Publications

DIALS Journal Articles

• Laue-DIALS: Open-source software for polychromatic x-ray diffraction data

  Hewitt RA, Dalton KM, Mendez DA, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR.

  Struct Dyn 11, 054701 (1 Sep 2024). [PMID:39386198] [PMC reprint: PMC11462730]
• xia2.multiplex: a multi-crystal data-analysis pipeline

  Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G.

  Acta Crystallogr D Struct Biol 78, 752-769 (01 Jun 2022). [PMID:35647922] [PMC reprint: PMC9159281]
• DIALS as a toolkit

  Winter G, Beilsten-Edmands J, Devenish N, Gerstel M, Gildea RJ, McDonagh D, Pascal E, Waterman DG, Williams BH, Evans G.

  Protein Sci 31, 232-250 (1 Jan 2022). [PMID:34747533] [PMC reprint: PMC8740827]
• Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling

  Beilsten-Edmands J, Winter G, Gildea R, Parkhurst J, Waterman D, Evans G.

  Acta Crystallogr D Struct Biol 76, 385-399 (01 Apr 2020). [PMID:32254063] [PMC reprint: PMC7137103]
• SAD phasing of XFEL data depends critically on the error model

  Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK.

  Acta Crystallogr D Struct Biol 75, 959-968 (01 Nov 2019). [PMID:31692470] [PMC reprint: PMC6834081]
• How best to use photons

  Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR.

  Acta Crystallogr D Struct Biol 75, 242-261 (01 Mar 2019). [PMID:30950396] [PMC reprint: PMC6450062]
• Improving signal strength in serial crystallography with DIALS geometry refinement

  Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Young ID, O’Riordan LJ, Yano J, Winter G, Evans G, Sauter NK.

  Acta Crystallogr D Struct Biol 74, 877-894 (01 Sep 2018). [PMID:30198898] [PMC reprint: PMC6130462]
• Electron diffraction data processing with DIALS

  Clabbers MTB, Gruene T, Parkhurst JM, Abrahams JP, Waterman DG.

  Acta Crystallogr D Struct Biol 74, 506-518 (01 Jun 2018). [PMID:29872002] [PMC reprint: PMC6096487]

  Data and processing instructions associated with this paper can be found here.

• Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity

  Gildea RJ, Winter G.

  Acta Crystallogr D Struct Biol 74, 405-410 (01 May 2018). [PMID:29717711] [PMC reprint: PMC5930348]
• DIALS: implementation and evaluation of a new integration package

  Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G.

  Acta Crystallogr D Struct Biol 74, 85-97 (01 Feb 2018). [PMID:29533234] [PMC reprint: PMC5947772]
• Background modelling of diffraction data in the presence of ice rings

  Parkhurst JM, Thorn A, Vollmar M, Winter G, Waterman DG, Fuentes-Montero L, Gildea RJ, Murshudov GN, Evans G.

  IUCrJ 4, 626-638 (01 Sep 2017). [PMID:28989718] [PMC reprint: PMC5619854]
• Robust background modelling in DIALS

  Parkhurst JM, Winter G, Waterman DG, Fuentes-Montero L, Gildea RJ, Murshudov GN, Evans G.

  J Appl Crystallogr 49, 1912-1921 (01 Dec 2016). [PMID:27980508] [PMC reprint: PMC5139990]
• Diffraction-geometry refinement in the DIALS framework

  Waterman DG, Winter G, Gildea RJ, Parkhurst JM, Brewster AS, Sauter NK, Evans G.

  Acta Crystallogr D Struct Biol 72, 558-75 (1 Apr 2016). [PMID:27050135] [PMC reprint: PMC4822564]
• New methods for indexing multi-lattice diffraction data

  Gildea RJ, Waterman DG, Parkhurst JM, Axford D, Sutton G, Stuart DI, Sauter NK, Evans G, Winter G.

  Acta Crystallogr D Biol Crystallogr 70, 2652-66 (1 Oct 2014). [PMID:25286849] [PMC reprint: PMC4188007]
• dxtbx: the diffraction experiment toolbox

  Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G.

  J Appl Crystallogr 47, 1459-1465 (01 Aug 2014). [PMID:25242914] [PMC reprint: PMC4119952]
• Diffuse X-ray scattering to model protein motions

  Wall ME, Adams PD, Fraser JS, Sauter NK.

  Structure 22, 182-4 (04 Feb 2014). [PMID:24507780] [PMC reprint: PMC4070675] (Reprint)
• New Python-based methods for data processing

  Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N.

  Acta Crystallogr D Biol Crystallogr 69, 1274-82 (1 Jul 2013). [PMID:23793153] [PMC reprint: PMC3689530]
• Automatic Fortran to C++ conversion with FABLE

  Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD.

  Source Code Biol Med 7, 5 (28 May 2012). [PMID:22640868] [PMC reprint: PMC3448510]

DIALS Application to XFEL Crystallography

• Structure of a ribonucleotide reductase R2 protein radical

  Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M.

  Science 382, 109-113 (06 Oct 2023). [PMID:37797025] [PMC reprint: PMC7615503]
• Structural evidence for intermediates during O₂ formation in photosystem II

  Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK.

  Nature 617, 629-636 (1 May 2023). [PMID:37138085] [PMC reprint: PMC10191843]
• Chemical crystallography by serial femtosecond X-ray diffraction

  Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN.

  Nature 601, 360-365 (1 Jan 2022). [PMID:35046599] [PMC reprint: PMC8770144]
• Structures of the intermediates of Kok's photosynthetic water oxidation clock

  Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.

  Nature 563, 421-425 (1 Nov 2018). [PMID:30405241] [PMC reprint: PMC6485242]
• XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

  Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.

  Proc Natl Acad Sci U S A 114, 13357-13362 (19 Dec 2017). [PMID:28835537] [PMC reprint: PMC5754760]
• Structure of photosystem II and substrate binding at room temperature

  Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.

  Nature 540, 453-457 (15 Dec 2016). [PMID:27871088] [PMC reprint: PMC5201176]
• De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure

  Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS.

  Nature 539, 43-47 (03 Nov 2016). [PMID:27680699] [PMC reprint: PMC5161637]
• Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

  Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS.

  Elife 4 (30 Sep 2015). [PMID:26422513] [PMC reprint: PMC4721965]
• Structure of the toxic core of α-synuclein from invisible crystals

  Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS.

  Nature 525, 486-90 (24 Sep 2015). [PMID:26352473] [PMC reprint: PMC4791177]
• Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis

  Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT.

  Nature 525, 62-7 (03 Sep 2015). [PMID:26280336] [PMC reprint: PMC4607316]
• A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

  Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A, Grimes JM, Sauter NK, Sutton G, Stuart DI.

  Acta Crystallogr D Biol Crystallogr 71, 1400-10 (1 Jun 2015). [PMID:26057680] [PMC reprint: PMC4461207]
• Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

  Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI.

  Elife 4 (17 Mar 2015). [PMID:25781634] [PMC reprint: PMC4397907]
• Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

  Ginn HM, Messerschmidt M, Ji X, Zhang H, Axford D, Gildea RJ, Winter G, Brewster AS, Hattne J, Wagner A, Grimes JM, Evans G, Sauter NK, Sutton G, Stuart DI.

  Nat Commun 6, 6435 (09 Mar 2015). [PMID:25751308] [PMC reprint: PMC4403592]
• XFEL diffraction: developing processing methods to optimize data quality

  Sauter NK.

  J Synchrotron Radiat 22, 239-48 (1 Mar 2015). [PMID:25723925] [PMC reprint: PMC4344359]
• Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

  Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK.

  Acta Crystallogr D Biol Crystallogr 71, 357-66 (1 Feb 2015). [PMID:25664747] [PMC reprint: PMC4321489]
• Data Exploration Toolkit for serial diffraction experiments

  Zeldin OB, Brewster AS, Hattne J, Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Zhao M, Weis WI, Sauter NK, Brunger AT.

  Acta Crystallogr D Biol Crystallogr 71, 352-6 (1 Feb 2015). [PMID:25664746] [PMC reprint: PMC4321488]
• Improved crystal orientation and physical properties from single-shot XFEL stills

  Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD.

  Acta Crystallogr D Biol Crystallogr 70, 3299-309 (01 Dec 2014). [PMID:25478847] [PMC reprint: PMC4257623] (Reprint)
• Goniometer-based femtosecond crystallography with X-ray free electron lasers

  Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO.

  Proc Natl Acad Sci U S A 111, 17122-7 (02 Dec 2014). [PMID:25362050] [PMC reprint: PMC4260607]
• Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

  Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I, Eisenberg DS.

  Proc Natl Acad Sci U S A 111, 12769-74 (02 Sep 2014). [PMID:25136092] [PMC reprint: PMC4156696]
• Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

  Kern J, Hattne J, Tran R, Alonso-Mori R, Laksmono H, Gul S, Sierra RG, Rehanek J, Erko A, Mitzner R, Wernet P, Bergmann U, Sauter NK, Yachandra V, Yano J.

  Philos Trans R Soc Lond B Biol Sci 369, 20130590 (17 Jul 2014). [PMID:24914169] [PMC reprint: PMC4052878]
• The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser

  Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra VK.

  Philos Trans R Soc Lond B Biol Sci 369, 20130324 (17 Jul 2014). [PMID:24914152] [PMC reprint: PMC4052861]
• Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy

  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.

  Nat Commun 5, 4371 (09 Jul 2014). [PMID:25006873] [PMC reprint: PMC4151126]
• Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

  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.

  Nat Methods 11, 545-8 (1 May 2014). [PMID:24633409] [PMC reprint: PMC4008696]
• Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature

  Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J.

  Science 340, 491-5 (26 Apr 2013). [PMID:23413188] [PMC reprint: PMC3732582]
• Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

  Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK.

  Proc Natl Acad Sci U S A 109, 9721-6 (19 Jun 2012). [PMID:22665786] [PMC reprint: PMC3382516]

DIALS Synchrotron Applications

• Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

  Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC.

  Proc Natl Acad Sci U S A 111, 17887-92 (16 Dec 2014). [PMID:25453071] [PMC reprint: PMC4273327]
• Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

  Pothineni SB, Venugopalan N, Ogata CM, Hilgart MC, Stepanov S, Sanishvili R, Becker M, Winter G, Sauter NK, Smith JL, Fischetti RF.

  J Appl Crystallogr 47, 1992-1999 (01 Dec 2014). [PMID:25484844] [PMC reprint: PMC4248568] (Reprint)

DIALS Newsletter Articles

• XFEL Detectors and ImageCIF

  Brewster AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK.

  Computational Crystallography Newsletter 5, 19-24 (2014).
• The DIALS framework for integration software

  Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, Brewster A, Sauter NK, Evans G.

  CCP4 Newsletter on Protein Crystallography 49, 16-19 (2013).

  (Reprint)
• Viewing diffraction images in CCTBX

  Echols N, Hattne J, Gildea RJ, Adams PD, Sauter NK.

  Computational Crystallography Newsletter 3, 14-17 (2012).
• An extremely fast spotfinder for real-time beamline applications

  Sauter NK.

  Computational Crystallography Newsletter 2, 93 (2011).

DIALS Reports

• DIALS Framework Report

  • The requirements for and the design of the DIALS framework is described in this report, submitted as the first project deliverable for the BioStruct-X 18 month report.