2014 Tutorials

Welcome

Four example datasets from the LCLS are described here, with complete instructions for full data processing.

Aug. 21-22 Data Analysis Workshop.

Getting Started

Go here to set up your environment.

List of Examples

Dataset	File Paths	Reference & purpose	CXIDB
L220 Lysozyme	/reg/d/psdm/cxi/cxi84914/xtc/e60	Boutet, 2012 (initial report) Hattne, 2014 (cctbx reprocessing)	17
Gd-Lysozyme	/reg/d/psdm/cxi/cxi84914/xtc/e239 /reg/d/psdm/cxi/cxi84914/xtc/e240	Barends, 2013 (SAD anomalous phasing)	22
Gd-Lysozyme-psana Tutorial revised for psana migration	/reg/d/psdm/cxi/cxi84914/xtc/e239 /reg/d/psdm/cxi/cxi84914/xtc/e240	Barends, 2013 (SAD anomalous phasing)	22
L498 Thermolysin	/reg/d/psdm/cxi/cxi84914/xtc/e157	Hattne, 2014 (cctbx processing & weak Zn anomalous signal)	23
LB67 Thermolysin	/reg/d/psdm/cxi/cxi84914/xtc/e350	unpublished (illustrate CSPAD hi/lo gain settings)

References

• Hattne et al (2014): Accurate Macromolecular Structures Using Minimal Measurements from X-ray Free-electron Lasers. Nature Methods 11, 545-548. Reprint
• Brewster et al (2014): XFEL Detectors and ImageCIF. Computational Crystallography Newsletter 5, 19-24. Reprint
• Tran et al (2014): The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Phil. Trans. R. Soc. B 369, 20130324. Reprint
• Kern et al (2014): Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. Phil. Trans. R. Soc. B 369, 20130590. Reprint
• Parkhurst et al (2014): dxtbx: the diffraction experiment toolbox. J. Appl. Cryst. 47, 1459-1465. Reprint
• Kern et al (2014): Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications 5, 4371.
• Sawaya et al (2014): Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proc Natl Acad Sci USA, epub 18 Aug 2014.
• Waterman et al (2013): The DIALS framework for integration software. CCP4 Newsletter on Protein Crystallography 49, 16-19. Reprint
• Kern et al (2013) Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 340, 491-495.
• Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N (2012) New Python-based methods for data processing. Acta Crystallographica Section D: Biological Crystallography D69, 1274-1282. Reprint
• Sierra et al (2012): Nanoflow electrospinning serial femtosecond crystallography. Acta Cryst. D68, 1584-1587. Reprint
• Kern et al (2012) Room temperature femtosecond X-ray diffraction of photosytem II microcrystals. Proc. Natl. Acad. Sci. USA 109, 9721-9726. Reprint