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diff --git a/doc/articles/electrons.rst b/doc/articles/electrons.rst index 00d326a8..e04b0905 100644 --- a/doc/articles/electrons.rst +++ b/doc/articles/electrons.rst @@ -3,11 +3,15 @@ Processing electron diffraction data with CrystFEL ================================================== Electron diffraction data is fully supported in recent versions of CrystFEL. -For some background, see this paper: +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 <https://doi.org/10.1038/s41467-020-14793-0>`_ +* 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 <https://doi.org/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. @@ -17,7 +21,7 @@ Setting the wavelength You can set the accelerating voltage in the geometry file:: - electron_voltage 300 kV + electron_voltage 200 kV This should be the accelerating voltage, not the relativistically-corrected energy of the accelerated electrons (the difference is small). Alternatively, @@ -53,8 +57,8 @@ Note that the coordinates are shifts of the *detector* (not the *beam*) in the 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:: +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 @@ -84,18 +88,20 @@ 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``). +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``). 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. +``--wavelength-estimate``. However, neither of these are usually necessary for +electron diffraction data. Saving and re-loading indexing results |