WebAug 5, 2024 · The phenix.refine (Afonine et al., 2012) engine is used when a file containing reflections in either MTZ or mmCIF format is provided, and phenix.real_space_refine … WebAug 7, 2024 · The structure was iteratively built using COOT and refined using phenix.refine with atomic scattering factors for electrons, automatic weighting of the geometry term, …
phenix.pdbtools: PDB model manipulations and statistics
WebJan 11, 2024 · All model building was performed using Coot 0.8.9.2 56 and refinement steps were performed with phenix.refine (v1.17.1.3660) within the PHENIX suite. 53,56 Restraints for the red and green chromophores were generated using phenix.elbow, 57 starting from coordinates available in the Protein Data Bank 58 (PDB ligand ID: NRQ or CH6 for red or ... WebMar 16, 2012 · phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. grand trunk rec center edmonton
Improved chemistry restraints for crystallographic …
Webphenix.den_refine: DEN refinement in Phenix Deformable elastic network (DEN) refinement is a refinement protocol that uses a sparse restraint network to maintain local model geometry while allowing for larger global domain motions over the course of several macrocycles of slow-cooling simulated annealing. WebWe compared Rosetta-Phenix refinement (phenix.rosetta_ refine) to three different low-resolution refinement strategies. As a control, structures were refined for 20 cycles in phenix.refine, optimizing X-ray weight at each cycle. We also refined structures in CNS. 1. 4 WebNov 8, 2024 · In a standard default Phenix refinement, the weight w is a combination of a value based on the ratio of gradient norms (Brünger et al., 1989; Adams et al., 1997) and a … grand trunk indian clothes