[phenixbb] geometry of disulfide and NAG

Li-Zhi Mi mi at idi.harvard.edu
Thu Jan 22 07:06:17 PST 2009

  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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