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Abstract
Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy of a map. Here, the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows the incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between the macromolecule and solvent are visible, and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here, model bias is reduced by using ensemble models that allow an estimation of model uncertainty. A test of model bias is presented that suggests that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map.
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Affiliation(s)
- Thomas C. Terwilliger
- New Mexico Consortium, Los Alamos, NM 87544, USA
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
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Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. Acta Crystallogr D Biol Crystallogr 2015; 71:646-66. [PMID: 25760612 PMCID: PMC4356370 DOI: 10.1107/s1399004714028132] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 12/25/2014] [Indexed: 11/29/2022]
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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Affiliation(s)
- Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Marat Mustyakimov
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Oleg V. Sobolev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | | | - Dusan Turk
- Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, 54506 Vandoeuvre-lès-Nancy, France
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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