From 60a4fee9e1dd04558db01a90a7c0eaa43d110020 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 17 May 2021 14:14:06 +0200 Subject: Add 'article' about electron diffraction --- doc/articles/electrons.rst | 122 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 doc/articles/electrons.rst (limited to 'doc') diff --git a/doc/articles/electrons.rst b/doc/articles/electrons.rst new file mode 100644 index 00000000..c1a7ab2c --- /dev/null +++ b/doc/articles/electrons.rst @@ -0,0 +1,122 @@ +================================================== +Processing electron diffraction data with CrystFEL +================================================== + +Electron diffraction data is fully supported in recent versions of CrystFEL. +For some background, see this paper: + +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 `_ + +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 300 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 the number of available CPU +cores. It's also useful to try indexing each pattern only once (`--no-retry`). + +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`. 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. -- cgit v1.2.3