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electrons.rst

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Processing electron diffraction data with CrystFEL

Electron diffraction data is fully supported in recent versions of CrystFEL. For some background, see these papers:

  • R. Bücker, P. Hogan-Lamarre, P. Mehrabi, E. C. Schulz et al. "Serial protein crystallography in an electron microscope". Nature Communications 11 (2020) 996. doi:10.1038/s41467-020-14793-0
  • Robert Bücker, Pascal Hogan-Lamarre, R. J. Dwayne Miller. "Serial Electron Diffraction Data Processing with diffractem and CrystFEL" https://arxiv.org/abs/2011.02977

Here are some tips to get you started with your own data.

Setting the wavelength

You can set the accelerating voltage in the geometry file:

electron_voltage = 200 kV

This should be the accelerating voltage, not the relativistically-corrected energy of the accelerated electrons (the difference is small). Alternatively, give the wavelength directly:

wavelength = 2.51e-12 m

You can also use V instead of kV and A (Angstroms) instead of m.

Obviously, do not use photon_energy - that's only for electromagnetic radiation.

Lens distortions and variable direct beam position

Depending on the method of data acquisition, the central beam may vary from frame to frame quite a lot. These shifts will need to be determined and stored in the image headers as part of a pre-processing step such as that performed by diffractem. Specify the location of the shifts in the geometry file, for example:

detector_shift_x = /%/shots/shift_x_mm mm
detector_shift_y = /%/shots/shift_y_mm mm

The location (/%/shots/shift_x_mm) will, of course, depend on your pre-processing. These are the correct locations for data from diffractem.

Note that the coordinates are shifts of the detector (not the beam) in the laboratory coordinate system (see man crystfel_geometry). Shifts in "detector coordinates" (i.e. detector_shift_fs) would only make sense for single-panel detectors and are therefore not implemented.

Correcting elliptical distortions of the projector lens can be done quite well by setting the panel direction vectors (see man crystfel_geometry again) to be non-orthogonal. For example:

p0/fs = +0.9934x -0.0092y
p0/ss = -0.0092x +1.0067y

This is also covered by diffractem.

Indexing patterns

The only indexing method suitable for electrons is PinkIndexer, but more methods might be added in the future. As well as selecting the indexing method using --indexing=pinkindexer, you will need to configure PinkIndexer's assumption about the size of a reflection in reciprocal space using --pinkIndexer-reflection-radius=0.003:

indexamajig -g sample.geom -i input-files.lst -o sample.stream \
            --indexing=pinkindexer --pinkIndexer-reflection-radius=0.003 \
            --peaks=zaef --threshold=300 --min-squared-gradient=50000

That's it! You will have to tune the peak search parameters as usual, of course, but this should already be enough to get started with electron diffraction data.

The default parameters give quick and reasonably good indexing. You can get more accurate results by increasing the granularity of refinement within Pinkindexer using --pinkIndexer-refinement-type=N, with N from 0 (least precise and fastest) to 5 (most precise and slowest). The default value is 1.

For speed, you might want to add --max-indexer-threads=N, where N is the number of threads that PinkIndexer should use within itself. You should also use -j M to specify the number of frames that indexamajig should process in parallel. The sum of N and M should be roughly equal to the number of available CPU cores. It's also helpful to disable the default indexamajig behaviour of making multiple attempts to index each pattern (--no-retry) - this doesn't gain much when using PinkIndexer.

If the camera length is specified in the geometry file by referencing values from image file headers, then you will also need to give an estimate of the camera length using --camera-length-estimate. The same applies if the wavelength is specified indirectly, in which case you will need --wavelength-estimate. However, neither of these are usually necessary for electron diffraction data.

Saving and re-loading indexing results

Indexing patterns with PinkIndexer can take a long time, which makes it painful to try (for example) different integration parameters. To mitigate this, you can store the results from one run of indexamajig and re-run the process using the previous indexing results instead of repeating the PinkIndexer step.

First, create a solution file from the stream using the stream2sol.py program from the CrystFEL scripts folder:

stream2sol.py -i sample.stream -o sample.sol

Then, run indexamajig using --indexing=file and giving the filename:

indexamajig -g sample.geom -i input-files.lst -o output.stream \
            --indexing=file --fromfile-input-file=sample.sol \
            --no-refine --no-check-peaks --no-retry \
            --int-radius=10,12,14

Note the options --no-refine --no-check-peaks --no-retry are added to skip the checks and refinement stages normally performed after indexing - these are not necessary when replaying solutions like this.