#!/bin/bash
# Reconstruction script for the 70S ribosome example.

# Initial stage.
gmm-rec.py ribosome_input.mrc -v -o coarse.mrc -s 5000 100 100 -g -r 10000 -d 32 -N 2000 -K 200 -a 2.82 -A 2 -p 8

gmm-plot-stack.py -i coarse_input.mrc coarse_initial_projections.mrc coarse_final_projections.mrc -r 4 -c 6
gmm-plot-stats.py -i coarse_*_stats.csv -o coarse

# Refinement stage.
gmm-rec.py ribosome_input.mrc -v -o refine.mrc -s 1000 -K 500 -t coarse_transformations.csv -d 64 -N 10000 -a 2.82 -A 2

gmm-plot-stack.py -i refine_input.mrc refine_initial_projections.mrc refine_final_projections.mrc -r 4 -c 6
gmm-plot-stats.py -i refine_stats.csv -o refine
