WebJan 17, 2024 · We refined this model against the composite cryo-EM map using phenix.real_space_refine 56, followed by manual model building in Coot 57 and subsequent refinement in phenix.real_space_refine ... WebJan 1, 2013 · The final model was refined in real space with Phenix.real_space_refinement with secondary structure restraints 67, 68 . For validation of the refinement, FSC (FSC sum ) between the...
[phenixbb] refinement of EM models with hydrogens using …
Webphenix.refine: Carry out refinement of a model phenix.secondary_structure_restraints: generate pseudo H-bond restraints for alpha helices, beta sheets, and nucleic acid base pairs Validation phenix.b_factor_statistics: Display summary of atomic displacement parameters for a model (or atom selection) WebExamples. Refinement of 1akg structure at 1.1 A resolution. In this series of examples we review the simple refinement with all default parameters, automatic picking and refinement of solvent molecules, switching from isotropic to anisotropic ADP refinement, practice monitoring of Rfactors change during refinement and experience the effect of adding and … fulton street pub and grill grand rapids mi
Structure refinement in PHENIX
http://phenix.lbl.gov/pipermail/phenixbb/2024-October/025185.html WebSep 28, 2024 · Pavel Afonine explains phenix.real_space_refine. Webreal_space_optimize_x_h_orientation = True ; xh_bond_distance_deviation_limit = 0.0 Idealize XH bond distances if deviation from ideal is greater than … Phenix Documentation - version unknown. Crystallography Cryo-EM Predicted … The graphical interface for phenix.refine runs the unmodified command-line … These examples specify hydrogen atoms, water molecules (detected by residue … fulton street station mta