CrystFEL

CrystFEL is a suite of programs to process data from "serial crystallography" experiments.

305
mentions
25
contributors

Cite this software

What CrystFEL can do for you

CrystFEL is a suite of programs to process data from "serial crystallography" experiments. Datasets from this type of experiment consist of many thousands of individual diffraction patterns, each one of which was produced by X-rays scattering from a tiny crystal. This technique is most often used for investigating the structure of biological molecules such as proteins, but other types of matter have been investigated as well. The X-rays can come from a synchrotron storage ring such as PETRA III, or from a free-electron laser such as the European XFEL. Electron beams in a transmission electron microscope can also be used. The "serial" mode of data acquisition is particularly relevant for time-resolved experiments -
making so-called "molecular movies".

To process the data, each diffraction pattern has to be analysed individually. The first step is to find the sharp "Bragg" peaks in the pattern, from which the orientation of the crystal as well as the geometrical parameters of the crystal lattice can be determined. The intensities of the Bragg peaks then need to be measured, including very weak peaks whose presence can be inferred from the crystal parameters despite not being found by the initial peak search. The intensities from all the patterns are then merged together to produce a final combined dataset which can be used to determine the structure of the crystal.

CrystFEL contains programs to perform each of these steps, brought together with a graphical user interface. High performance computing is often needed due to the sizes of the datasets, so the GUI can submit jobs directly via a batch system such as Slurm. Recently, streaming data interfaces (for example, based on ZeroMQ) have been implemented, enabling real-time data processing without any intermediate storage of data.

The CrystFEL website contains further information including presentation slides, a screencast, citation lists, API reference and a detailed tutorial.

Screenshot of the CrystFEL graphical user interface.Screenshot of the CrystFEL graphical user interface being used to examine a serial crystallography dataset acquired at SwissFEL.

See also a presentation video about CrystFEL.

Logo of CrystFEL
Keywords
Programming languages
  • C 90%
  • Julia 3%
  • Python 3%
  • Shell 2%
  • Meson 1%
License
  • GPL-3.0-or-later
</>Source code
Packages

Participating organisations

Arizona State University
Hamburg University of Technology
Max
SLA
Van
Diamond Light Source
RIK
Uni
Deutsches Elektronen-Synchrotron DESY

Mentions

Contributors

TW
Thomas White
Developer
Deutsches Elektronen-Synchrotron DESY
VM
Valerio Mariani
Developer
SLAC National Accelerator Lab
HG
Helen Ginn
Contributor
Deutsches Elektronen-Synchrotron DESY
YG
Yaroslav Gevorkov
Contributor
Center for Free-Electron Laser Science
AT
Aleksandra Tolstikova
Developer
Deutsches Elektronen-Synchrotron DESY
CG
Cornelius Gati
Contributor
Deutsches Elektronen-Synchrotron DESY
TN
Takanori Nakane
Contributor
MRC Laboratory of Molecular Biology
PH
Pascal Hogan-Lamarre
Contributor
Max-Planck-Institut für Struktur und Dynamik der Materie
RK
Richard A Kirian
Contributor
Arizona State University
AA
Andrew Aquila
Contributor
SLAC National Accelerator Laboratory
PT
Parthasarathy Tirumalai
Continuous Integration and Deployment engineer
Deutsches Elektronen-Synchrotron DESY
OY
Oleksandr Yefanov
Contributor
Center for Free Electron Laser Science