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 10: Line 14:
| style="padding: 5px;"| File Paths
| style="padding: 5px;"| File Paths
| style="padding: 5px;"| Reference & purpose
| style="padding: 5px;"| Reference & purpose
| style="padding: 5px;"| CXIDB
|-
|-
| style="padding: 10px;"| '''L220 Lysozyme'''
| style="padding: 10px;"| '''L220 Lysozyme'''
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e60</code>
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e60</code>
| style="padding: 5px;"| Boutet, 2012 (initial report)<br>Hattne, 2014 (cctbx reprocessing)
| style="padding: 5px;"| Boutet, 2012 (initial report)<br>Hattne, 2014 (cctbx reprocessing)
| 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;" | <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)
| style="padding: 5px;"| [http://cxidb.org/id-22.html 22]
|-
|-
| style="padding: 10px;"| '''L498 Thermolysin'''  
| 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;"| Barends, 2013 (SAD anomalous phasing)
| style="padding: 5px;"| [http://cxidb.org/id-22.html 22]
|-
| style="padding: 10px;"| '''[[L498 Thermolysin]]'''
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e157</code>
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e157</code>
| style="padding: 5px;"| Hattne, 2014 (cctbx processing & weak Zn anomalous signal)
| style="padding: 5px;"| Hattne, 2014 (cctbx processing & weak Zn anomalous signal)
| style="padding: 5px;"| [http://cxidb.org/id-23.html 23]
|-  
|-  
| style="padding: 10px;"| '''LB67 Thermolysin'''
| style="padding: 10px;"| '''[[LB67 Thermolysin]]'''
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e350</code>
| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e350</code>
| 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
/reg/d/psdm/cxi/cxi84914/xtc/e240 		Barends, 2013 (SAD anomalous phasing) 22
Gd-Lysozyme-psana
Tutorial revised for psana migration 		/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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