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To B or not to B: a question of resolution?

In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is...

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Autor principal: Merritt, Ethan A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322606/
https://www.ncbi.nlm.nih.gov/pubmed/22505267
http://dx.doi.org/10.1107/S0907444911028320
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author Merritt, Ethan A.
author_facet Merritt, Ethan A.
author_sort Merritt, Ethan A.
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description In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is important to validate the choice of parameters as well as validating their refined values. One recurring task is to choose the best model for describing the displacement of each atom about its mean position. At atomic resolution one has the option of devoting six model parameters (a ‘thermal ellipsoid’) to describe the displacement of each atom. At medium resolution one typically devotes at most one model parameter per atom to describe the same thing (a ‘B factor’). At very low resolution one cannot justify the use of even one parameter per atom. Furthermore, this aspect of the structure may be described better by an explicit model of bulk displacements, the most common of which is the translation/libration/screw (TLS) formalism, rather than by assigning some number of para­meters to each atom individually. One can sidestep this choice between atomic displacement parameters and TLS descriptions by including both treatments in the same model, but this is not always statistically justifiable. The choice of which treatment is best for a particular structure refinement at a particular resolution can be guided by general considerations of the ratio of model parameters to the number of observations and by specific statistics such as the Hamilton R-­factor ratio test.
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spelling pubmed-33226062012-04-16 To B or not to B: a question of resolution? Merritt, Ethan A. Acta Crystallogr D Biol Crystallogr Research Papers In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is important to validate the choice of parameters as well as validating their refined values. One recurring task is to choose the best model for describing the displacement of each atom about its mean position. At atomic resolution one has the option of devoting six model parameters (a ‘thermal ellipsoid’) to describe the displacement of each atom. At medium resolution one typically devotes at most one model parameter per atom to describe the same thing (a ‘B factor’). At very low resolution one cannot justify the use of even one parameter per atom. Furthermore, this aspect of the structure may be described better by an explicit model of bulk displacements, the most common of which is the translation/libration/screw (TLS) formalism, rather than by assigning some number of para­meters to each atom individually. One can sidestep this choice between atomic displacement parameters and TLS descriptions by including both treatments in the same model, but this is not always statistically justifiable. The choice of which treatment is best for a particular structure refinement at a particular resolution can be guided by general considerations of the ratio of model parameters to the number of observations and by specific statistics such as the Hamilton R-­factor ratio test. International Union of Crystallography 2012-03-16 /pmc/articles/PMC3322606/ /pubmed/22505267 http://dx.doi.org/10.1107/S0907444911028320 Text en © Merritt 2012 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Merritt, Ethan A.
To B or not to B: a question of resolution?
title To B or not to B: a question of resolution?
title_full To B or not to B: a question of resolution?
title_fullStr To B or not to B: a question of resolution?
title_full_unstemmed To B or not to B: a question of resolution?
title_short To B or not to B: a question of resolution?
title_sort to b or not to b: a question of resolution?
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322606/
https://www.ncbi.nlm.nih.gov/pubmed/22505267
http://dx.doi.org/10.1107/S0907444911028320
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