phenix.refine is a program within the PHENIX package 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. Several hundred parameters enable extensive customizations for complex use cases. Multiple user‐defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X‐ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The high‐intensity time‐of‐flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM ...II at Garching close to Munich, Germany. Because of the world‐wide 3He crisis in 2009, the authors promptly initiated the development of 3He‐free detector alternatives that are tailor‐made for the requirements of large‐area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular‐ and wavelength‐dependent data from the POWTEX detector, unfortunately damaged by a 50g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A, 764, 156–166. The final part of the data treatment chain, namely a novel multi‐dimensional refinement using a modified version of the GSAS‐II software suite Toby & Von Dreele (2013). J. Appl. Cryst.46, 544–549, is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS‐II. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly‐user sample, BaZn(NCN)2. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi‐dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN)2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large‐area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.
The first real‐world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular‐ and wavelength‐dispersive Rietveld refinement using a modified version of GSAS‐II.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior ...conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (
B
factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in
REFMAC
5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using
REFMAC
5 and related tools distributed as part of the
CCP
4 suite is discussed.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The concept of isogeometric analysis is proposed. Basis functions generated from NURBS (Non-Uniform Rational B-Splines) are employed to construct an exact geometric model. For purposes of analysis, ...the basis is refined and/or its order elevated without changing the geometry or its parameterization. Analogues of finite element
h- and
p-refinement schemes are presented and a new, more efficient, higher-order concept,
k-refinement, is introduced. Refinements are easily implemented and exact geometry is maintained at all levels without the necessity of subsequent communication with a CAD (Computer Aided Design) description. In the context of structural mechanics, it is established that the basis functions are complete with respect to affine transformations, meaning that all rigid body motions and constant strain states are exactly represented. Standard patch tests are likewise satisfied. Numerical examples exhibit optimal rates of convergence for linear elasticity problems and convergence to thin elastic shell solutions. A
k-refinement strategy is shown to converge toward monotone solutions for advection–diffusion processes with sharp internal and boundary layers, a very surprising result. It is argued that isogeometric analysis is a viable alternative to standard, polynomial-based, finite element analysis and possesses several advantages.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
While smoothed-particle hydrodynamics (SPH) simulations are usually performed using uniform particle distributions, local particle refinement techniques have been developed to concentrate fine ...spatial resolutions in identified areas of interest. Although the formalism of this method is relatively easy to implement, its robustness at coarse/fine interfaces can be problematic. Analysis performed in 16 shows that the radius of refined particles should be greater than half the radius of unrefined particles to ensure robustness. In this article, the basics of an Adaptive Particle Refinement (APR) technique, inspired by AMR in mesh-based methods, are presented. This approach ensures robustness with alleviated constraints. Simulations applying the new formalism proposed achieve accuracy comparable to fully refined spatial resolutions, together with robustness, low CPU times and maintained parallel efficiency.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
This article describes the implementation of real‐space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...calculation, which in turn makes it possible to identify optimal data‐restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low‐resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary‐structure and rotamer‐specific restraints, as well as restraints or constraints on internal molecular symmetry. The re‐refinement of 385 cryo‐EM‐derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
A description is provided of the implementation of real‐space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re‐refinement of cryo‐EM‐derived models.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
This study investigates and evaluates applications of the adjoint problem and its solution in frequency-domain computational electromagnetics (CEM). The study establishes and validates adjoint-based ...applications including higher order parameter sampling, a posteriori error estimate evaluation, and <inline-formula> <tex-math notation="LaTeX">p </tex-math></inline-formula>- and <inline-formula> <tex-math notation="LaTeX">h </tex-math></inline-formula>-refinements. These applications can improve the efficiency, automation, and robustness of CEM methods. We employ a 1-D finite-element-method scattering solver, simplifying the implementation, replicability, clarity, and intuitiveness of analysis results and conclusions, which then extend naturally to higher dimensional solvers and more complicated CEM problems. While demonstrated with a higher order solver, the derived techniques apply to low-order methodology as well. This is the first demonstration of the applicability of adjoint-based a posteriori error estimation techniques to adaptive discretization refinement in frequency-domain CEM with arbitrary-order basis functions. This work introduces the application of dual-weighted residual error estimation and selective adaptivity based on error cancellation. The proposed targeted, adaptive mesh/model <inline-formula> <tex-math notation="LaTeX">p </tex-math></inline-formula>- and/or <inline-formula> <tex-math notation="LaTeX">h </tex-math></inline-formula>-refinement heuristics informed by adjoint element-wise error contribution estimates show near-monotonic reduction of the quantity-of-interest error with increased numbers of refined elements. In general, adjoint techniques are underutilized in CEM, and another goal of this work is to promote their future use for refinement, optimization, and uncertainty quantification.
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high‐fidelity interactive remodelling/refinement of macromolecular models into electron‐density ...maps. ISOLDE combines interactive molecular‐dynamics flexible fitting with modern molecular‐graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo‐EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low‐resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low‐resolution model.
ISOLDE is an interactive molecular‐dynamics environment for rebuilding models against experimental cryo‐EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low‐resolution data.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
PDF
