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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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View of macromolecule and bulk-solvent areas for PDB entry 1nh2. The map from (1) (a) and the FEM (b) contoured at 1.0σ. The macromolecule and the bulk-solvent interface are shown.
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fig19: View of macromolecule and bulk-solvent areas for PDB entry 1nh2. The map from (1) (a) and the FEM (b) contoured at 1.0σ. The macromolecule and the bulk-solvent interface are shown.

Mentions: The map from (1) is unusually noisy and notoriously patchy for this structure. Fig. 18 ▶ shows an example of typical map improvement throughout the entire model. Fig. 19 ▶ provides an overall view of the macromolecule–solvent interface and shows significant noise reduction in the bulk-solvent region as a result of applying FEM.


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)

View of macromolecule and bulk-solvent areas for PDB entry 1nh2. The map from (1) (a) and the FEM (b) contoured at 1.0σ. The macromolecule and the bulk-solvent interface are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig19: View of macromolecule and bulk-solvent areas for PDB entry 1nh2. The map from (1) (a) and the FEM (b) contoured at 1.0σ. The macromolecule and the bulk-solvent interface are shown.
Mentions: The map from (1) is unusually noisy and notoriously patchy for this structure. Fig. 18 ▶ shows an example of typical map improvement throughout the entire model. Fig. 19 ▶ provides an overall view of the macromolecule–solvent interface and shows significant noise reduction in the bulk-solvent region as a result of applying FEM.

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