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Andrews LC, Bernstein HJ, Sauter NK. Approximating lattice similarity. Acta Crystallogr A Found Adv 2023; 79:480-484. [PMID: 37485824 PMCID: PMC10483589 DOI: 10.1107/s2053273323003200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/06/2023] [Indexed: 07/25/2023] Open
Abstract
A method is proposed for choosing unit cells for a group of crystals so that they all appear as nearly similar as possible to a selected cell. Related unit cells with varying cell parameters or indexed with different lattice centering can be accommodated.
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Affiliation(s)
| | - Herbert J. Bernstein
- Ronin Institute, c/o NSLS-II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Nicholas K. Sauter
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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Bernstein HJ, Andrews LC, Diaz JA, Jakoncic J, Nguyen T, Sauter NK, Soares AS, Wei JY, Wlodek MR, Xerri MA. Best practices for high data-rate macromolecular crystallography (HDRMX). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014302. [PMID: 31934601 PMCID: PMC6952294 DOI: 10.1063/1.5128498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/11/2019] [Indexed: 05/13/2023]
Abstract
In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.
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Affiliation(s)
- Herbert J Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Lawrence C Andrews
- Ronin Institute for Independent Scholarship, 9515 NE 137th St., Kirkland, Washington 98034, USA
| | - Jorge A Diaz
- Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Jean Jakoncic
- Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA
| | - Thu Nguyen
- Stony Brook University, Stony Brook, New York 11794, USA
| | - Nicholas K Sauter
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - Alexei S Soares
- Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA
| | - Justin Y Wei
- Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USA
| | | | - Mario A Xerri
- Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USA
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Terwilliger TC, Bricogne G. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2533-43. [PMID: 25286839 PMCID: PMC4188001 DOI: 10.1107/s1399004714017040] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/23/2014] [Indexed: 11/22/2022]
Abstract
Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.
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Affiliation(s)
- Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507, USA
| | - Gerard Bricogne
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX, England
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