Phenix refine anisotropic b factors

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Webcommand phenix.refine--show_defaults=alland then take the parameters that you want to use. Refinement scenarios Refining group isotropic B-factors: % phenix.refine data.hkl … WebFeb 18, 2015 · Four-stranded structures known as G-quadruplexes have been implicated in cellular processes and found potential applications in therapeutics and nanotechnology. G-quadruplex structures are highly polymorphic, but so far, only right-handed helical forms have been observed.

Structure of a left-handed DNA G-quadruplex PNAS

WebAug 26, 2014 · Structure Factors (CIF) Structure Factors (CIF - gz) Validation Full PDF; Validation (XML - gz) ... b = 143.307: β = 90: c = 120.512: γ = 120: Software Package: … http://phenix.lbl.gov/pipermail/phenixbb/2012-July/018742.html robust in software engineering

[phenixbb] scattering factors - phenix.lbl.gov

WebTemperature Factor Modeling; Anisotropic B[1][1] ... Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] RMS Deviations; Key Refinement Restraint Deviation; f_dihedral_angle_d ... 1243: Nucleic Acid Atoms: Solvent Atoms: 59: Heterogen Atoms: 28: Software. Software; Software Name Purpose; PHENIX: refinement: xia2: data reduction: xia2 ... WebJan 1, 2003 · In fact, if the anisotropy is small, the same benefit may be obtained by applying global B factors to each molecule, but such a case is included automatically in the TLS refinement. We therefore recommend that TLS refinement at the level of molecules should be considered for all refinements. WebApr 19, 2016 · The model was refined against all of the diffraction data using PHENIX . At the end of structure refinement, anisotropic B-factors were refined resulting in an R factor of 14.5% and an R free]. The refined structure comprises residues 10–125 of TTR, 2 TBBPA molecules, 1 sodium ion, and 202 water molecules. There are no Ramachandran outliers ... robust independence lathe

Experiment: 7EYX

http://phenix.lbl.gov/pipermail/phenixbb/2012-July/018744.html WebMany of the programs in Phenix, and phenix.refine in particular, allow (or require) you to specify selections of atoms in a model. Common examples include: TLS (constrained … robust indicationWebphenix.refine allows multi-step complex refinement jobs, for example, containing: rigid body refinement, Simulated Annealing, individual or grouped B-factors combined with TLS … robust in statistics meaning

"WebR-Factor (Observed) R-Work R-Free Mean Isotropic B; X-RAY DIFFRACTION ... Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] RMS Deviations; Key Refinement Restraint Deviation ... 5988: Nucleic Acid Atoms: Solvent Atoms: 775: Heterogen Atoms: 44: Software. Software; Software Name Purpose; PHENIX ... " - Phenix refine anisotropic b factors

Phenix refine anisotropic b factors

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WebRefinement of atomic displacement parameters (commonly named as ADP or B-factors) An ADP in phenix.refine is defined as a sum of three contributions: Utotal = Ulocal + Utls + … WebNov 18, 2013 · B factors will be refined as anisotropic if the resolution is better than 1.5 Å, or if the resolution is worse than 2.5 Å and the atomic number is at least 19 (potassium). Because the procedure depends on the accurate placement of isolated single atoms, it is generally not suitable for low-resolution structures.

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WebApr 1, 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. WebJul 2, 2012 · >>phenix.refine (version 1.7.3) it is not very clear (at least for me) >>if the refinement was with TLS groups and individual isotropic >>B-factors or with anisotropic B …

Webphenix.refine and phenix.model_vs_data use the same code to perform the bulk solvent correction and scaling, so they should report approximately the same R-factors given … WebOptions include coordinate refinement (individually against reciprocal-space data or real-space maps; or as rigid-body groups against reciprocal-space data); B-factor or ADP …

WebTemperature Factor Modeling; Anisotropic B[1][1] ... Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] Non-Hydrogen Atoms Used in Refinement; Non-Hydrogen Atoms Number; Protein Atoms: 5726: Nucleic Acid Atoms: Solvent Atoms: Heterogen Atoms: 64: Software. Software; Software Name Purpose; PHENIX: refinement: REFMAC: refinement: … WebOct 27, 2015 · The phenix.ensemble_refinement method [ 8] uses electron density to bias molecular dynamics simulations, then assembles snapshots from this trajectory into a multi-copy ensemble model. However, energy barriers of the simulation may prevent sampling of well separated backbone conformations.

WebMay 3, 2024 · Anisotropic B-factor refinement was not possible for the S complex at room temperature so no entropy estimates from anisotropic B-factors are presented. These results suggest that the room temperature B -factors provide a more realistic picture of movements in the protein, although the entropies are still ∼5 times higher than those …

http://www.uoxray.uoregon.edu/local/manuals/phenix-1.24.1b/phenix/structure_refinement.html robust indonesiahttp://phenix.lbl.gov/pipermail/phenixbb/2011-June/017302.html robust indexWebRefinement 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 … Other links Bibliography Dictionary Index Find a program or regression test Citing … Individual B-factors is restrained atomic B-factor refinement, and is usually appro… Many of the programs in Phenix, and phenix.refine in particular, allow (or require) … robust inference for dyadic dataWebThe densification of integrated circuits requires thermal management strategies and high thermal conductivity materials 1-3.Recent innovations include the development of … robust indoor localization with ads-bWeb(Anecdotally, we have found that phenix.refine often refines to much tighter RMSDs with similar R-frees to other programs. This may reflect different approaches used in the … robust indoor gun racksWebphenix.ensemble_refinement is designed to combine X-ray structure refinement with molecular dynamics in order to produce ensemble models fitted to diffraction data. These ensemble models can contain ~50-500 individual structures and simultaneously account for anisotopic and anharmonic distributions. Burnley BT, Afonine PV, Adams PD, Gros P. 2012. robust indiahttp://phenix.lbl.gov/pipermail/phenixbb/2008-April/012174.html robust industry