2014 Tutorials: Difference between revisions

From cctbx_xfel
Jump to navigation Jump to search
No edit summary
Line 31: Line 31:
| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)
| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)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, 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

Retrieved from "http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=2014_Tutorials&oldid=531"