scholarly journals Improving signal strength in serial crystallography with DIALS geometry refinement

2018 ◽  
Vol 74 (9) ◽  
pp. 877-894 ◽  
Author(s):  
Aaron S. Brewster ◽  
David G. Waterman ◽  
James M. Parkhurst ◽  
Richard J. Gildea ◽  
Iris D. Young ◽  
...  
Keyword(s):  
Heavy Atom ◽  
Incident Beam ◽  
Nonlinear Least Squares ◽  
Small Time ◽  
Unit Cell ◽  
Detector Position ◽  
Computational Performance ◽  
Anomalous Peak ◽  
Serial Crystallography ◽  
Fitting In

The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.

Determination of the structure of bis(propyldithiocarbamate)nickel(II)

1990 ◽  
Vol 55 (4) ◽  
pp. 1010-1014 ◽  
Author(s):  
Jiří Kameníček ◽  
Richard Pastorek ◽  
František Březina ◽  
Bohumil Kratochvíl ◽  
Zdeněk Trávníček
Keyword(s):  
Molecular Structure ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Planar Configuration ◽  
Compound C ◽  
Heavy Atom Method

The crystal and molecular structure of the title compound (C8H16N2NiS4) was solved by the heavy atom method and the structure was refined anisotropically to a final R factor of R = 0.029 (wR = 0.037) for 715 observed reflections. The crystal is monoclinic, space group P21/c with a = 948.3(2), b = 776.9(2), c = 1 167.4(2) pm, β = 125.14(2)°, Z = 2. The molecule contains two four-membered NiSCS rings of approximately planar configuration with the Ni atom situated at a centre of symmetry. The molecules are arranged in chains along the c-axis of the unit cell.

scholarly journals Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites

2009 ◽  
Vol 42 (2) ◽  
pp. 259-264 ◽  
Author(s):  
Xinguo Hong ◽  
Quan Hao
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Unit Cell ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Molecular Envelope ◽  
Waxs Data ◽  
Ray Scattering

Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the programGASBORat 5 Å resolution (qmax= 1.25 Å−1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2σ level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax= 0.25 Å−1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination ofFSEARCHand WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.

Nanoindentation Method for Determining the Initial Contact and Adhesion Characteristics of Soft Polydimethylsiloxane

2005 ◽  
Vol 20 (8) ◽  
pp. 2004-2011 ◽  
Author(s):  
Yifang Cao ◽  
Dehua Yang ◽  
Wole Soboyejoy
Keyword(s):  
Indentation Depth ◽  
Contact Point ◽  
Nonlinear Least Squares ◽  
Soft Materials ◽  
Work Of Adhesion ◽  
Contact Radius ◽  
Initial Contact ◽  
Combined Use ◽  
Fitting In ◽  
Load Indentation

In this paper, we present a method for determining the initial contact point and nanoindentation load–indentation depth characteristics for soft materials. The method is applied to the prediction of the load–indentation depth characteristics of polydimethylsiloxane. It involves the combined use of Johnson–Kendall–Roberts and Maugis–Dugdale adhesion theories and nonlinear least squares fitting in the determination of the initial contact point, the transition parameter, and the contact radius at zero contact load. The elastic modulus and the work of adhesion are also extracted from the load–indentation depth curves.

Nonlinear least-squares data fitting in Excel spreadsheets

2010 ◽  
Vol 5 (2) ◽  
pp. 267-281 ◽  
Author(s):  
Gerdi Kemmer ◽  
Sandro Keller
Keyword(s):  
Least Squares ◽  
Nonlinear Least Squares ◽  
Data Fitting ◽  
Fitting In

The crystal structure of bis(ethyldiazoacetate) mercury(II) Hg(CN2CO2C2H5)2

1977 ◽  
Vol 55 (20) ◽  
pp. 3527-3529 ◽  
Author(s):  
R. A. Smith ◽  
M. Torres ◽  
O. P. Strausz
Keyword(s):  
Crystal Structure ◽  
Diffuse Scattering ◽  
Heavy Atom ◽  
Unit Cell ◽  
Thermal Parameters ◽  
Fold Axis ◽  
Axis Of Symmetry ◽  
Cell Data ◽  
Unit Cell Data

Bis(ethyldiazoacetate) mercury(II) is orthorhombic with the following unit cell data at 20 °C: Fdd2, a = 19.810(8), b = 14.387(5), c = 9.015(2) Å, V = 2569.3 Å3, ρ0 = 2.17(2), ρc = 2.21, Z = 8 ([Formula: see text]λ = 0.70930 Å). The structure was solved by heavy atom methods and refined to R = 2.2% for 706 reflections. The molecule has a 2-fold axis of symmetry and all thermal parameters are large in the direction of this axis; diffuse scattering was observed in the rotation photograph taken about this axis. As expected the diazoacetate portion is planar.

A Translation-Function Approach for Heavy-Atom Location in Macromolecular Crystallography

1998 ◽  
Vol 54 (3) ◽  
pp. 400-402 ◽  
Author(s):  
Alexei Vagin ◽  
Alexei Teplyakov
Keyword(s):  
Heavy Atom ◽  
Unit Cell ◽  
Function Approach ◽  
Macromolecular Crystallography ◽  
Heavy Atoms ◽  
Anomalous Data ◽  
Translation Function ◽  
Full Symmetry

A method for locating heavy atoms in the unit cell of macromolecular crystals by a full-symmetry translation function is described. The approach has been implemented in the program TRAHALO and tested on experimental isomorphous and anomalous data.

scholarly journals Serial Crystallography with Multi-stage Merging oi 1000’s of Images

2017 ◽  
Author(s):  
Herbert J. Bernstein ◽  
Lawrence C. Andrews ◽  
James Foadi ◽  
Martin R. Fuchs ◽  
Jean Jakoncic ◽  
...  
Keyword(s):  
Data Clustering ◽  
Clustering Algorithms ◽  
Unit Cell ◽  
Physical Parameters ◽  
Data Sets ◽  
Cell Parameters ◽  
Cell Clustering ◽  
Multi Stage ◽  
Cluster Data ◽  
Serial Crystallography

KAMO and Blend provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options to increase the sensitivity to differences in unit cell parameters and to allow for clustering of nearly complete datasets on the basis of intensity or amplitude differences. If datasets are already sufficiently complete to permit it, apply KAMO once, just for reflections. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step either the simple cell vector distance of the original Blend is used, or the more sensitive NCDist, to find clusters to merge to achieve sufficient completeness to allow intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections at the common HKLs to merge clusters in a way sensitive to structural differences that may not perturb the cell parameters sufficiently to make meaningful clusters.Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which can then be merged to, hopefully, yield the electron density from a single protein iso-form. What is striking about many of these physical parameters is that they are largely independent from one another. Consequently, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy was to use unit-cell clustering until merged data was of sufficient completeness to then use intensity based clustering. We have demonstrated that, using this strategy, we were able to accurately cluster data sets from crystals that had subtle differences.

scholarly journals Pattern-matching indexing of Laue and monochromatic serial crystallography data for applications in materials science

2020 ◽  
Vol 53 (3) ◽  
pp. 824-836
Author(s):  
Catherine Dejoie ◽  
Nobumichi Tamura
Keyword(s):  
Pattern Matching ◽  
Materials Science ◽  
Reciprocal Lattice ◽  
Unit Cell ◽  
Crystallographic Structure ◽  
Experimental Conditions ◽  
Lattice Vector ◽  
Small Unit ◽  
Orientation Matrix ◽  
Serial Crystallography

Serial crystallography data can be challenging to index, as each frame is processed individually, rather than being processed as a whole like in conventional X-ray single-crystal crystallography. An algorithm has been developed to index still diffraction patterns arising from small-unit-cell samples. The algorithm is based on the matching of reciprocal-lattice vector pairs, as developed for Laue microdiffraction data indexing, combined with three-dimensional pattern matching using a nearest-neighbors approach. As a result, large-bandpass data (e.g. 5–24 keV energy range) and monochromatic data can be processed, the main requirement being prior knowledge of the unit cell. Angles calculated in the vicinity of a few theoretical and experimental reciprocal-lattice vectors are compared, and only vectors with the highest number of common angles are selected as candidates to obtain the orientation matrix. Global matching on the entire pattern is then checked. Four indexing options are available, two for the ranking of the theoretical reciprocal-lattice vectors and two for reducing the number of possible candidates. The algorithm has been used to index several data sets collected under different experimental conditions on a series of model samples. Knowing the crystallographic structure of the sample and using this information to rank the theoretical reflections based on the structure factors helps the indexing of large-bandpass data for the largest-unit-cell samples. For small-bandpass data, shortening the candidate list to determine the orientation matrix should be based on matching pairs of reciprocal-lattice vectors instead of triplet matching.

Enhancing XRPD Pattern Quality With Line-Profile-Fitting in Multiphase Systems

1993 ◽  
Vol 37 ◽  
pp. 95-99
Author(s):  
G. Kimmel ◽  
J. Sariel ◽  
I. Dahan ◽  
S. Nathan ◽  
U. Admon
Keyword(s):  
Line Profile ◽  
Systematic Errors ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Major Work ◽  
Cell Parameters ◽  
The Past ◽  
Profile Fitting ◽  
Pure Substances ◽  
Fitting In

In the past the powder diffraction data where presented as d-I sets as obtained experimentally and systematic errors were utilized only for the derivation of the unit cell parameters. This attitude was justified by the fact that the major work of XRPD made by Debye-Scherrer camera and it was assumed that most users would obtain the same systematic errors. Nowadays, diffractometry has taken over, and the diffractometers have lower systematic errors, which can minimized by calibration. Thus, they are now preferred. There are many phases which can be used as standards, but only four were selected, namely, Si, Ag, W, and mica (FP), which can easily be obtained as pure substances, have a limited number of diffraction lines and the distribution of intensities along 2θ is good. The calibration is made by fitting a polynomial which correlates the standard experimental peak positions versus the expected (calculated) values. However, while on the one hand, the more peaks which are used, the better the fit which can be achieved; on the other hand using a standard with many peaks enhances the probability for interference with the examined specimen peaks. Thus, it was decided to determine each line position by line profile fitting as was recommended elsewhere. In order to derive real observed data we do not link the diffraction lines between themselves by global structural or tine shape parameters. Thus, local variations in line profile parameters are treated. In the line-profile-fitting method suggested here the final structural details (atomic positions) are not required. Similar method have been used in the past for structure analysis, unit-cell refinement, and broadening analysis of pure substances. It was found that using the suggested method yields accurate unit cell parameters for each individual phase in the polyphase mixture. Several systems will be demonstrated in this work.

Crystal and molecular structure of the m-bromobenzoate derivative of bisnorquassin

1970 ◽  
Vol 48 (2) ◽  
pp. 307-311 ◽  
Author(s):  
H. Lynton
Keyword(s):  
Molecular Structure ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Unit Cell ◽  
Anisotropic Temperature ◽  
Cell Dimensions ◽  
Final Agreement ◽  
Unit Cell Dimensions ◽  
Heavy Atom Method ◽  
Atomic Parameters

The molecular structure of the m-bromobenzoate derivative of bisnorquassin, C27H27O7Br, has been determined by the heavy atom method. The compound crystallizes in the orthorhombic system, space group P212121, with unit cell dimensions a = 20.09 ± 0.02 Å, b = 14.63 ± 0.02 Å, c = 8.06 + 0.01 Å and 4 molecules in the unit cell. Final atomic parameters have been obtained from a blockdiagonal least-squares refinement using anisotropic temperature parameters. The final agreement residual for 1665 observed reflections is R = 0.107.The structure of bisnorquassin previously proposed by Findlay and Cropp, on the basis of spectroscopic and chemical evidence, is shown to be essentially correct.

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