[phenixbb] geometry of disulfide and NAG

Pavel Afonine pafonine at lbl.gov
Thu Jan 22 08:27:46 PST 2009

Hi Li-Zhi Mi,

- make sure that the restraints are actually used: look ".geo" file - it 
contains a list of all geometry restraints used in refinement;

- changing the wxc_scale will not necessarily help (although it might) 
since it is a global weight used for the whole target;

- try idealizing the geometry of this problem fragment before refinement;

- you can also edit the corresponding CIF file to decrease the sigmas 
for these particular restraints.


On 1/22/2009 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
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