site stats

Phenix refine pubmed

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 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 …

PAIREF: paired refinement also for Phenix users - PMC

Web8. 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. WebRefinement 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. flight vy7821 https://ppsrepair.com

Towards automated crystallographic structure refinement with phenix ...

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 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 software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without … flightvtracker tampa to austin

Phenix User Workshop 9/16/2024 - phenix.real_space_refine

Category:Accurate macromolecular crystallographic refinement ... - PubMed

Tags:Phenix refine pubmed

Phenix refine pubmed

Towards automated crystallographic structure refinement with phenix …

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 … 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

Did you know?

Webphenix-online.org Web12. 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,...

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. … 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....

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 … 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. …

WebTo improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement …

WebWe developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray … greater anglia trains strike datesWeb1. júl 2024 · PAIREF: paired refinement also for Phenix users. In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for … flight vy6616Web1. jún 2024 · Real-space refinement in PHENIX for cryo-EM and crystallography. This article describes the implementation of real-space refinement in the phenix.real_space_refine … greater anglia trains strikesWeb18. 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 ). greater anglia trains stationsWeb1. 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 … greater anglia train strike datesWeb8. 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 … greater anglia trains timetable 2021Web10. 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 ). flight vte xkh