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Serial Femtosecond Crystallography at SACLA

This wiki provides useful information for serial femtosecond crystallography (SFX) experiments at SACLA. Please note that this is an unofficial documentation; the author is a power user of SACLA but not a member of the facility.

In case of trouble, please contact me by mail or through the "Issues" page.

Currently (Feb, 2020), this tutorial and the pipeline use CrystFEL 0.6.3. Newer versions of CrystFEL up to 0.9.0 are also available on the SACLA HPC system.

NOTE: To access the tutorial dataset on the SACLA HPC, you have to add LLST_PATH="/gpfs/:/home/software/examples/ExpData/gpfs/" to your ~/.bashrc, because the dataset is old and stored in a different location. After you finish the tutorial, please remove this line; this line modifies the data path and prevents access to newer datasets.

References

First of all, we recommend all users to read the following documentations.

• CrystFEL website, especially tutorials and best practices.
• Data processing pipeline for serial femtosecond crystallography at SACLA
  Nakane et al. J. Appl. Crystallogr. 49.3 (2016), open access

Contents

• Basics

  • Running the pipeline
  • Running CrystFEL
  • Optimizing the result
  • SACLA HPC system
  • Online (realtime) analysis
  • Working with MPCCD images

• Advanced topics

  • Experimental phasing
  • Time resolved experiments (without timing tool)
  • Time resolved experiments (with timing tool)
  • Dealing with unusual geometry and mask
  • Processing MPCCD images by DIALS
  • Processing MPCCD images by cppxfel (needs developer version)

• Serial crystallography at synchrotrons

  • Processing EIGER images in CrystFEL
  • Processing EIGER images by DIALS

• Processing Examples

  • Experimental Phasing of Proteinase K