Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Moriarty, N.W.; Janowski, P.A.; Swails, J.M.; Nguyen, H.; Richardson, J.S.; Case, D.A.; Adams, P.D.

doi:10.1107/S2059798319015134

Acta Crystallographica Section D
Acta Crystallographica
Section D STRUCTURAL BIOLOGY

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Figure 3
Comparison plots of model-quality measures versus resolution for Amber (burnt orange) versus CDL/E&H (dark blue) refinements with error bars depicting the 95% confidence level of the standard error of the mean. The MolProbity score is a combination of all-atom clashscore and Ramachandran favored and rotamer outliers, weighted to approximate the expected score at the resolution of the structure. The hydrogen-bond fraction is calculated using cpptraj per 1000 atoms in the model. For all six plots, Amber (burnt orange) differs in the better direction.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 76| Part 1| January 2020| Pages 51-62

https://doi.org/10.1107/S2059798319015134

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