Dragonfly is a software package to analyze single particle diffractive imaging data. The package has the following parts:
- An implementation of the EMC single-particle reconstruction algorithm using MPI and OpenMP to merge diffraction patterns of approximately identical particles in random orientations.
- Data stream simulator, that generates noisy single-particle diffraction patterns from a PDB file.
pip install dragonfly-spi
Initialize a reconstruction directory with default configuration files:
dragonfly.init
cd recon_0001
Edit config.ini to set your PDB file, detector geometry and other parameters, then generate simulated data:
dragonfly.utils.sim_setup
Run the EMC reconstruction (here with 4 OpenMP threads for 10 iterations):
dragonfly.emc -t 4 10
Monitor progress with the plotting GUI:
dragonfly.autoplot
More detailed documentation can be found in the online docs.
Please cite the following publication if you use Dragonfly for your work:
Ayyer, K., Lan, T. Y., Elser, V., & Loh, N. D. (2016). Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imaging. Journal of applied crystallography, 49(4), 1320-1335.