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| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)
 
| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)
 
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==References==
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<ul>
 +
 +
<li>
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Hattne et al (2014):<B>
 +
Accurate Macromolecular Structures Using Minimal Measurements from X-ray Free-electron Lasers.
 +
</B>
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[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">
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<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, Gl&ouml;ckner 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 &Aring 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
/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

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