Cppxfel Post-refinement

Post-refinement by cppxfel of integrated intensities occurs after initial orientation matrix refinement. This is the penultimate stage of producing a viable MTZ file for structure solution. This is also the point at which indexing ambiguities are broken (note that only two-fold indexing ambiguities can be broken at the moment without an external reference MTZ).

Contents of refine.txt

This stage is controlled by the input file refine.txt generated by cppxfel.input_gen and uses a number of files generated at the previous stage. The contents of this file:

cat refine.txt

ORIENTATION_MATRIX_LIST refine-orientations.dat
MATRIX_LIST_VERSION 2.0
NEW_MATRIX_LIST refined.dat

PARTIALITY_CUTOFF 0.2

COMMANDS

REFINE_PARTIALITY

Executing refine.txt

This can be executed using the line

cppxfel.run -i refine.txt

This begins by generating an initial, merged MTZ file using an initial guess at the parameters of the image. For space group I23, this requires the indexing ambiguity to be broken, which can be followed by the values of the fx: lines during L-BFGS refinement. The processing statistics for the first merge are then displayed.

This is followed by a number of rounds of post-refinement (approximately 6). The major processing statistics for each image can be followed as they are produced, followed by a large output of all the parameters used in refinement after each cycle. The processing statistics for each subsequent merge are then displayed until refinement ends.