Difference between revisions of "2014 Tutorials"
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| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings) | | style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings) | ||
|} | |} | ||
+ | ==References== | ||
+ | <ul> | ||
+ | |||
+ | <li> | ||
+ | Hattne et al (2014):<B> | ||
+ | Accurate Macromolecular Structures Using Minimal Measurements from X-ray Free-electron Lasers. | ||
+ | </B> | ||
+ | [http://dx.doi.org/10.1038/nmeth.2887 <i>Nature Methods</i> <b>11</b>, 545-548]. | ||
+ | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008696/pdf/nihms571964.pdf (Reprint)] | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Brewster AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK (2014):<B> | ||
+ | XFEL Detectors and ImageCIF. | ||
+ | </B> | ||
+ | <a href="http://www.phenix-online.org/newsletter"> | ||
+ | <i>Computational Crystallography Newsletter</i> <b>5</b>, 19-24</a>. | ||
+ | <a href="http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf" | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | </li> | ||
+ | |||
+ | <P> | ||
+ | |||
+ | <li> | ||
+ | Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, | ||
+ | Yachandra V (2014):<B> | ||
+ | The Mn<sub>4</sub>Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy | ||
+ | and crystallography using an X-ray free-electron laser. | ||
+ | </B> | ||
+ | <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html"> | ||
+ | <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130324. | ||
+ | </a> | ||
+ | <a href="http://dx.doi.org/10.1098/rstb.2013.0324" | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | </li> | ||
+ | |||
+ | <P> | ||
+ | |||
+ | <li> | ||
+ | Kern J, Hattne J, Tran R, Alonso-Mori R, Laksmono H, Gul S, Sierra RG, Rehanek J, Erko A, Mitzner R, Wernet P, Bergman | ||
+ | n U, Sauter NK, Yachandra V, Yano J (2014):<B> | ||
+ | Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. | ||
+ | </B> | ||
+ | <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html"> | ||
+ | <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130590. | ||
+ | </a> | ||
+ | <a href="http://dx.doi.org/10.1098/rstb.2013.0590" | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | </li> | ||
+ | |||
+ | <P> | ||
+ | |||
+ | <li> | ||
+ | Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton, AW, Echols N, Evans G, Sauter NK, Winter | ||
+ | G (2014):<B> | ||
+ | <em>dxtbx</em>: the diffraction experiment toolbox. | ||
+ | </B> | ||
+ | <a href="http://dx.doi.org/10.1107/S1600576714011996"> | ||
+ | <i>J. Appl. Cryst.</i> <b>47</b>, 1459-1465. | ||
+ | <a | ||
+ | href="http://cci.lbl.gov/publications/download/jo5001_reprint.pdf" | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | </li> | ||
+ | |||
+ | <P> | ||
+ | |||
+ | <li> | ||
+ | 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 T-C, | ||
+ | Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sau | ||
+ | ter NK, Bergmann U, Yano J, Yachandra VK (2014):<B> | ||
+ | Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. | ||
+ | </B> | ||
+ | <a href="http://dx.doi.org/10.1038/ncomms5371"> | ||
+ | <i>Nature Communications</i> <b>5</b>, 4371</a>. | ||
+ | <a | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | |||
+ | <P> | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier J-P, Messerschmidt MM, Boutet S, | ||
+ | Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, | ||
+ | Park H-W, Federici BA, Sauter NK, Schlichting I, Eisenberg DS (2014):<B> | ||
+ | Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron | ||
+ | laser beam. | ||
+ | </B> | ||
+ | <a href="http://www.pnas.org/content/early/2014/08/14/1413456111"> | ||
+ | <i>Proc Natl Acad Sci USA</i><b></b>, epub 18 Aug 2014</a>. | ||
+ | <a | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | |||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, | ||
+ | Brewster A, Sauter NK, Evans G (2013):<B> | ||
+ | The DIALS framework for integration software. | ||
+ | </B> | ||
+ | <a href="http://www.ccp4.ac.uk/newsletters/newsletter49/content.html"> | ||
+ | <i>CCP4 Newsletter on Protein Crystallography</i> <b>49</b>, 16-19</a>. | ||
+ | <a href="http://cci.lbl.gov/publications/download/DIALS.pdf" | ||
+ | target=reprints | ||
+ | >(Reprint)</a> | ||
+ | <P> | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Kern et al (2013) <B> | ||
+ | Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. | ||
+ | </B> | ||
+ | [http://www.sciencemag.org/content/early/2013/02/13/science.1234273 <i>Science</i> <b>340</b>, 491-495]. | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N (2012) <B> | ||
+ | New Python-based methods for data processing. | ||
+ | </B> | ||
+ | [http://dx.doi.org/10.1107/S0907444913000863 <i>Acta Crystallographica Section D: Biological Crystallography</i> <b>D69</b>, 1274-1282]. | ||
+ | [http://cci.lbl.gov/publications/download/ba5193_reprint.pdf Reprint] | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Sierra et al (2012):<B> | ||
+ | Nanoflow electrospinning serial femtosecond crystallography. | ||
+ | </B> | ||
+ | [http://dx.doi.org/10.1107/S0907444912038152 <i>Acta Cryst. </i> <b>D68</b>, 1584-1587]. | ||
+ | [http://cci.lbl.gov/publications/download/lv5021.pdf Reprint] | ||
+ | </li> | ||
+ | |||
+ | <li> | ||
+ | Kern et al (2012) <B> | ||
+ | Room temperature femtosecond X-ray diffraction of photosytem II microcrystals. | ||
+ | </B> | ||
+ | [http://www.pnas.org/content/early/2012/05/31/1204598109.abstract <i>Proc. Natl. Acad. Sci. USA </i> <b>109</b>, 9721-9726]. | ||
+ | [http://cci.lbl.gov/publications/download/PNAS-2012-Kern-9721-6.pdf Reprint] | ||
+ | </li> |
Revision as of 20:30, 20 August 2014
Welcome
Four example datasets from the LCLS are described here, with complete instructions for full data processing.
Getting Started
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
|
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 AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK (2014): XFEL Detectors and ImageCIF. <a href="http://www.phenix-online.org/newsletter"> Computational Crystallography Newsletter 5, 19-24</a>. <a href="http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf" target=reprints >(Reprint)</a>
- Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra V (2014): The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html"> Phil. Trans. R. Soc. B 369, 20130324. </a> <a href="http://dx.doi.org/10.1098/rstb.2013.0324" target=reprints >(Reprint)</a>
- Kern J, Hattne J, Tran R, Alonso-Mori R, Laksmono H, Gul S, Sierra RG, Rehanek J, Erko A, Mitzner R, Wernet P, Bergman n U, Sauter NK, Yachandra V, Yano J (2014): Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. <a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html"> Phil. Trans. R. Soc. B 369, 20130590. </a> <a href="http://dx.doi.org/10.1098/rstb.2013.0590" target=reprints >(Reprint)</a>
- Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton, AW, Echols N, Evans G, Sauter NK, Winter G (2014): dxtbx: the diffraction experiment toolbox. <a href="http://dx.doi.org/10.1107/S1600576714011996"> J. Appl. Cryst. 47, 1459-1465. <a href="http://cci.lbl.gov/publications/download/jo5001_reprint.pdf" target=reprints >(Reprint)</a>
- 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 T-C, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sau ter NK, Bergmann U, Yano J, Yachandra VK (2014): Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. <a href="http://dx.doi.org/10.1038/ncomms5371"> Nature Communications 5, 4371</a>. <a target=reprints >(Reprint)</a> <P>
- Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier J-P, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park H-W, Federici BA, Sauter NK, Schlichting I, Eisenberg DS (2014): Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam. <a href="http://www.pnas.org/content/early/2014/08/14/1413456111"> Proc Natl Acad Sci USA, epub 18 Aug 2014</a>. <a target=reprints >(Reprint)</a>
- Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, Brewster A, Sauter NK, Evans G (2013): The DIALS framework for integration software. <a href="http://www.ccp4.ac.uk/newsletters/newsletter49/content.html"> CCP4 Newsletter on Protein Crystallography 49, 16-19</a>. <a href="http://cci.lbl.gov/publications/download/DIALS.pdf" target=reprints >(Reprint)</a> <P>
- 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
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