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Welcome to the EMC-for-SMX wiki!

Here we will demonstrate the step-by-step analysis using diffraction patterns of hen egg white lysozyme microcrystals collected at the Advanced Photon Source. The dataset is graciously provided by the authors of Martin-Garcia et al. (2017).

The analysis consists of four main steps:

1. Initialization
2. Data reduction
3. EMC reconstruction
4. Resolution estimation

For the test dataset, the data reduction step can be skipped for those who would like to try an EMC reconstruction immediately. This can be done by downloading the reduced data provided by us, which is described in Skipping data reduction

The workflow of the analysis is shown below:

The files and modules relevant to the analysis include:

1. config.ini: configuration file that records the reconstruction parameters.
2. init-recon.py: python script that initializes the reconstruction.
3. aux: directory that stores auxiliary files.
4. make-detector: maps detector pixels to reciprocal space.
5. make-background: generates pixel-wise background estimates and identifies Bragg peak candidates.
6. make-powder: generates pseudo-powder patterns.
7. make-quaternion: generates rotation samples.
8. orient-peak: finds probable orientations for each data frame.
9. reduce-data: converts data to the format used by the EMC algorithm.
10. make-Ematrix: creates mapping between Bragg peaks and detector pixels at different orientations.
11. low-res-emc: low-resolution reconstruction using the standard EMC algorithm.
12. rej-frames: rejects frames with no or multiple crystals.
13. setup-local: creates the necessary files for the high-resolution reconstruction.
14. local-update: high-resolution reconstruction using the local update scheme of the EMC algorithm.
15. cal-CC: splits data into two halves to implement two independent reconstructions to calculate the correlation coefficient, CC*.