2014 Tutorials: Difference between revisions
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[http://dx.doi.org/10.1038/nmeth.2887 <i>Nature Methods</i> <b>11</b>, 545-548]. | [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 | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008696/pdf/nihms571964.pdf Reprint] | ||
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[http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130590]. | [http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130590]. | ||
[http://dx.doi.org/10.1098/rstb.2013.0590 | [http://dx.doi.org/10.1098/rstb.2013.0590 Reprint] | ||
</li> | </li> | ||
<li> | <li> | ||
Parkhurst | Parkhurst et al (2014):<B> | ||
<em>dxtbx</em>: the diffraction experiment toolbox. | <em>dxtbx</em>: the diffraction experiment toolbox. | ||
</B> | </B> | ||
[http://dx.doi.org/10.1107/S1600576714011996 <i>J. Appl. Cryst.</i> <b>47</b>, 1459-1465]. | |||
<i>J. Appl. Cryst.</i> <b>47</b>, 1459-1465. | [http://cci.lbl.gov/publications/download/jo5001_reprint.pdf Reprint] | ||
</li> | </li> | ||
<li> | <li> | ||
Kern | Kern et al (2014):<B> | ||
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. | Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. | ||
</B> | </B> | ||
[http://dx.doi.org/10.1038/ncomms5371 <i>Nature Communications</i> <b>5</b>, 4371]. | |||
<i>Nature Communications</i> <b>5</b>, 4371 | |||
</li> | </li> | ||
<li> | <li> | ||
Sawaya | Sawaya et al (2014):<B> | ||
Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron | |||
Protein crystal structure obtained at 2.9 | |||
laser beam. | laser beam. | ||
</B> | </B> | ||
[http://www.pnas.org/content/early/2014/08/14/1413456111 <i>Proc Natl Acad Sci USA</i><b></b>, epub 18 Aug 2014]. | |||
<i>Proc Natl Acad Sci USA</i><b></b>, epub 18 Aug 2014 | |||
</li> | </li> | ||
Revision as of 20:36, 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 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 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>
- 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