1
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Zhou Q, Gao ZQ, Dong Z, Jiang YM, She Z, Geng Z, Dong YH. A reference-based multi-lattice indexing method integrating prior information correction and iterative refinement in protein crystallography. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:277-288. [PMID: 34196290 DOI: 10.1107/s2053273321003521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/01/2021] [Indexed: 11/10/2022]
Abstract
A new multi-lattice indexing method based on the principle of whole-pattern matching given cell dimensions and space-group symmetry is presented for macromolecular crystallography. The proposed method, termed the multi-crystal data processing suite (MCDPS), features a local correction for prior information accompanied by iterative refinement of experimental parameters, both of which are numerically and experimentally demonstrated to be critical for accurately identifying multiple crystal lattices. Further analysis of data reduction and structure determination with conventional single-crystal programs reveals that the processed multi-lattice data sets are comparable in quality to typical single-crystal ones in terms of crystallographic metrics. Importantly, it is confirmed that careful exclusion of overlapping reflections prior to scaling is necessary to guarantee an accurate data reduction result. The potential for multi-lattice indexing in solving the general macroscopic twinning problem is also explored.
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Affiliation(s)
- Qiang Zhou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zeng Qiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zheng Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yu Meng Jiang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhun She
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yu Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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2
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Beyerlein KR, White TA, Yefanov O, Gati C, Kazantsev IG, Nielsen NFG, Larsen PM, Chapman HN, Schmidt S. FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images. J Appl Crystallogr 2017; 50:1075-1083. [PMID: 28808433 PMCID: PMC5541352 DOI: 10.1107/s1600576717007506] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/21/2017] [Indexed: 01/31/2023] Open
Abstract
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on ([Formula: see text]10) facets.
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Affiliation(s)
- Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivan G. Kazantsev
- Institute of Computational Mathematics and Mathematical Geophysics, Lavrentieva 6, 630090 Novosibirsk, Russian Federation
| | | | - Peter M. Larsen
- Department of Physics, Technical University of Denmark, DK-2800, Denmark
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Søren Schmidt
- Department of Physics, Technical University of Denmark, DK-2800, Denmark
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3
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Gildea RJ, Waterman DG, Parkhurst JM, Axford D, Sutton G, Stuart DI, Sauter NK, Evans G, Winter G. New methods for indexing multi-lattice diffraction data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2652-66. [PMID: 25286849 PMCID: PMC4188007 DOI: 10.1107/s1399004714017039] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/23/2014] [Indexed: 11/10/2022]
Abstract
A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of diffraction data. The method takes advantage of a simplification of Fourier transform-based methods that is applicable when the unit-cell dimensions are known a priori. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from crystals of ∼1 µm in size, where it is shown that up to six lattices can be successfully indexed and subsequently integrated from a 1° wedge of data. Analysis is presented which shows that improvements in data-quality indicators can be obtained through accurate identification and rejection of overlapping reflections prior to scaling.
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Affiliation(s)
- Richard J. Gildea
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - David G. Waterman
- STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I. Stuart
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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4
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Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun 2014; 5:4371. [PMID: 25006873 PMCID: PMC4151126 DOI: 10.1038/ncomms5371] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/10/2014] [Indexed: 01/07/2023] Open
Abstract
The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Sheraz Gul
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hartawan Laksmono
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G. Sierra
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Richard J. Gildea
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | | | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Claudiu A. Stan
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Alyssa Lampe
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | | | - Alan R. Fry
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Gallo
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | - Jens Uhlig
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Petrus H. Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David E. Skinner
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael J. Bogan
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA,PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Pieter Glatzel
- European Synchrotron Radiation Facility, F-38043 Grenoble Cedex, France
| | - Garth J. Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany,Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
| | - Vittal K. Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Corresponding authors. (U.B.), , (J.Y.), (V.K.Y)
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5
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Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 2014; 11:545-8. [PMID: 24633409 DOI: 10.1038/nmeth.2887] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 02/04/2014] [Indexed: 01/19/2023]
Abstract
X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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Affiliation(s)
- Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Richard J Gildea
- 1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2]
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | | | - Alyssa Lampe
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sheraz Gul
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany
| | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Alan R Fry
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Alan Miahnahri
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - William E White
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Donald W Schafer
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M Marvin Seibert
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Tsu-Chien Weng
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jonas Sellberg
- 1] Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Department of Physics, AlbaNova, Stockholm University, Stockholm, Sweden
| | - Matthew J Latimer
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Pieter Glatzel
- European Synchrotron Radiation Facility, Grenoble, France
| | - Petrus H Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ralf W Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael J Bogan
- 1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA. [2] Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Athina Zouni
- 1] Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany. [2] Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Uwe Bergmann
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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6
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Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N. New Python-based methods for data processing. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1274-82. [PMID: 23793153 PMCID: PMC3689530 DOI: 10.1107/s0907444913000863] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/09/2013] [Indexed: 11/16/2022]
Abstract
Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h(-1)) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units.
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Affiliation(s)
- Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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7
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Powell HR, Johnson O, Leslie AGW. Autoindexing diffraction images with iMosflm. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1195-203. [PMID: 23793145 PMCID: PMC3689522 DOI: 10.1107/s0907444912048524] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/26/2012] [Indexed: 12/03/2022]
Abstract
The principles of one-dimensional FFT-based autoindexing of diffraction images are described together with practical issues that may arise. A procedure for indexing multiple lattices as implemented in iMosflm is presented. An overview of autoindexing diffraction images based on one-dimensional fast Fourier transforms is presented. The implementation of the algorithm in the Mosflm/iMosflm program suite is described with a discussion of practical issues that may arise and ways of assessing the success or failure of the procedure. Recent developments allow indexing of images that show multiple lattices, and several examples demonstrate the success of this approach in real cases.
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Affiliation(s)
- Harold R Powell
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England
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8
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Sørensen HO, Schmidt S, Wright JP, Vaughan GBM, Techert S, Garman EF, Oddershede J, Davaasambuu J, Paithankar KS, Gundlach C, Poulsen HF. Multigrain crystallography. ACTA ACUST UNITED AC 2012. [DOI: 10.1524/zkri.2012.1438] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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