A program to analyze the distributions of unmeasured reflections

2011 ◽  
Vol 44 (4) ◽  
pp. 865-872 ◽  
Author(s):  
Ludmila Urzhumtseva ◽  
Alexandre Urzhumtsev
Keyword(s):  
Spatial Distribution ◽  
Missing Data ◽  
Computer Program ◽  
Diffraction Data ◽  
Reciprocal Space ◽  
Data Set ◽  
Data Completeness ◽  
Significant Time ◽  
Cumulative Data ◽  
Structure Solution

Crystallographic Fourier maps may contain barely interpretable or non-interpretable regions if these maps are calculated with an incomplete set of diffraction data. Even a small percentage of missing data may be crucial if these data are distributed non-uniformly and form connected regions of reciprocal space. Significant time and effort can be lost trying to interpret poor maps, in improving them by phase refinement or in fighting against artefacts, whilst the problem could in fact be solved by completing the data set. To characterize the distribution of missing reflections, several types of diagrams have been suggested in addition to the usual plots of completeness in resolution shells and cumulative data completeness. A computer program,FOBSCOM, has been developed to analyze the spatial distribution of unmeasured diffraction data, to search for connected regions of unmeasured reflections and to obtain numeric characteristics of these regions. By performing this analysis, the program could help to save time during structure solution for a number of projects. It can also provide information about a possible overestimation of the map quality and model-biased features when calculated values are used to replace unmeasured data.

scholarly journals SUPERFLIP– a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions

2007 ◽  
Vol 40 (4) ◽  
pp. 786-790 ◽  
Author(s):  
Lukáš Palatinus ◽  
Gervais Chapuis
Keyword(s):  
Computer Program ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Periodic Structures ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Modulated Structures ◽  
Structure Solution ◽  
Matching Procedure ◽  
Arbitrary Dimensions

SUPERFLIPis a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure.SUPERFLIPis written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.

scholarly journals Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals

IUCrJ ◽  
2019 ◽  
Vol 6 (1) ◽  
pp. 34-45 ◽  
Author(s):  
Cecilia M. Casadei ◽  
Karol Nass ◽  
Anton Barty ◽  
Mark S. Hunter ◽  
Celestino Padeste ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Diffraction Data ◽  
Structure Factor ◽  
Large Scale ◽  
Reciprocal Space ◽  
Protein Crystals ◽  
Two Dimensional ◽  
Data Set ◽  
Redundant Data ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump–probe experiments.

scholarly journals PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction data

2010 ◽  
Vol 43 (2) ◽  
pp. 370-376 ◽  
Author(s):  
Silvina Pagola ◽  
Peter W. Stephens
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Space Structure ◽  
Molecular Solids ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Structure Solution

This work describes the computer programPSSP(powder structure solution program) for the crystal structure solution of molecular solids from X-ray powder diffraction data. This direct-space structure solution program uses the simulated annealing global optimization algorithm to minimize the difference between integrated intensities calculated from trial models and those extracted in a Le Bail fit of the experimental pattern, using a cost function for dealing with peak overlap through defined intensity correlation coefficients, computationally faster to calculate thanRwp. The methodology outlined is applicable to organic solids composed of moderately complex rigid and flexible molecules, using diffraction data up to relatively low resolution.PSSPperformance tests using 11 molecular solids with six to 20 degrees of freedom are analyzed.

WCEN: a computer program for initial processing of fiber diffraction patterns

2006 ◽  
Vol 39 (5) ◽  
pp. 752-756 ◽  
Author(s):  
Wen Bian ◽  
Hong Wang ◽  
Ian McCullough ◽  
Gerald Stubbs
Keyword(s):  
Computer Program ◽  
Single Crystal ◽  
Diffraction Data ◽  
Plant Viruses ◽  
Reciprocal Space ◽  
Parameter Determination ◽  
Input And Output ◽  
Fiber Diffraction ◽  
Diffraction Patterns ◽  
Initial Processing

Processing of fiber diffraction patterns is generally more difficult than for single-crystal patterns, and requires different algorithms and software. The programWCENhas been developed to determine experimental and specimen parameters and to convert diffraction data from detector to reciprocal space, and offers a variety of input and output formats, running under Mac OS X and Linux. The program is described and examples from oriented sols of filamentous plant viruses, illustrating different strategies for parameter determination and refinement, are given.

scholarly journals Extending the charge-flipping method towards structure solution from incomplete data sets

2007 ◽  
Vol 40 (3) ◽  
pp. 456-462 ◽  
Author(s):  
Lukáš Palatinus ◽  
Walter Steurer ◽  
Gervais Chapuis
Keyword(s):  
Experimental Data ◽  
Missing Data ◽  
Incomplete Data ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Data Sets ◽  
Data Set ◽  
Density Maps ◽  
Structure Solution ◽  
Unknown Structure

The charge-flipping method tends to fail if applied to an incomplete diffraction data set. The reason is artifacts induced in the density maps by Fourier transforming the data. It is shown that the missing data can be sufficiently well approximated on the basis of the Patterson map of the unknown structure optimized by the maximum entropy method (MEM). Structures that could not be solved by the original charge-flipping algorithm can be solved by the proposed method. The method has been tested on experimental data of one inorganic and two organic structures and on several types of missing data. In many cases, up to 50% of missing reflections, or even more, can be tolerated and the structure can still be reconstructed by charge flipping.

FIDDLE. Simultaneous Indexing and Structure Solution from Powder Diffraction Data using a Genetic Algorithm and Correlation Functions

2019 ◽  
Author(s):  
Carmen Guguta ◽  
Jan M.M. Smits ◽  
Rene de Gelder
Keyword(s):  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Correlation Functions ◽  
Cross Correlation ◽  
Simultaneous Optimization ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Matching Technique

A method for the determination of crystal structures from powder diffraction data is presented that circumvents the difficulties associated with separate indexing. For the simultaneous optimization of the parameters that describe a crystal structure a genetic algorithm is used together with a pattern matching technique based on auto and cross correlation functions.<br>

scholarly journals Do galactic bars depend on environment?: an information theoretic analysis of Galaxy Zoo 2

2020 ◽  
Vol 501 (1) ◽  
pp. 994-1001
Author(s):  
Suman Sarkar ◽  
Biswajit Pandey ◽  
Snehasish Bhattacharjee
Keyword(s):  
Spatial Distribution ◽  
Mutual Information ◽  
Local Density ◽  
Statistical Significance ◽  
Distribution Functions ◽  
Cumulative Distribution ◽  
Host Galaxy ◽  
Data Sets ◽  
Data Set ◽  
Information Theoretic

ABSTRACT We use an information theoretic framework to analyse data from the Galaxy Zoo 2 project and study if there are any statistically significant correlations between the presence of bars in spiral galaxies and their environment. We measure the mutual information between the barredness of galaxies and their environments in a volume limited sample (Mr ≤ −21) and compare it with the same in data sets where (i) the bar/unbar classifications are randomized and (ii) the spatial distribution of galaxies are shuffled on different length scales. We assess the statistical significance of the differences in the mutual information using a t-test and find that both randomization of morphological classifications and shuffling of spatial distribution do not alter the mutual information in a statistically significant way. The non-zero mutual information between the barredness and environment arises due to the finite and discrete nature of the data set that can be entirely explained by mock Poisson distributions. We also separately compare the cumulative distribution functions of the barred and unbarred galaxies as a function of their local density. Using a Kolmogorov–Smirnov test, we find that the null hypothesis cannot be rejected even at $75{{\ \rm per\ cent}}$ confidence level. Our analysis indicates that environments do not play a significant role in the formation of a bar, which is largely determined by the internal processes of the host galaxy.

scholarly journals Handling Complex Missing Data Using Random Forest Approach for an Air Quality Monitoring Dataset: A Case Study of Kuwait Environmental Data (2012 to 2018)

2021 ◽  
Vol 18 (3) ◽  
pp. 1333
Author(s):  
Ahmad R. Alsaber ◽  
Jiazhu Pan ◽  
Adeeba Al-Hurban 
Keyword(s):  
Air Quality ◽  
Missing Data ◽  
Random Forest ◽  
Missing Values ◽  
Imputation Method ◽  
Environmental Data ◽  
Environmental Research ◽  
Quality Data ◽  
Data Set ◽  
Air Quality Data

In environmental research, missing data are often a challenge for statistical modeling. This paper addressed some advanced techniques to deal with missing values in a data set measuring air quality using a multiple imputation (MI) approach. MCAR, MAR, and NMAR missing data techniques are applied to the data set. Five missing data levels are considered: 5%, 10%, 20%, 30%, and 40%. The imputation method used in this paper is an iterative imputation method, missForest, which is related to the random forest approach. Air quality data sets were gathered from five monitoring stations in Kuwait, aggregated to a daily basis. Logarithm transformation was carried out for all pollutant data, in order to normalize their distributions and to minimize skewness. We found high levels of missing values for NO2 (18.4%), CO (18.5%), PM10 (57.4%), SO2 (19.0%), and O3 (18.2%) data. Climatological data (i.e., air temperature, relative humidity, wind direction, and wind speed) were used as control variables for better estimation. The results show that the MAR technique had the lowest RMSE and MAE. We conclude that MI using the missForest approach has a high level of accuracy in estimating missing values. MissForest had the lowest imputation error (RMSE and MAE) among the other imputation methods and, thus, can be considered to be appropriate for analyzing air quality data.

scholarly journals Potential value of the current mental health monitoring of children in state care in England

BJPsych Open ◽  
2018 ◽  
Vol 4 (6) ◽  
pp. 486-491 ◽  
Author(s):  
Christine Cocker ◽  
Helen Minnis ◽  
Helen Sweeting
Keyword(s):  
Mental Health ◽  
Missing Data ◽  
Mental Health Problems ◽  
Population Level ◽  
Cross Sectional ◽  
Data Set ◽  
Looked After Children ◽  
Education Data ◽  
Sample Attrition ◽  
Aggregate Population

BackgroundRoutine screening to identify mental health problems in English looked-after children has been conducted since 2009 using the Strengths and Difficulties Questionnaire (SDQ).AimsTo investigate the degree to which data collection achieves screening aims (identifying scale of problem, having an impact on mental health) and the potential analytic value of the data set.MethodDepartment for Education data (2009–2017) were used to examine: aggregate, population-level trends in SDQ scores in 4/5- to 16/17-year-olds; representativeness of the SDQ sample; attrition in this sample.ResultsMean SDQ scores (around 50% ‘abnormal’ or ‘borderline’) were stable over 9 years. Levels of missing data were high (25–30%), as was attrition (28% retained for 4 years). Cross-sectional SDQ samples were not representative and longitudinal samples were biased.ConclusionsMental health screening appears justified and the data set has research potential, but the English screening programme falls short because of missing data and inadequate referral routes for those with difficulties.Declaration of interestNone.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

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