Phenix real space refine rotemers
WebThis article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost.
Phenix real space refine rotemers
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WebCCP4 WebThe crystallographic refinement was carried out with PHENIX with restrained refinement and TLS refinement implemented in the final stages. The model building and real-space refinement were performed in COOT [ 47 ] and upon completion of the refinement 99% of the residues were in Ramachandran favored or allowed regions, while 1% were outliers.
Webphenix.real_space_refinetool can be applied to refine cryo-EM-derived models in real space. This program computes Real Space Correlationcoefficients between map and model-derived map and, additionally, it assesses the geometry and dihedral-angle combinations of atomic structures with the aim of getting the best map-fitted structure by 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 …
Web17. jan 2024 · This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Web1. jan 2013 · phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of …
WebA complete graphical interface for phenix.refine is available; it includes integration with several refinement-related utilities such as phenix.ready_set, …
Web1. apr 2012 · phenix.refineis a program within the PHENIXpackage 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. indigo chapter important pointsWeb1. jún 2024 · In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary- structure … indigo chapters bayers lakeWeb10. jan 2024 · The real-space refinement algorithm includes a fast and efficient search for the optimal relative weight of restraints, a procedure that is extremely challenging for … lockwood at lyons houstonWebPhenix Workshop 4/14/2024 (cryo-EM) - Real Space Refinement Phenix Tutorials 1.82K subscribers Subscribe 3.1K views 1 year ago Phenix user workshops Pavel Afonine … indigo change flight chargesWeb1. jún 2024 · The real-space refinement algorithm includes a fast and efficient search for the optimal relative weight of restraints, a procedure that is extremely challenging for … lockwood assisted living waterfordWeb1. jún 2024 · This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified … indigo chapter questions and answers ncertWeb21. feb 2024 · The coordinates of the obtained single-chain model were modified manually using Coot and refined with repeated rounds of Phenix real-space refine function. The structure was further refined in real-space in PHENIX with secondary structure restraint . The atomic models were validated using the Cryo-EM validation tools of Phenix . Briefly, each ... indigo chapters canada books