scholarly journals SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data

IUCrJ ◽  
2019 ◽  
Vol 6 (1) ◽  
pp. 72-84 ◽  
Author(s):  
Chufeng Li ◽  
Xuanxuan Li ◽  
Richard Kirian ◽  
John C. H. Spence ◽  
Haiguang Liu ◽  
...  
Keyword(s):  
Simulated Data ◽  
Peptide Ligand ◽  
Acta Cryst ◽  
Inorganic Molecule ◽  
Cell Parameters ◽  
Unit Cells ◽  
Single Pattern ◽  
Diffraction Patterns ◽  
Time Required

SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.

TexPat – a program for quantitative analysis of oblique texture electron diffraction patterns

2004 ◽  
Vol 219 (1) ◽  
Author(s):  
Peter Oleynikov ◽  
Sven Hovmöller ◽  
Xiaodong Zou ◽  
Anatoliy P. Zhukhlistov ◽  
Maxim S. Nickolsky ◽  
...  
Keyword(s):  
Automated Detection ◽  
Unit Cell ◽  
Published Data ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Symmetry Properties ◽  
Speed Up ◽  
Diffraction Patterns ◽  
Integrated Intensities

AbstractWe have developed a program – TexPat for quantification of texture patterns in order to facilitate, speed up and improve the accuracy of this analytical method. The program introduces new approaches for automated detection of centre and symmetry axes and simplifies the process of indexing and calculating the unit cell parameters. The main algorithm of the program uses the symmetry properties of the texture pattern images. The successive steps help to process the reflections of the pattern using the peak shape extracted from well-separated peaks. The program generates a list of unit cell parameters, all processed reflections with Miller indices and their integrated intensities. The quality of the results obtained by TexPat is compatible with published data.

Systematic crystallographic refinement of triclinic unit cells

1998 ◽  
Vol 13 (1) ◽  
pp. 22-31
Author(s):  
Ludo K. Frevel
Keyword(s):  
Powder Diffraction ◽  
Unit Cell ◽  
Simultaneous Equations ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Triclinic Phase ◽  
Unit Cells ◽  
Diffraction Patterns ◽  
Limits Of Error

Combining the exhaustive indexing of triclinic powder diffraction patterns with a crystallographic determination of unit cell parameters from pinacoid and prism reflections yields unit cell parameters with realistic limits of error. Additionally a referee method has been developed by which the six reciprocal cell parameters of a triclinic phase are determined by solving an exhaustive set of linear simultaneous equations in six unknowns.

Unit cell dimensions of the hydrated aluminium phosphate–sulphate minerals sanjuanite, kribergite, and hotsonite

1989 ◽  
Vol 53 (371) ◽  
pp. 385-386 ◽  
Author(s):  
H. De Bruiyn ◽  
G. J. Beukes ◽  
W. A. Van Der Westhuizen ◽  
E. A. W. Tordiffe
Keyword(s):  
Unit Cell ◽  
X Ray Diffraction ◽  
Aluminium Phosphate ◽  
Powder Diffraction File ◽  
Cell Parameters ◽  
Cell Dimensions ◽  
Unit Cells ◽  
Diffraction Patterns ◽  
Unit Cell Dimensions ◽  
Hydrated Aluminium

AT the time when the hydrated aluminium phosphate-sulphate hotsonite (Beukes et al., 1984a) and its equally rare relative zaherite (Beukes et al., 1984b; De Bruiyn et al., 1985) were discovered near Pofadder, South Africa, very little was known about the unit cells of the other two hydrated aluminium phosphate-sulphate minerals sanjuanite and kribergite, originally described by De Abeledo et al. (1968) from Argentina and Sweden, respectively. Although the Powder Diffraction file (PDF) contains the X-ray diffraction patterns for sanjuanite and kribergite (PDF 20-47 and 20-48 respectively), they had not been indexed nor have their unit cell parameters been calculated thus far.

Improvement of X-ray powder diffraction patterns of the spin transition polymer [Fe(Htrz)3](ClO4)2⋅1.85H2O

2001 ◽  
Vol 16 (1) ◽  
pp. 37-41 ◽  
Author(s):  
E. Smit ◽  
B. Manoun ◽  
S. M. C. Verryn ◽  
D. de Waal
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Spin Transition ◽  
Powder Diffraction Data ◽  
High Quality ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters ◽  
Diffraction Patterns

The effects of proper drying and grinding of [Fe(Htrz)3](ClO4)2⋅1.85H2O specimens on the quality of X-ray powder patterns are illustrated (Htrz=1H-1,2,4-Triazole). A procedure is suggested to achieve high-quality, reproducible X-ray powder patterns of the compound. The observed powder diffraction data of the compound are reported together with preliminary indices calculated for a monoclinic system with cell parameters a=15.8160 Å, b=20.6134 Å, c=13.0321 Å, β=103.83° and Volume=4125.633 Å3, with reliability factors: M15=10.4, F15=22.0 (0.0100; 68) and space group P21/m. This compound is very similar to the compound [Cu(Hyetrz)3](ClO4)2⋅3H2O and a comparison is made between the cell parameters of the two compounds

THE USE OF THE PROFILE ANALYSIS OF DIFFRACTION PEAKS FOR DETERMINATION OF THE PHASE RELATIONSHIPS IN THE SYSTEM (1 -2x)BiScO3 xPbTiO3 • xPbMg1/3Nb2/3O3 NEAR THE MORPHOTROPIC BOUNDAR

2019 ◽  
Vol 85 (4) ◽  
pp. 22-27
Author(s):  
Vladimir R. Sirotinkin ◽  
Alexandr A. Bush ◽  
Alexandr I. Spitsin ◽  
Andrei G. Segalla
Keyword(s):  
Profile Analysis ◽  
Cubic Symmetry ◽  
Cell Parameters ◽  
Unit Cells ◽  
Diffraction Peaks ◽  
Diffraction Patterns ◽  
Two Phases ◽  
Xrd Patterns ◽  
System 1 ◽  
Phase Relationships

To determine the phase relationships in the system (1 - 2x)BiSc03 • xPbTi03 • xPbMg1/3Nb2/303 near the morphotropic boundary, the ceramic samples for x = 0.34 and x = 0.46 were studied by the XRD method. The profiles of nine regions of the XRD patterns were analyzed using WinFit software. In both cases, a much better agreement with the experimental data was observed with the introduction of additional phases with cubic symmetry. The simulation of the full x-ray diffraction patterns of the samples using the Le Bail method was also carried out. The studied samples contain two phases: the main with a cubic (o = 4.0432 A) (x = 0.34) and tetragonal (o = 3,9963 А, с = 4.0580 A) (x = 0.46) unit cells and additional one. The additional phases with broad diffraction peaks can be considered cubic (with the unit cell parameters a - 4.045 A and a - 4.017 A, respectively).

Anisotropic radiation damage of potassium tetracyano platinate (KCP)

1978 ◽  
Vol 36 (1) ◽  
pp. 392-393
Author(s):  
N. Uyeda ◽  
E. J. Kirkland ◽  
B. M. Siegel
Keyword(s):  
Electron Diffraction ◽  
Radiation Damage ◽  
Structural Changes ◽  
High Resolution Electron Microscopy ◽  
Radiation Sensitivity ◽  
Resolution Electron ◽  
Damage Process ◽  
Diffraction Patterns ◽  
Fading Rate

The direct observation of structural change by high resolution electron microscopy will be essential for the better understanding of the damage process and its mechanism. However, this approach still involves some difficulty in quantitative interpretation mostly being due to the quality of obtained images. Electron diffraction, using crystalline specimens, has been the method most frequently applied to obtain a comparison of radiation sensitivity of various materials on the quantitative base. If a series of single crystal patterns are obtained the fading rate of reflections during the damage process give good comparative measures. The electron diffraction patterns also render useful information concerning the structural changes in the crystal. In the present work, the radiation damage of potassium tetracyano-platinate was dealt with on the basis two dimensional observation of fading rates of diffraction spots. KCP is known as an ionic crystal which possesses “one dimensional” electronic properties and it would be of great interest to know if radiation damage proceeds in a strongly asymmetric manner.

Spot-scan imaging of ice-embedded catalase crystal on a slow-scan CCD camera in a 400-kV electron cryomicroscope

1994 ◽  
Vol 52 ◽  
pp. 98-99
Author(s):  
Wah Chiu ◽  
Michael Sherman ◽  
Jaap Brink
Keyword(s):  
Electron Diffraction ◽  
Ccd Camera ◽  
Protein Crystal ◽  
Modulation Transfer ◽  
Measured Intensity ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Diffraction Patterns ◽  
Complex Crystal

In protein electron crystallography, both low dose electron diffraction patterns and images are needed to provide accurate amplitudes and phases respectively for a 3-dimensional reconstruction. We have demonstrated that the Gatan 1024x1024 model 679 slow-scan CCD camera is useful to record electron diffraction intensities of glucose-embedded crotoxin complex crystal to 3 Å resolution. The quality of the electron diffraction intensities is high on the basis of the measured intensity equivalence ofthe Friedel-related reflections. Moreover, the number of patterns recorded from a single crystal can be as high as 120 under the constraints of radiation damage and electron statistics for the reflections in each pattern.A limitation of the slow-scan CCD camera for recording electron images of protein crystal arises from the relatively large pixel size, i.e. 24 μm (provided by Gatan). The modulation transfer function of our camera with a P43 scintillator has been determined for 400 keV electrons and shows an amplitude fall-off to 0.25 at 1/60 μm−1.

Heat Transfer Enhancement in Separation Process of Ethanol from Ethanol Water Mixture by Using Surfactants

2020 ◽  
pp. 9-14 ◽  
Author(s):  
Acharya Anil Ramchandra ◽  
R. Kadam ◽  
A. T. Pise
Keyword(s):  
Heat Transfer ◽  
Ammonium Chloride ◽  
Sodium Dodecyl ◽  
Water Mixture ◽  
Transfer Enhancement ◽  
Surface Tension Reduction ◽  
Surface Active Agents ◽  
Surface Active ◽  
Time Required

Here the investigations are done while distillation of ethanol-water mixture for separating ethanol from fermentation process. Focus is to study reduction in time required and hence saving in energy for the distillation process of ethanol-water mixture under the influence of surface-active agents (Surfactants). This novelty is from observation of these surfactants to enhance heat transfer rate because of surface tension reduction in aqueous solutions. SDS (Sodium Dodecyl Sulphate), NH4Cl (Ammonium Chloride) and SLBS (Sodium lauryl benzene sulphonate) surfactants in different concentration are experimented. The concentration of these surfactant is varied from 1700 ppm to 2800 ppm. This range is decided by observing critical micelle concentration of used surfactants. Results showed that time is reduced and hence energy consumption is also reduced. Results shown by NH4Cl are found to be more useful as it is ecofriendly surfactant which is not affecting ethanol-water mixture. Use of ammonium chloride as surfactant in distillation is actually useful to reduce energy without hampering the quality of process is the novelty of this work.

scholarly journals Public Awareness and Disaster Risk Reduction: Just-in-Time Networks and Learning

2008 ◽  
Vol 23 (3) ◽  
pp. 286-288 ◽  
Author(s):  
Ali Ardalan ◽  
Faina Linkov ◽  
Eugene Shubnikov ◽  
Ronald E. LaPorte
Keyword(s):  
Hurricane Katrina ◽  
Wide Spectrum ◽  
Public Awareness ◽  
Just In Time ◽  
Educational Levels ◽  
Hazard And Risk ◽  
Time Required ◽  
Expert Network ◽  
Core Materials

AbstractImproving public awareness through education has been recognized widely as a basis for reducing the risk of disasters. Some of the first disaster just-in-time (JIT) education modules were built within 3–6 days after the south Asia tsunami, Hurricane Katrina, and the Bam, Pakistan, and Indonesia earthquakes through a Supercourse. Web monitoring showed that visitors represented a wide spectrum of disciplines and educational levels from 120 developed and developing countries. Building disaster networks using an educational strategy seizes the opportunity of increased public interest to teach and find national and global expertise in hazard and risk information. To be effective, an expert network and a template for the delivery of JIT education must be prepared before an event occurs, focusing on developing core materials that could be customized rapidly, and then be based on the information received from a recent disaster. The recyclable process of the materials would help to improve the quality of the teaching, and decrease the time required for preparation. The core materials can be prepared for disasters resulting from events such as earthquakes, hurricanes, tsunamis, floods, and bioterrorism.

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