Metrics for crystallographic diffraction- and fit-data: a review of existing ones and the need for new ones

Henn, Julian

doi:10.1080/0889311x.2019.1607845

Cited by 7 publications

(10 citation statements)

References 158 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As mentioned before, the suitability of using 2 (or more commonly, the goodness of fit, GooF) as an agreement factor depends on the quality of the standard uncertainties -these should be, as far as possible, free from systematic errors (Henn, 2019). Specifically, the use of the statistical weighting scheme requires that the residuals (Á 2 i ) and the have no significant correlation, which is fulfilled when…”

Section: Summary and Discussionmentioning

confidence: 99%

“…(ii) If possible, reintegrate the data to a desired resolution instead of applying cutoffs. In this way the chances of having systematic errors can be reduced (Henn, 2019).…”

Section: Summary and Discussionmentioning

confidence: 99%

“…The employment of the statistical weighting scheme assumes that the measurement errors are uncorrelated and, therefore, the variance-covariance matrix is diagonal. However, this requirement is not always met, in which case the use of the 2 function as an agreement factor may be unreliable (Henn, 2019). This situation will be explored later in this work.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

See 2 more Smart Citations

The influence of refinement strategies on the wavefunctions derived from an experiment

Landeros‐Rivera¹,

Contreras‐García²,

Dominiak³

2021

Acta Crystallogr B Struct Sci Cryst Eng Mater

View full text Add to dashboard Cite

The synergy between theory and experiment found in X-ray wavefunction refinement (XWR) makes it one of the most compelling techniques available for chemical physics. The foremost benefit of XWR – obtaining wavefunctions constrained to experimental data – is at the same time its Achilles heel, because of the dependence of the results on the quality of both empirical and theoretical data. The purpose of this work is to answer the following: What is the effect of the refinement strategy and manipulation of input data on the physical properties obtained from XWR? With that in mind, cutoffs based on data resolution and F/σ(F) ratios were applied for both steps of XWR, the Hirshfeld atom refinement (HAR) and the X-ray constrained wavefunction fitting (XCW), for four selected systems: sulfur dioxide, urea, carbamazepine and oxalic acid. The effects of changing the weighting scheme or the method to transform σ(F 2) to σ(F) were also analysed. The results show that while HAR always reaches the same result, XCW is extremely sensitive to crystallographic data manipulation. This is a result of the variability of the experimental uncertainties for different resolution shells, and of not having proper standard uncertainties. Therefore, the use of distinct constraints for each resolution interval in XCW is proposed to fix this instability.

show abstract

Section: Summary and Discussionmentioning

confidence: 99%

“…(ii) If possible, reintegrate the data to a desired resolution instead of applying cutoffs. In this way the chances of having systematic errors can be reduced (Henn, 2019).…”

Section: Summary and Discussionmentioning

confidence: 99%

Section: Theoretical Frameworkmentioning

confidence: 99%

See 1 more Smart Citation

The influence of refinement strategies on the wavefunctions derived from an experiment

Landeros‐Rivera¹,

Contreras‐García²,

Dominiak³

2021

Acta Crystallogr B Struct Sci Cryst Eng Mater

View full text Add to dashboard Cite

show abstract

“…It is an important question, though, as significantly large absolute deviations of the mean value of the weighted residuals from zero larger than three are widespread. In the 127 data sets published by IUCrData (https://iucrdata.iucr.org/) and discussed by Henn (2019), they appeared in 66 (52%) cases, but remained unmentioned -and most likely undetected -in all publications where they appeared. On average, the absolute significance of the deviation of residuals from zero for the 127 data sets was 4.30.…”

Section: Shift In the Significance Of The Mean Of The Residuals As Gi...mentioning

confidence: 99%

Progress in detection of and correction for low-energy contamination

Domagala,

Nourd,

Diederichs

et al. 2023

J Appl Cryst

View full text Add to dashboard Cite

Contamination with low-energy radiation leads to an increased number of weighted residuals being larger in absolute terms than three standard uncertainties. For a Gaussian distribution, these rare events occur only in 0.27% of all cases, which is a small number for small- to medium-sized data sets. The correct detection of rare events – and an adequate correction procedure – thus relies crucially on correct standard uncertainties, which are often not available [Henn (2019), Crystallogr. Rev. 25, 83–156]. It is therefore advisable to use additional, more robust, metrics to complement the established ones. These metrics are developed here and applied to reference data sets from two different publications about low-energy contamination. Other systematic errors were found in the reference data sets. These errors compromise the correction procedures and may lead to under- or overcompensation. This can be demonstrated clearly with the new metrics. Empirical correction procedures generally may be compromised or bound to fail in the presence of other systematic errors. The following systematic errors, which were found in the reference data sets, need to be corrected for prior to application of the low-energy contamination correction procedure: signals of 2λ contamination, extinction, disorder, twinning, and too-large or too-low standard uncertainties (this list may not be complete). All five reference data sets of one publication show a common resolution-dependent systematic error of unknown origin. How this affects the correction procedure can be stated only after elimination of this error. The methodological improvements are verified with data published by other authors.

show abstract

“…In chemical crystallography, aside from the R factor, various other parameters are checked such as resolution, redundancy, weighting parameters, goodness of fit and wR2; the differences between F obs versus F calc are also checked as a further validation tool. Note that the presence of systematic errors and concerns about the goodness of fit have been expressed in a data review of a large number of chemical crystal structures (Henn, 2019).…”

Section: Reliabilitymentioning

confidence: 99%

The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability

Helliwell¹,

Massera²

2022

J Appl Cryst

View full text Add to dashboard Cite

Within science, of which crystallography is a key part, there are questions posed to all fields that challenge the trust in results. The US National Academies of Sciences, Engineering and Medicine published a thorough report in 2019 on the Reproducibility and Replicability of Science: replicability being where a totally new study attempts to confirm if a phenomenon can be seen independently of another study. Data reuse is a key term in the FAIR data accord [Wilkinson et al. (2016). Sci. Data, 3, 160018], where the acronym FAIR means findable, accessible, interoperable and reusable. In the social sciences, the acronym FACT (namely fairness, accuracy, confidentiality and transparency) has emerged, the idea being that data should be FACTual to ensure trust [van der Aalst et al. (2017). Bus. Inf. Syst. Eng. 59, 311–313]. A distinction also must be made between accuracy and precision; indeed, the authors' lectures at the European Crystallography School ECS6 independently emphasized the need for use of other methods as well as crystal structure analysis to establish accuracy in biological and chemical/material functional contexts. The efforts by disparate science communities to introduce new terms to ensure trust have merit for discussion in crystallographic teaching commissions and possible adoption by crystallographers too.

show abstract

Metrics for crystallographic diffraction- and fit-data: a review of existing ones and the need for new ones

Cited by 7 publications

References 158 publications

The influence of refinement strategies on the wavefunctions derived from an experiment

The influence of refinement strategies on the wavefunctions derived from an experiment

Progress in detection of and correction for low-energy contamination

The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability

Contact Info

Product

Resources

About