Robert H. Blessing

Bio: Robert H. Blessing is an academic researcher from Hauptman-Woodward Medical Research Institute. The author has contributed to research in topics: Crystal structure & Hydrogen bond. The author has an hindex of 24, co-authored 73 publications receiving 10644 citations. Previous affiliations of Robert H. Blessing include University at Buffalo & Woodward, Inc..

An empirical correction for absorption anisotropy

Abstract: A least-squares procedure is described for modeling an empirical transmission surface as sampled by multiple symmetry-equivalent and/or azimuth rotation-equivalent intensity measurements. The fitting functions are sums of real spherical harmonic functions of even order, ylm(− u0) + ylm(u1), 2 ≤ l = 2n ≤ 8. The arguments of the functions are the components of unit direction vectors, −u0 for the reverse incident beam and u1 for the scattered beam, referred to crystal-fixed Cartesian axes. The procedure has been checked by calculations against standard absorption test data.

Outlier Treatment in Data Merging

Abstract: Experience with a variety of diffraction data-reduction problems has led to several strategies for dealing with mismeasured outliers in multiply measured data sets. Key features of the schemes employed currently include outlier identification based on the values ymedian = median(|Fi|2), σmedian = median[σ(|Fi|2)], and |Δ|median = median(|Δi|) = median[||Fi|2-median (|Fi|2)|] in samples with i = 1, 2 ..... n and n ≥ 2 measurements; and robust/resistant averaging weights based on values of |zi| = |Δi|/max{σmedian, |Δ|median[n/(n−1)]1/2}. For outlier discrimination or down-weighting, sample median values have the advantage of being much less outlier-based than sample mean values would be.

Data Reduction and Error Analysis for Accurate Single Crystal Diffraction Intensities

Abstract: Principles and procedures of diffraction data processing are described. Reflection integration limits are obtained from a least squares analysis of peak profile widths, based on the principles of convolution synthesis of peak profiles. An approximate, empirical thermal diffuse scattering correction is obtained from a least squares analysis of thermal diffuse scattering (TDS) intensity estimates, based on fitting intersecting straight lines to the background profile near the peak limits. Time-dependent scaling according to standard reference reflection intensities is based on least squares fitted scaling polynomials and may be weighted by anisotropic, intensity-dependent or scattering-angle-dependent factors. Inter-set scaling of data subsets and averaging of replicate and equivalent measurements, which includes several criteria for detecting and rejecting outlier measurements, provide a basis for a bivariate analysis of variance on F2 0 and (sin θ)/λ. Error analysis at each stage of the data proc...

Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

Abstract: The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.

WinGX suite for small-molecule single-crystal crystallography

Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.

WinGX and ORTEP for Windows: an update

Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.

Scaling and assessment of data quality

Abstract: The various physical factors affecting measured diffraction intensities are discussed, as are the scaling models which may be used to put the data on a consistent scale. After scaling, the intensities can be analysed to set the real resolution of the data set, to detect bad regions (e.g. bad images), to analyse radiation damage and to assess the overall quality of the data set. The significance of any anomalous signal may be assessed by probability and correlation analysis. The algorithms used by the CCP4 scaling program SCALA are described. A requirement for the scaling and merging of intensities is knowledge of the Laue group and point-group symmetries: the possible symmetry of the diffraction pattern may be determined from scores such as correlation coefficients between observations which might be symmetry-related. These scoring functions are implemented in a new program POINTLESS.

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Abstract: While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non Gly, Pro) backbone CMAP potential has been refined against experimental solution NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mechanical energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mechanical energy surfaces, followed by additional empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against data not used to guide parametrization: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equilibrium folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.