FEM: feature-enhanced map

Acta Crystallographica. Section D, Biological Crystallography
Pavel V AfoninePaul D Adams

Abstract

A method is presented that modifies a 2mFobs - DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs - DFmodel σA-weighted map.

References

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Citations

Jan 9, 2016·Science·Jeremy BakelarNicholas Noinaj
Dec 22, 2015·Journal of Molecular Biology·Niloufar AtaieHo Leung Ng
Jan 21, 2016·Nature·Bernhard C LechtenbergStefan J Riedl
Nov 4, 2015·Biological Chemistry·Jan PippelNorbert Sträter
Feb 20, 2016·Acta Crystallographica. Section D, Structural Biology·Maja Holch NielsenLasse Bohl Jenner
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Dec 18, 2015·Nature Communications·Dianfan LiMartin Caffrey
Nov 23, 2015·Chemistry & Biology·Daria M ShcherbakovaVladislav V Verkhusha
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Apr 23, 2015·Nature·Heena KhatterBruno P Klaholz
Apr 8, 2015·Acta Crystallographica. Section D, Biological Crystallography·Mads Beich-FrandsenMaria J Macias
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Sep 11, 2018·Acta Crystallographica. Section D, Structural Biology·Pavel V AfonineAlexandre Urzhumtsev
Sep 15, 2016·Science Advances·Valentina SperanziniAndrea Mattevi
Jun 5, 2019·Proceedings of the National Academy of Sciences of the United States of America·Sandra ZakrzewskaHartmut Michel
Jul 17, 2019·Nature Communications·Martin MeagherEric J Enemark
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Oct 17, 2019·Science Advances·Hanseong KimUhn-Soo Cho
Dec 3, 2016·The Journal of Biological Chemistry·Dustin T KingNatalie C J Strynadka

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Methods Mentioned

BETA
electron-microscopy
X-ray

Software Mentioned

cctbx
Coot
OMIT
phenix
map comparison
SHELX
_ refine
refine
MAIN
Anisotropy Correction Server

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