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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.

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.

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Effect of map sharpening using unsharp masking and exponential (B-factor) sharpening methods. See §2.6.2 for details. For easier comparison all maps are scaled to have their maximum value equal to 1.
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fig11: Effect of map sharpening using unsharp masking and exponential (B-factor) sharpening methods. See §2.6.2 for details. For easier comparison all maps are scaled to have their maximum value equal to 1.

Mentions: To illustrate the effect of the two map-sharpening options, exponential and unsharp masking, we consider a test example similar to that used in the previous section: C and N atoms are placed in the middle of a P1 box at about a distance of 1.45 Å apart. Each atom has unit occupancy and a fixed B factor of 15 Å2. Fig. 11 ▶ shows five curves: blue is the exact electron-density distribution calculated using the Gaussian approximation formula [see, for example, formula 12 in Afonine & Urzhumtsev (2004 ▶) implemented as described in Grosse-Kunstleve et al. (2004 ▶)] and red is for its Fourier image calculated at 1.5 Å resolution. Both exponential (green) and unsharp masking (purple) sharpen the map similarly, while applied together they act synergistically (black).


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)

Effect of map sharpening using unsharp masking and exponential (B-factor) sharpening methods. See §2.6.2 for details. For easier comparison all maps are scaled to have their maximum value equal to 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig11: Effect of map sharpening using unsharp masking and exponential (B-factor) sharpening methods. See §2.6.2 for details. For easier comparison all maps are scaled to have their maximum value equal to 1.
Mentions: To illustrate the effect of the two map-sharpening options, exponential and unsharp masking, we consider a test example similar to that used in the previous section: C and N atoms are placed in the middle of a P1 box at about a distance of 1.45 Å apart. Each atom has unit occupancy and a fixed B factor of 15 Å2. Fig. 11 ▶ shows five curves: blue is the exact electron-density distribution calculated using the Gaussian approximation formula [see, for example, formula 12 in Afonine & Urzhumtsev (2004 ▶) implemented as described in Grosse-Kunstleve et al. (2004 ▶)] and red is for its Fourier image calculated at 1.5 Å resolution. Both exponential (green) and unsharp masking (purple) sharpen the map similarly, while applied together they act synergistically (black).

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