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Measuring and using information gained by observing diffraction data
The information gained by making a measurement, termed the Kullback–Leibler divergence, assesses how much more precisely the true quantity is known after the measurement was made (the posterior probability distribution) than before (the prior probability distribution). It provides an upper bound for...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057217/ https://www.ncbi.nlm.nih.gov/pubmed/32133988 http://dx.doi.org/10.1107/S2059798320001588 |
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author | Read, Randy J. Oeffner, Robert D. McCoy, Airlie J. |
author_facet | Read, Randy J. Oeffner, Robert D. McCoy, Airlie J. |
author_sort | Read, Randy J. |
collection | PubMed |
description | The information gained by making a measurement, termed the Kullback–Leibler divergence, assesses how much more precisely the true quantity is known after the measurement was made (the posterior probability distribution) than before (the prior probability distribution). It provides an upper bound for the contribution that an observation can make to the total likelihood score in likelihood-based crystallographic algorithms. This makes information gain a natural criterion for deciding which data can legitimately be omitted from likelihood calculations. Many existing methods use an approximation for the effects of measurement error that breaks down for very weak and poorly measured data. For such methods a different (higher) information threshold is appropriate compared with methods that account well for even large measurement errors. Concerns are raised about a current trend to deposit data that have been corrected for anisotropy, sharpened and pruned without including the original unaltered measurements. If not checked, this trend will have serious consequences for the reuse of deposited data by those who hope to repeat calculations using improved new methods. |
format | Online Article Text |
id | pubmed-7057217 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-70572172020-03-06 Measuring and using information gained by observing diffraction data Read, Randy J. Oeffner, Robert D. McCoy, Airlie J. Acta Crystallogr D Struct Biol Ccp4 The information gained by making a measurement, termed the Kullback–Leibler divergence, assesses how much more precisely the true quantity is known after the measurement was made (the posterior probability distribution) than before (the prior probability distribution). It provides an upper bound for the contribution that an observation can make to the total likelihood score in likelihood-based crystallographic algorithms. This makes information gain a natural criterion for deciding which data can legitimately be omitted from likelihood calculations. Many existing methods use an approximation for the effects of measurement error that breaks down for very weak and poorly measured data. For such methods a different (higher) information threshold is appropriate compared with methods that account well for even large measurement errors. Concerns are raised about a current trend to deposit data that have been corrected for anisotropy, sharpened and pruned without including the original unaltered measurements. If not checked, this trend will have serious consequences for the reuse of deposited data by those who hope to repeat calculations using improved new methods. International Union of Crystallography 2020-02-25 /pmc/articles/PMC7057217/ /pubmed/32133988 http://dx.doi.org/10.1107/S2059798320001588 Text en © Read et al. 2020 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Ccp4 Read, Randy J. Oeffner, Robert D. McCoy, Airlie J. Measuring and using information gained by observing diffraction data |
title | Measuring and using information gained by observing diffraction data |
title_full | Measuring and using information gained by observing diffraction data |
title_fullStr | Measuring and using information gained by observing diffraction data |
title_full_unstemmed | Measuring and using information gained by observing diffraction data |
title_short | Measuring and using information gained by observing diffraction data |
title_sort | measuring and using information gained by observing diffraction data |
topic | Ccp4 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057217/ https://www.ncbi.nlm.nih.gov/pubmed/32133988 http://dx.doi.org/10.1107/S2059798320001588 |
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