[phenixbb] geometry in phenix.refine

Jianghai Zhu jzhu at cbr.med.harvard.edu
Thu Feb 21 14:45:07 PST 2008

> the difference is most likely because of H atoms, indeed (deferent
> "ideal" values used by phenix.reduce and Monomer Library that is  
> used in
> phenix.refine). In the next version of phenix.refine the geometry of H
> atoms will always be regularized (unless free refinement is  
> requested at
> ultra-high resolution), so it will be always consistent with the  
> Monomer
> Library definitions.

Why not just the same value to start with?

> Also, I think H atoms should be excluded from geometry statistics
> calculations if riding model is used. I will add this as well.

Then you need to change the geometry statistics output by  
phenix.refine when riding H atoms are present.


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