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Automated map sharpening by maximization of detail and connectivity

An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high le...

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Autores principales: Terwilliger, Thomas C., Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096490/
https://www.ncbi.nlm.nih.gov/pubmed/29872005
http://dx.doi.org/10.1107/S2059798318004655
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author Terwilliger, Thomas C.
Sobolev, Oleg V.
Afonine, Pavel V.
Adams, Paul D.
author_facet Terwilliger, Thomas C.
Sobolev, Oleg V.
Afonine, Pavel V.
Adams, Paul D.
author_sort Terwilliger, Thomas C.
collection PubMed
description An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures in a metric termed the ‘adjusted surface area’, map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map–model correlation that can reproduce visual choices of optimally sharpened maps was used. The map–model correlation is calculated using a model with B factors (atomic displacement factors; ADPs) set to zero. This model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening.
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spelling pubmed-60964902018-08-24 Automated map sharpening by maximization of detail and connectivity Terwilliger, Thomas C. Sobolev, Oleg V. Afonine, Pavel V. Adams, Paul D. Acta Crystallogr D Struct Biol Research Papers An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures in a metric termed the ‘adjusted surface area’, map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map–model correlation that can reproduce visual choices of optimally sharpened maps was used. The map–model correlation is calculated using a model with B factors (atomic displacement factors; ADPs) set to zero. This model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening. International Union of Crystallography 2018-05-18 /pmc/articles/PMC6096490/ /pubmed/29872005 http://dx.doi.org/10.1107/S2059798318004655 Text en © Terwilliger et al. 2018 http://creativecommons.org/licenses/by/2.0/uk/ 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/2.0/uk/
spellingShingle Research Papers
Terwilliger, Thomas C.
Sobolev, Oleg V.
Afonine, Pavel V.
Adams, Paul D.
Automated map sharpening by maximization of detail and connectivity
title Automated map sharpening by maximization of detail and connectivity
title_full Automated map sharpening by maximization of detail and connectivity
title_fullStr Automated map sharpening by maximization of detail and connectivity
title_full_unstemmed Automated map sharpening by maximization of detail and connectivity
title_short Automated map sharpening by maximization of detail and connectivity
title_sort automated map sharpening by maximization of detail and connectivity
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096490/
https://www.ncbi.nlm.nih.gov/pubmed/29872005
http://dx.doi.org/10.1107/S2059798318004655
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