- Effective automation of the procedures described in Kingston and Millane (2022), IUCrJ, 9, 648-665.
- Envelope and phase determination steps are parallelized.
Major changes
- Envelope comparison and clustering now allows for inversion symmetry.
- The way the apodization function is specified has changed.
- Checks on the magnitude of missing terms are now based entirely on the Wilson model.
- Agreement of the data with the Wilson model is reported.
- New procedures introduced for controlling the amplitudes of missing data during Fourier space projection onto the constraints
- A much more flexible method of defining the update rules and constraints was introduced.
- During DBSCAN clustering of envelopes, "k-distances" are now evaluated. Optionally use the k-distance distribution to set threshold value ε.
- Internal handling of Fourier data was reworked. Fourier coefficients beyond the current "effective resolution limit" are now removed, speeding up the calculations with heavily apodized data.
- Ouput from analysis of overall scale and B-factor (method of Rogers) is now reported in the summary log file for the job.
- Parameterization of the envelope determination step has changed, significantly improving algorithm performance for some test cases.
Major changes
- Code restructuring to allow user to define the major steps to be perfomed and how the inputs and outputs of those steps are handled.
- Updated parameter file syntax, allowing better control of what happens at each iteration.
- Better procedures for detection and removal of outliers in the input diffraction data.
- Addition of RRR and RAAR algorithms and their reversed variants.
- Implementation of procedures to add error to an existing phase set using appropriate circular probability distributions.
- Changes to the way the apodzation function is applied.
- Better procedures for handling random number generation, facilitating algorithm comparisons.
- Algorithms optimized to increase speed of execution.
- Added ability to average phases over the algorithm trajectory, following convergence to the solution, and to calculate the phase retrival transfer function.