2014 Tutorials: Difference between revisions
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Four example datasets from the LCLS are described here, with complete instructions for full data processing. | Four example datasets from the LCLS are described here, with complete instructions for full data processing. | ||
Aug. 21-22 [https://www.bioxfel.org/resources/2014-data-analysis-workshop Data Analysis Workshop]. | |||
== [[ 2014 Prerequisites | Getting Started]]== | == [[ 2014 Prerequisites | Getting Started]]== | ||
[[ 2014 Prerequisites | Go here to set up your environment.]] | |||
== List of Examples == | == List of Examples == | ||
| Line 17: | Line 21: | ||
| style="padding: 5px;"| [http://cxidb.org/id-17.html 17] | | style="padding: 5px;"| [http://cxidb.org/id-17.html 17] | ||
|- | |- | ||
| style="padding: 10px;"| '''Gd-Lysozyme''' | | style="padding: 10px;"| '''[[Gd-Lysozyme]]''' | ||
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e239<br>/reg/d/psdm/cxi/cxi84914/xtc/e240</code> | |||
| style="padding: 5px;"| Barends, 2013 (SAD anomalous phasing) | |||
| style="padding: 5px;"| [http://cxidb.org/id-22.html 22] | |||
|- | |||
| style="padding: 10px;"| '''[[Gd-Lysozyme-psana]]''' <br>Tutorial revised for psana migration | |||
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e239<br>/reg/d/psdm/cxi/cxi84914/xtc/e240</code> | | style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e239<br>/reg/d/psdm/cxi/cxi84914/xtc/e240</code> | ||
| style="padding: 5px;"| Barends, 2013 (SAD anomalous phasing) | | style="padding: 5px;"| Barends, 2013 (SAD anomalous phasing) | ||
| Line 31: | Line 40: | ||
| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings) | | style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings) | ||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 et al (2014):<B> | |||
XFEL Detectors and ImageCIF. | |||
</B> | |||
[http://www.phenix-online.org/newsletter <i>Computational Crystallography Newsletter</i> <b>5</b>, 19-24]. | |||
[http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf Reprint] | |||
</li> | |||
<li> | |||
Tran et al (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> | |||
[http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130324]. | |||
[http://dx.doi.org/10.1098/rstb.2013.0324 Reprint] | |||
</li> | |||
<li> | |||
Kern et al (2014):<B> | |||
Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers. | |||
</B> | |||
[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 Reprint] | |||
</li> | |||
<li> | |||
Parkhurst et al (2014):<B> | |||
<em>dxtbx</em>: the diffraction experiment toolbox. | |||
</B> | |||
[http://dx.doi.org/10.1107/S1600576714011996 <i>J. Appl. Cryst.</i> <b>47</b>, 1459-1465]. | |||
[http://cci.lbl.gov/publications/download/jo5001_reprint.pdf Reprint] | |||
</li> | |||
<li> | |||
Kern et al (2014):<B> | |||
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. | |||
</B> | |||
[http://dx.doi.org/10.1038/ncomms5371 <i>Nature Communications</i> <b>5</b>, 4371]. | |||
</li> | |||
<li> | |||
Sawaya et al (2014):<B> | |||
Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron | |||
laser beam. | |||
</B> | |||
[http://www.pnas.org/content/early/2014/08/14/1413456111 <i>Proc Natl Acad Sci USA</i><b></b>, epub 18 Aug 2014]. | |||
</li> | |||
<li> | |||
Waterman et al (2013):<B> | |||
The DIALS framework for integration software. | |||
</B> | |||
[http://www.ccp4.ac.uk/newsletters/newsletter49/content.html <i>CCP4 Newsletter on Protein Crystallography</i> <b>49</b>, 16-19]. | |||
[http://cci.lbl.gov/publications/download/DIALS.pdf Reprint] | |||
</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> | |||
Latest revision as of 23:41, 23 November 2014
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
|
Barends, 2013 (SAD anomalous phasing) | 22 |
| Gd-Lysozyme-psana Tutorial revised for psana migration |
/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 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