Difference between revisions of "2014 Tutorials"

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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 ==
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| style="padding: 5px;"| [http://cxidb.org/id-17.html 17]
 
| style="padding: 5px;"| [http://cxidb.org/id-17.html 17]
 
|-
 
|-
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| style="padding: 10px;"| '''Gd-Lysozyme'''
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| style="padding: 10px;"| '''[[Gd-Lysozyme]]'''
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| style="padding: 5px;" | <code>/reg/d/psdm/cxi/cxi84914/xtc/e239<br>/reg/d/psdm/cxi/cxi84914/xtc/e240</code>
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| style="padding: 5px;"| Barends, 2013 (SAD anomalous phasing)
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| style="padding: 5px;"| [http://cxidb.org/id-22.html 22]
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|-
 +
| 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)
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| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)
 
| style="padding: 5px;"| unpublished (illustrate CSPAD hi/lo gain settings)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==
 
==References==
 
<ul>
 
<ul>
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</B>
 
</B>
 
[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 (Reprint)]
+
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008696/pdf/nihms571964.pdf Reprint]
 
</li>
 
</li>
  
 
<li>
 
<li>
−
Brewster AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK (2014):<B>
+
Brewster et al (2014):<B>
 
XFEL Detectors and ImageCIF.
 
XFEL Detectors and ImageCIF.
 
</B>
 
</B>
−
<a href="http://www.phenix-online.org/newsletter">
+
[http://www.phenix-online.org/newsletter <i>Computational Crystallography Newsletter</i> <b>5</b>, 19-24].
−
<i>Computational Crystallography Newsletter</i> <b>5</b>, 19-24</a>.
+
[http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf Reprint]
−
<a href="http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf"
+
−
  target=reprints
+
−
>(Reprint)</a>
+
 
</li>
 
</li>
−
 
−
<P>
 
  
 
<li>
 
<li>
−
Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J,
+
Tran et al (2014):<B>
−
Yachandra V (2014):<B>
+
 
The Mn<sub>4</sub>Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy
 
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.
 
and crystallography using an X-ray free-electron laser.
 
</B>
 
</B>
−
<a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html">
+
[http://rstb.royalsocietypublishing.org/content/369/1647/20130324.full.pdf+html <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130324].
−
<i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130324.
+
[http://dx.doi.org/10.1098/rstb.2013.0324 Reprint]
−
</a>
+
−
<a href="http://dx.doi.org/10.1098/rstb.2013.0324"
+
−
  target=reprints
+
−
>(Reprint)</a>
+
 
</li>
 
</li>
−
 
−
<P>
 
  
 
<li>
 
<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
+
Kern et al (2014):<B>
−
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.
 
Methods development for diffraction and spectroscopic studies of metalloenzymes at X-ray free electron lasers.
 
</B>
 
</B>
−
<a href="http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html">
+
[http://rstb.royalsocietypublishing.org/content/369/1647/20130590.full.pdf+html <i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130590].
−
<i>Phil. Trans. R. Soc. B</i> <b>369</b>, 20130590.
+
[http://dx.doi.org/10.1098/rstb.2013.0590 Reprint]
−
</a>
+
−
<a href="http://dx.doi.org/10.1098/rstb.2013.0590"
+
−
  target=reprints
+
−
>(Reprint)</a>
+
 
</li>
 
</li>
−
 
−
<P>
 
  
 
<li>
 
<li>
−
Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton, AW, Echols N, Evans G, Sauter NK, Winter
+
Parkhurst et al (2014):<B>
−
G (2014):<B>
+
 
<em>dxtbx</em>: the diffraction experiment toolbox.
 
<em>dxtbx</em>: the diffraction experiment toolbox.
 
</B>
 
</B>
−
<a href="http://dx.doi.org/10.1107/S1600576714011996">
+
[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]
−
<a
+
−
href="http://cci.lbl.gov/publications/download/jo5001_reprint.pdf"
+
−
  target=reprints
+
−
>(Reprint)</a>
+
 
</li>
 
</li>
−
 
−
<P>
 
  
 
<li>
 
<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
+
Kern et al (2014):<B>
−
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.
 
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.
 
</B>
 
</B>
−
<a href="http://dx.doi.org/10.1038/ncomms5371">
+
[http://dx.doi.org/10.1038/ncomms5371 <i>Nature Communications</i> <b>5</b>, 4371].
−
<i>Nature Communications</i> <b>5</b>, 4371</a>.
+
−
<a
+
−
  target=reprints
+
−
>(Reprint)</a>
+
−
 
+
−
<P>
+
 
</li>
 
</li>
  
 
<li>
 
<li>
−
Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier J-P, Messerschmidt MM, Boutet S,
+
Sawaya et al (2014):<B>
−
Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP,
+
Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron
−
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.
 
  laser beam.
 
</B>
 
</B>
−
<a href="http://www.pnas.org/content/early/2014/08/14/1413456111">
+
[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</a>.
+
−
<a
+
−
  target=reprints
+
−
>(Reprint)</a>
+
−
 
+
 
</li>
 
</li>
  
 
<li>
 
<li>
−
Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J,
+
Waterman et al (2013):<B>
−
Brewster A, Sauter NK, Evans G (2013):<B>
+
 
The DIALS framework for integration software.
 
The DIALS framework for integration software.
 
</B>
 
</B>
−
<a href="http://www.ccp4.ac.uk/newsletters/newsletter49/content.html">
+
[http://www.ccp4.ac.uk/newsletters/newsletter49/content.html <i>CCP4 Newsletter on Protein Crystallography</i> <b>49</b>, 16-19].
−
<i>CCP4 Newsletter on Protein Crystallography</i> <b>49</b>, 16-19</a>.
+
[http://cci.lbl.gov/publications/download/DIALS.pdf Reprint]
−
<a href="http://cci.lbl.gov/publications/download/DIALS.pdf"
+
−
  target=reprints
+
−
>(Reprint)</a>
+
−
<P>
+
 
</li>
 
</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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