Phenix refine pubmed

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August undefined, 2024

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. júl 2024 · PAIREF: paired refinement also for Phenix users. In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for …

PHENIX : a comprehensive Python-based system for macromolecular …

Web1. jún 2024 · In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure … Webscientific article (publication date: April 2012) cynthia neill

PAIREF: paired refinement also for Phenix users - PMC

Web8. nov 2024 · Similarly, Phenix uses ribose-pucker- and base-type-dependent torsional restraints for RNA (Jain et al., 2015 ). For bond lengths and angles, protein side chains … Web27. júl 2016 · PHENIX (Adams et al., 2010) is the widely popular suite of software for integrated crystallography that includes the phenix.refine (Afonine et al., 2012) application for refinement; AFITT (v.2.4.0.4; http://www.eyesopen.com/afitt; Wlodek et al., 2006) is OpenEye's package for automated ligand placement in real-space density. Web1. 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 … cynthia nelli

Use of knowledge-based restraints in phenix.refine to improve ...

Real-space refinement in PHENIX for cryo-EM and crystallography

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 ... cynthia nava lpcWeb12. apr 2024 · SignificanceIron is an essential nutrient for bacteria but has poor bioavailability in the environment and in host organisms due to its sequestration and low solubility. To overcome this challenge,... cynthia neipris

"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 … " - Phenix refine pubmed

Phenix refine pubmed

Web18. 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 ). Webphenix.refine - general purpose crystallographic structure refinement program Contents Overview Graphical interface Citation reference and comprehensive methodology details …

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WebThe standard ERRASER-Phenix pipeline consists of three major stages: an initial Phenix refinement, followed by iterative ERRASER refinement, and a final Phenix refinement (Fig. … WebHere, the implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described. …

Webphenix.reﬁne is a program within the PHENIX package that supports crystallographic structure reﬁnement against experi-mental 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. Several Web29. sep 2013 · An approach combining the sampling methodology and energy function of Rosetta with the X-ray refinement methodology of Phenix enables improved low …

Web7. júl 2024 · The refinement approach of phenix.refine differs from that of REFMAC5 in several aspects (Shabalin et al., 2024 ), such as bulk-solvent modeling (Weichenberger et … Web1. nov 2010 · This starting model was used for joint X-ray/neutron refinement in Phenix 15, 16 where H/D occupancy and position was experimentally modelled based on the neutron diffraction data. The final room ...

WebPavel Afonine explains phenix.real_space_refine.

Web8. okt 2009 · Phenix.refine is the state-of-the-art crystallographic structure-refinement engine of PHENIX. The foundational refinement machinery is a combination of highly … cynthia nerea sereno diazWeb1. apr 2012 · To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the … cynthia ni google scholarWeb10. 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 ). cynthia nell cannonWebphenix-online.org cynthia nicoliniWebThe 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. cynthia nolascophenix.refine is a program within the PHENIX package that supports … cynthia noto triconWebThe PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE … cynthia nicol ubc