dragonfly-spi 0.1.0

Suite of XFEL single particle imaging tools

Dragonfly

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.

Installation

pip install dragonfly-spi

Quick Start

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.

Citation

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.