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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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An example of a misfitted ligand in PDB entry 1se6. (a) The incorrect fit shown in the map from (1). The FEM is shown calculated with (b) and without (c) the incorrectly fitted ligand included in the calculations. The composite residual OMIT map is shown with (d) and without (e) the incorrectly fitted ligand included in the calculations. (f) RESOLVE density-modified map. (g) Ligand-omit map from (1) after correcting the ligand fit followed by a round of refinement. All maps are shown at 1σ or equivalent.
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fig22: An example of a misfitted ligand in PDB entry 1se6. (a) The incorrect fit shown in the map from (1). The FEM is shown calculated with (b) and without (c) the incorrectly fitted ligand included in the calculations. The composite residual OMIT map is shown with (d) and without (e) the incorrectly fitted ligand included in the calculations. (f) RESOLVE density-modified map. (g) Ligand-omit map from (1) after correcting the ligand fit followed by a round of refinement. All maps are shown at 1σ or equivalent.

Mentions: Pozharski et al. (2013 ▶) pointed out a misfitted ligand in this entry. While the Fourier map from (1) does not clearly identify the ligand at 1σ (Fig. 22 ▶a), feature-enhanced maps calculated both with (Fig. 22 ▶b) and without (Fig. 22 ▶c) the ligand present in the input model file better identified the ligand. Also, composite residual OMIT maps calculated with (Fig. 22 ▶d) and without (Fig. 22 ▶e) the ligand both unambiguously confirm its identity. A RESOLVE density-modified map barely shows the ligand density. Correcting the ligand fit is obvious based on the residual OMIT or FEM maps, and a subsequent round of refinement yields a clear ligand-omit Fourier map from (1).


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)

An example of a misfitted ligand in PDB entry 1se6. (a) The incorrect fit shown in the map from (1). The FEM is shown calculated with (b) and without (c) the incorrectly fitted ligand included in the calculations. The composite residual OMIT map is shown with (d) and without (e) the incorrectly fitted ligand included in the calculations. (f) RESOLVE density-modified map. (g) Ligand-omit map from (1) after correcting the ligand fit followed by a round of refinement. All maps are shown at 1σ or equivalent.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig22: An example of a misfitted ligand in PDB entry 1se6. (a) The incorrect fit shown in the map from (1). The FEM is shown calculated with (b) and without (c) the incorrectly fitted ligand included in the calculations. The composite residual OMIT map is shown with (d) and without (e) the incorrectly fitted ligand included in the calculations. (f) RESOLVE density-modified map. (g) Ligand-omit map from (1) after correcting the ligand fit followed by a round of refinement. All maps are shown at 1σ or equivalent.
Mentions: Pozharski et al. (2013 ▶) pointed out a misfitted ligand in this entry. While the Fourier map from (1) does not clearly identify the ligand at 1σ (Fig. 22 ▶a), feature-enhanced maps calculated both with (Fig. 22 ▶b) and without (Fig. 22 ▶c) the ligand present in the input model file better identified the ligand. Also, composite residual OMIT maps calculated with (Fig. 22 ▶d) and without (Fig. 22 ▶e) the ligand both unambiguously confirm its identity. A RESOLVE density-modified map barely shows the ligand density. Correcting the ligand fit is obvious based on the residual OMIT or FEM maps, and a subsequent round of refinement yields a clear ligand-omit Fourier map from (1).

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