Cb of its disulfide partner. For NAG part,
> > C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a
> > way to adjust these violations?
> >   Thanks in advance for the helps,
> >   Li-Zhi Mi,
> >
> >
> >
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> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
> >   

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