[phenixbb] geometry of disulfide and NAG

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Jan 22 08:59:21 PST 2009


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.


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

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