Discovering internal dynamics of proteins by fitting against their diffuse scattering intensities. The package is used in the following preprint:

P Mazumder, K Ayyer, "Understanding conformational dynamics from macromolecular crystal diffuse scattering", bioRxiv 2021.02.11.429988

This is a pure-python package using CuPy for GPU computation. Create a conda environment or virtualenv and install Cupy using the documentation given here (you shouldn't need to compile it by installing using pip). Diffuser itself is installed using the command in the root directory of the repository:

$ pip install -e .

This will add the scripts described in the next section to your path in the environment.

Go to the examples/ folder for a basic tutorial.

All scripts take their parameters from a config file.

• diffuser.rbdiff - Rigid body diffuse scattering calculated from an electron density map and from disorder parameters
• diffuser.traj_diff - Diffuse scattering from an MD trajectory
• diffuser.process_md - Process MD trajectory to get pcincipal-component modes and average structure
• diffuser.pcdiff - Diffuse scattering by distorting the molecule along principal-component modes
• diffuser.bgo_optimize - Bayesian optimization by tuning the weights in pcdiff to fit against a target intensity distribution