This is a list of references for software and instruments available to the MX users at MAX IV for data collection and processing. Please make sure that you include the appropriate references in your publications.

Acknowledging data collected at BioMAX

The general format for MAX IV beamtime acknowledgement is available on the MAX IV user policy pages

Please also cite the BioMAX paper, see Beamline software and instrumentation: BioMAX below.

Beamline software and instrumentation

  • BioMAX: Ursby, T.; Åhnberg, K.; Appio, R.; Aurelius, O.; Barczyk, A.; Bartalesi, A.; Bjelčić, M.; Bolmsten, F.; Cerenius, Y.; Doak, R. B.; Eguiraun, M.; Eriksson, T.; Friel, R. J.; Gorgisyan, I.; Gross, A.; Haghighat, V.; Hennies, F.; Jagudin, E.; Norsk Jensen, B.; Jeppsson, T.; Kloos, M.; Lidon-Simon, J.; de Lima, G. M. A.; Lizatovic, R.; Lundin, M.; Milan-Otero, A.; Milas, M.; Nan, J.; Nardella, A.; Rosborg, A.; Shilova, A.; Shoeman, R. L.; Siewert, F.; Sondhauss, P.; Talibov, V. O.; Tarawneh, H.; Thånell, J.; Thunnissen, M.; Unge, J.; Ward, C.; Gonzalez, A.; Mueller, U. BioMAX – the First Macromolecular Crystallography Beamline at MAX IV Laboratory. J. Synchrotron Radiat. 2020, 27 (5), 1415–1429. DOI: 10.1107/s1600577520008723
  • MXCube3: Mueller, U.; Thunnissen, M.; Nan, J.; Eguiraun, M.; Bolmsten, F.; Milàn-Otero, A.; Guijarro, M.; Oscarsson, M.; de Sanctis, D.; Leonard, G. MXCuBE3: A New Era of MX-Beamline Control Begins. Synchrotron Radiat. News 2017, 30 (1), 22–27. DOI: 10.1080/08940886.2017.1267564
  • ISPyB: Delagenière, S.; Brenchereau, P.; Launer, L.; Ashton, A. W.; Leal, R.; Veyrier, S.; Gabadinho, J.; Gordon, E. J.; Jones, S. D.; Levik, K. E.; Mcsweeney, S. M.; Monaco, S.; Nanao, M.; Spruce, D.; Svensson, O.; Walsh, M. A.; Leonard, G. A. ISPyB: An Information Management System for Synchrotron Macromolecular Crystallography. Bioinformatics 2011, 27 (22), 3186–3192. DOI: 10.1093/bioinformatics/btr535
  • FragMAX: Lima, G. M. A.; Talibov, V. O.; Jagudin, E.; Sele, C.; Nyblom, M.; Knecht, W.; Logan, D. T.; Sjögren, T.; Mueller, U. FragMAX: The Fragment-Screening Platform at the MAX IV Laboratory. Acta Crystallogr. Sect. D, Struct. Biol. 2020, 76 (8), 771–777. DOI: 10.1107/S205979832000889X
  • Serial crystallography: Shilova, A.; Lebrette, H.; Aurelius, O.; Nan, J.; Welin, M.; Kovacic, R.; Ghosh, S.; Safari, C.; Friel, R. J.; Milas, M.; Matej, Z.; Högbom, M.; Brändén, G.; Kloos, M.; Shoeman, R. L.; Doak, B.; Ursby, T.; Håkansson, M.; Logan, D. T.; Mueller, U. Current Status and Future Opportunities for Serial Crystallography at MAX IV Laboratory. J. Synchrotron Radiat. 2020, 27 (5), 1095–1102. DOI: 10.1107/S1600577520008735
  • Energy scans: Gorgisyan, I.; Bell, P.; Cascella, M.; Eguiraun, M.; Freitas, Á.; Lidon-Simon, J.; Nan, J.; Takahashi, C.; Tarawneh, H.; Ursby, T.; Gonzalez, A. Fast, automated, continuous energy scans for experimental phasing at the BioMAX beamline. J. Synchrotron Radiat. 2023, 30 (5). DOI: 10.1107/S1600577523005738

Automated pipelines for data processing

  • EDNA: Incardona, M. F.; Bourenkov, G. P.; Levik, K.; Pieritz, R. A.; Popov, A. N.; Svensson, O. EDNA: A Framework for Plugin-Based Applications Applied to X-Ray Experiment Online Data Analysis. J. Synchrotron Radiat. 2009, 16 (6), 872–879. DOI: 10.1107/S0909049509036681
  • autoPROC: Vonrhein, C.; Flensburg, C.; Keller, P.; Sharff, A.; Smart, O.; Paciorek, W.; Womack, T.; Bricogne, G. Data Processing and Analysis with the AutoPROC Toolbox. Acta Crystallogr. Sect. D Biol. Crystallogr. 2011, 67 (4), 293–302. DOI: 10.1107/S0907444911007773
  • Fast DP/Fast EP: Winter, G.; McAuley, K. E. Automated Data Collection for Macromolecular Crystallography. Methods 2011, 55 (1), 81–93. DOI: 10.1016/j.ymeth.2011.06.010
  • Xia2: Winter, G. xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Cryst. 2010 43, 186-190. DOI: 10.1107/S0021889809045701

Software included in PReSTO

You can find the list of software packages and programs included in PReSTO in the NSC site. Please acknowledge the individual packges that you use.

Other MX software installed at MAX IV

  • CCP4 package: Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Basle, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Marmol, J. J., Berrisford, J. M., Bond, P. S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A. G., Cowtan, K. D., Croll, T. I., Debreczeni, J. E., Devenish, N. E., Dodson, E. J., Drevon, T. R., Emsley, P., Evans, G., Evans, P. R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E. F., Gerstel, M., Gildea, R. J., Hatti, K., Hekkelman, M. L., Heuser, P., Hoh, S. W., Hough, M. A., Jenkins, H. T., Jimenez, E., Joosten, R. P., Keegan, R. M., Keep, N., Krissinel, E. B., Kolenko, P., Kovalevskiy, O., Lamzin, V. S., Lawson, D. M., Lebedev, A. A., Leslie, A. G. W., Lohkamp, B., Long, F., Maly, M., McCoy, A. J., McNicholas, S. J., Medina, A., Millan, C., Murray, J. W., Murshudov, G. N., Nicholls, R. A., Noble, M. E. M., Oeffner, R., Pannu, N. S., Parkhurst, J. M., Pearce, N., Pereira, J., Perrakis, A., Powell, H. R., Read, R. J., Rigden, D. J., Rochira, W., Sammito, M., Sanchez Rodriguez, F., Sheldrick, G. M., Shelley, K. L., Simkovic, F., Simpkin, A. J., Skubak, P., Sobolev, E., Steiner, R. A., Stevenson, K., Tews, I., Thomas, J. M. H., Thorn, A., Valls, J. T., Uski, V., Uson, I., Vagin, A., Velankar, S., Vollmar, M., Walden, H., Waterman, D., Wilson, K. S., Winn, M. D., Winter, G., Wojdyr, M. & Yamashita, K. Acta Crystallogr. Sect. D Struct. Biol. 2023, 79 (6), 449-461. DOI: 10.1107/S2059798323003595
  • DIALS: Winter, G.; Waterman, D. G.; Parkhurst, J. M.; Brewster, A. S.; Gildea, R. J.; Gerstel, M.; Fuentes-Montero, L.; Vollmar, M.; Michels-Clark, T.; Young, I. D.; Sauter, N. K.; Evans, G. DIALS: Implementation and Evaluation of a New Integration Package. Acta Crystallogr. Sect. D Struct. Biol. 2018, 74 (2), 85–97. DOI: 10.1107/S2059798317017235
  • IMosfilm: Battye, T. G. G.; Kontogiannis, L.; Johnson, O.; Powell, H. R.; Leslie, A. G. W. IMOSFLM: A New Graphical Interface for Diffraction-Image Processing with MOSFLM. Acta Crystallogr. Sect. D Biol. Crystallogr. 2011, 67 (4), 271–281. DOI: 10.1107/S0907444910048675
  • PHENIX: Adams, P. D.; Afonine, P. V.; Bunkóczi, G.; Chen, V. B.; Davis, I. W.; Echols, N.; Headd, J. J.; Hung, L. W.; Kapral, G. J.; Grosse-Kunstleve, R. W.; McCoy, A. J.; Moriarty, N. W.; Oeffner, R.; Read, R. J.; Richardson, D. C.; Richardson, J. S.; Terwilliger, T. C.; Zwart, P. H. PHENIX: A Comprehensive Python-Based System for Macromolecular Structure Solution. Acta Crystallogr. Sect. D Biol. Crystallogr. 2010, 66 (2), 213–221. DOI: 10.1107/S0907444909052925
  • Shelxc/d/e/l: Sheldrick, G. M. A Short History of SHELX. Acta Crystallogr. Sect. A Found. Crystallogr. 2008, 64 (1), 112–122. DOI: 10.1107/S0108767307043930
  • XDS and XSCALE: Kabsch, W. Integration, Scaling, Space-Group Assignment and Post-Refinement. Acta Crystallogr. Sect. D Biol. Crystallogr. 2010, 66 (2), 133–144. DOI: 10.1107/S0907444909047374
Page manager: Ana Gonzalez July 15, 2024