Phenix refine pubmed
Web1. júl 2024 · PAIREF: paired refinement also for Phenix users. In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for … WebThe PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The …
Phenix refine pubmed
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Webphenix-online.org WebThe PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without …
Web1. apr 2012 · PubMed; License; CC BY 2.0; Project: Phenix; Authors: ... phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a ... Web15. mar 2012 · The resulting models with the best Phaser likelihood scores are then refined with phenix.refine and used to create a new set of density-modified maps. These maps are averaged to yield a single averaged density-modified map. ... Article PubMed CAS Google Scholar Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L (2004) The …
Webphenix.refine - general purpose crystallographic structure refinement program Contents Overview Graphical interface Citation reference and comprehensive methodology details … WebThe graphical interface for phenix.refine runs the unmodified command-line version; default settings are unchanged. All parameters should be configurable through the GUI, although some of these (such as NCS restraint groups) are handled in a non-standard way.
WebYou can launch phenix.refine directly from Phaser by clicking the button labeled "Run phenix.refine". This will load the output model and the MTZ file; you should also input the sequence (this is not actually used in refinement, but the post-refinement validation will check for sequence errors in the model).
WebNational Center for Biotechnology Information channels around the worldWeb10. jan 2024 · In this paper, we describe the implementation of the phenix.real_space_refine program and demonstrate its performance by applications to simulated data and to cryo-EM models in the PDB (Bernstein et al., 1977; Berman et al., 2000) and corresponding maps in the EMDB (Henrick et al., 2003 ). harley stretch bagsWeb18. dec 2012 · Analysis of all 20 datasets showed that ensemble refinement improved the Rfree by between 0.3 and 4.9 percentage points compared to single structures re-refined using the same program package, that is Phenix ( Afonine et al., 2012 ), with a mean improvement of 1.8% in Rfree values ( Table 1, Figure 2A ). harley street wellbeing centre clinic prioryWeb1. apr 2012 · To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine.... channels available on spectrum tvWeb1. júl 2011 · 2.2. Pre-refinement correction of rotamer outliers. To improve the performance of refinement with a reference model, we added a complementary method to identify and correct rotamer outliers in the working model by comparison with the reference model. Outliers are identified with phenix.rotalyze (Adams et al., 2010), which uses the … harley stretched bagsWeb1. jún 2024 · In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure … harley stretched baggerWebscientific article (publication date: April 2012) channels available on sling orange and blue