Phenix refine pubmed

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August undefined, 2024

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 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 …

PAIREF: paired refinement also for Phenix users - PMC

Web1. 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.... WebUse of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (Q35878822) From Wikidata. Jump to navigation Jump to search. scientific article published on 16 March 2012. edit. Language Label Description terry doyle facebook

Modelling dynamics in protein crystal structures by ensemble refinement …

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 … 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 … Webphenix-online.org terry down there somewhere

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

Improved low-resolution crystallographic refinement with Phenix …

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 … 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 ). terry downes v sugar ray robinsonWebYou 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). terry d oxford

"Web16. mar 2012 · This article is from Acta Crystallographica Section D: Biological Crystallography, volume 68.Abstractphenix.refine is a program within the PHENIX package that... " - Phenix refine pubmed

Phenix refine pubmed

Improved low-resolution crystallographic refinement with Phenix …

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. 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 …

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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 … WebThe PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE …

Web1. júl 2024 · PAIREF: paired refinement also for Phenix users. In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for … Web16. mar 2012 · Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Item Preview remove-circle Share or Embed This Item. Share to Twitter. Share to Facebook. Share to Reddit. Share to Tumblr.

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. …

Web10. 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 ). trigon metals previously kombat copperWebRefinement of Atomic Displacement Parameters (ADP or B-factors) An ADP in phenix.refine is defined as a sum of three contributions: Utotal = Ulocal + Utls + Ucryst. where Utotal is the total ADP, Ulocal reflects the local atomic vibration (also named as residual B) and Ucryst reflects global lattice vibrations. terry doyle beatrice neWebphenix.refine - general purpose crystallographic structure refinement program Contents Overview Graphical interface Citation reference and comprehensive methodology details … terry dragon prince transWebWe developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray … trigon methodWeb8. okt 2009 · PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. terry dq6Web12. 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,... trigonmetry pdfphenix.refine is a program within the PHENIX package that supports … trigon liability and workman\\u0027s comp