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FEM: feature-enhanced map.

Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: 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.

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Affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.

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.

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(a) The original map from (1), (b) the FEM and (c) a RESOLVE density-modified map for PDB entry 2g38, where the data are known to be affected by severe anisotropy. Note the reduction in the effect of map anisotropy along the vertical direction in both the FEM and RESOLVE maps.
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fig21: (a) The original map from (1), (b) the FEM and (c) a RESOLVE density-modified map for PDB entry 2g38, where the data are known to be affected by severe anisotropy. Note the reduction in the effect of map anisotropy along the vertical direction in both the FEM and RESOLVE maps.

Mentions: This is a classical example of data with severe anisotropy and has served as an example for the Anisotropy Correction Server (Strong et al., 2006 ▶). The original diffraction data were kindly provided by the author (Michael Sawaya), as the corresponding PDB entry contains only an anisotropy-corrected version of the measured intensities. Fig. 21 ▶ shows three maps: the original map from (1), the FEM and a density-modified RESOLVE map. The latter two maps show a notable reduction in anisotropy effects (elongation of map contours along the vertical direction).


FEM: feature-enhanced map.

Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2015)

(a) The original map from (1), (b) the FEM and (c) a RESOLVE density-modified map for PDB entry 2g38, where the data are known to be affected by severe anisotropy. Note the reduction in the effect of map anisotropy along the vertical direction in both the FEM and RESOLVE maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356370&req=5

fig21: (a) The original map from (1), (b) the FEM and (c) a RESOLVE density-modified map for PDB entry 2g38, where the data are known to be affected by severe anisotropy. Note the reduction in the effect of map anisotropy along the vertical direction in both the FEM and RESOLVE maps.
Mentions: This is a classical example of data with severe anisotropy and has served as an example for the Anisotropy Correction Server (Strong et al., 2006 ▶). The original diffraction data were kindly provided by the author (Michael Sawaya), as the corresponding PDB entry contains only an anisotropy-corrected version of the measured intensities. Fig. 21 ▶ shows three maps: the original map from (1), the FEM and a density-modified RESOLVE map. The latter two maps show a notable reduction in anisotropy effects (elongation of map contours along the vertical direction).

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.

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.

Show MeSH