LCLS serial femtosecond crystallography data analysis instructions

By Nadia Zatsepin

Arizona State University

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Abstract

The links below will take you to detailed instructions and sound advice from experienced LCLS data analysts. These pages are focused on serial femtosecond crystallography (SFX), but much of it applies to other X-ray diffraction or imaging experiments at LCLS. 

  1. Brief introduction to serial femtosecond crystallography & slides from "Software for serial femtosecond crystallography data analysis" from IUCr 2014.  
  2. Before your beamtime
  3. During your beamtime
  4. Accessing your data at LCLS
  5. Detectors and geometry
  6. Data reduction and hit finding: Cheetah
  7. Live monitoring and hit finding parameter tweaker: OnDA
  8. Working with LCLS data remotely
  9. Managing your LCLS data after the beamtime
  10. Indexing, merging, evaluating crystal diffraction data: CrystFEL

  The SFX data analysis pipeline we will be referring to is outlined here. These pages will describe the CSPAD/DAQ, Cheetah and CrystFEL steps.

SFX data analysis pipeline  

Additionally, you will find links to

  1. Useful data analysis scripts, all free for your use and modification. These were contributed by BioXFEL members and collaborators. 
  2. 2015 Data Analysis Workshop at ACA, Philadelphia, including PDF's of presentations. 
  3. 2015 Phenix workshop at Rice University, to help with analyzing your merged serial crystallography data after CrystFEL
  4. Videos and presentations from our 2014 data analysis (serial femtosecond crystallography) workshop held at LBNL
  5. Presentation by BioXFEL researcher Marc Messerschmidt about crystallography with an XFEL. 
  6. Cheetah documentation: page 1, page 2, keywords and hit finding algorithms.

  If you see typos or errors or would like more detail about a particular topic, please email the authors (top of this page).   

References

1. LCLS Data Analysis pages (getting started, python modules, detector calibration GUI, TimeTool etc):  https://confluence.slac.stanford.edu/display/PSDM/LCLS+Data+Analysis   2. SFX Data analysis workshop at  ACA 2015 Workshop spreadsheet   3. BioXFEL   data analysis group :    https://www.bioxfel.org/groups/dataanalysis 4. Resources for BioXFEL data analysis group:  https://www.bioxfel.org/groups/dataanalysis/resources 5.  GitHub  repository of scripts:  https://github.com/bioxfel/scripts    

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In This Series

  1. Cheetah documentation page 2

    23 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard Kirian

    Cheetah documentation Page 2. Click here for Page 1. Click here for a list of all keywords.  The official Cheetah website is http://www.desy.de/~barty/cheetah/   These pages will not reproduce all the content from the Cheetah site, but are meant as an addendum.   Running Cheetah …

  2. Cheetah documentation

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    What is Cheetah and how do you use it?

  3. Cheetah documentation - all keywords

    21 Jul 2015 | Series | Contributor(s): Richard Kirian, Nadia Zatsepin

    List of all Cheetah's keywords

  4. 1. Before your beamtime

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Advice for preparing for an LCLS beamtime, especially for data analysts.

  5. 2. During your beamtime

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Important tasks for data analysts during the LCLS beamtime.  Explanation of LCLS eLog.

  6. 3. Accessing your data

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Where is your LCLS data? How long will it be there? 

  7. 5. Data reduction and hit finding

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard A Kirian

    LCLS data reduction and hit finding. Running Cheetah at LCLS. Tuning hit finding parameters and understanding Cheetah's output.

  8. 9. Indexing, merging, evaluation crystal diffraction data: CrystFEL

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Indexing, merging, evaluation serial crystallography data

  9. 7. Working with LCLS data remotely

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Working with LCLS data remotely

  10. 4. Detectors and geometry

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    CXI detectors and geometry

  11. 8. Managing and copying LCLS data

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    LCLS data management and transfer.

  12. Data Analysis Scripts

    21 Jul 2015 | Downloads

    A repository of useful scripts for the analysis of XFEL data. 

  13. Crystallography with an XFEL

    21 Jul 2015 | Seminars | Contributor(s): Marc Messerschmidt

    Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for …

  14. 6. Live data monitoring and interactive hit finding refinement: OnDA

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    OnDA - live data monitoring and interactive hit finding refinement

  15. Introduction to serial femtosecond crystallography data analysis

    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Tom Grant

    Introduction to serial femtosecond crystallography (SFX) with X-ray free electron lasers.  Presentation on software for SFX. 

  16. 2015 Phenix Workshop at Rice University

    03 Apr 2015 | Workshops | Contributor(s): Tom Grant, George Phillips

    The Gulf Coast Consortia, BioXFEL, and Rice University present an instructional workshop on Phenix, the Python-based Hierarchical Environment for Intergrated Xtallography. Topics include experimental phasing, molecular replacement, model refinement and structure validation.

  17. 2014 Data Analysis Workshop

    26 Aug 2014 | Workshops | Contributor(s): Tom Grant, Nadia Zatsepin

    Video and interactive web presentations with PDF slides available for download. Description Serial crystallography is a rapidly growing field with a correspondingly rapidly growing user base. One of the main bottlenecks in serial crystallography is the ability to efficiently filter and analyze …