Structure refinement in PHENIX
WEBRigid body refinement. phenix.refine implementation of rigid body refinement is highly and efficient (large convergence radius, no need to cut high-resolution data). We call this MZ protocol (multiple zones).
Real-space refinement (cryo-EM) - phenix-online.org
WEBThe program used to refine atomic models in real space is phenix.real_space_refine. The algorithm uses a simplified refinement target function that speeds up calculations, so optimal data-restraint weights can be identified with little runtime cost.
Phenix
WEBPhenix is a comprehensive software package for macromolecular structure determination that handles data from diffraction (X-ray, neutron and electron) and electron cryo-microscopy. Tasks include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition.
Tutorial: Molecular replacement, refinement, and rebuilding …
WEBOverview. This tutorial is intended for users who are completely unfamiliar with macromolecular crystallography and/or Phenix. It outlines the procedure for solving a structure by molecular replacement, performing initial refinement, and rebuilding the structure in Coot.
Structure refinement in PHENIX - University of Oregon
WEBStructure refinement in PHENIX. phenix.refine is run from the command line: % phenix.refine <pdb-file (s)> <reflection-file (s)> <monomer-library-file (s)>. When you do this a number of things happen:
WEBphenix.refine allows multi-step complex refinement jobs, for example, containing: rigid body refinement, Simulated Annealing, individual or grouped B-factors combined with TLS refinement, constrained occupancy refinement, automatic water picking to …
Towards automated crystallographic structure refinement with phenix…
WEBphenix.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.
WEBX-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.
Real-space refinement in PHENIX for cryo-EM and crystallography
WEBJun 1, 2018 · 1. Introduction. Improvements in the cryo-electron microscopy (cryo-EM) technique have led to a rapid increase in the number of high-resolution three-dimensional reconstructions that can be interpreted with atomic models (Fig. 1).
Frequently asked questions for phenix.refine
WEBSimulated annealing (SA) is most useful early in refinement, when the model is far from convergence. Manually built models, or MR solutions involving significant local conformational changes, are common inputs where SA can improve over simple gradient-driven refinement.