Hekstra Lab

mdtools

Tools for running MD simulations in OpenMM

colav

Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).

SFcalculator

laue-index-assigner

A robust algorithm for assigning miller indices to Laue data from approximate indexing solutions.

microutil

Python utils for working microscopy datasets

napari-labeller

EF-X-crystal-MD

Setup and analysis of MD simulations mimicking the application of an external electric field to a protein crystal.

raman-analysis

Spontaneous Raman analysis library

SFcalculator_torch

Differentiable pipeline connecting protein atomic models and crystallography structure factors

Devices_Optics

Code to collect and analyze data using the spectroscopic setup & data collected

disco

Generate feasible Laue Bragg spots from randomly oriented crystals

marccd

Read, write, and manipulate diffraction images that use the MarCCD format

SFcalculator_jax

cog

Wrapper for Precognition to simplify Laue data reduction

dw

jupyter notebooks exploring the double-Wilson model

dw-examples

Examples of merging crystallographic intensities with a bivariate prior

envs

conda environment repository

fasrc-ood-jupyter

OnDemand app for serving Jupyter notebooks out of your local path

fast-overlap

meep meep

hadamuxer

Demultiplex Hadamard-encoded diffraction images.

hekstra-lab.github.io

Essentially a custom 404 in case anyone tries this URL

landfill

Machine learning tools to estimate spatiotemporally resolved background intentensities

regroup

Determine new space groups for analyzing pump-probe crystallography experiments

room-of-requirement

Useful Lab Utilities

russell-thesis

Jupyter notebooks that were used for data analysis and figure making for John Russell's Ph.D. Thesis.

scramble

A tool for disambiguating serial laue data

SFcalculator_tf

spectra-baseline

Fast implementations of baseline subtraction for raman spectra

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

yeast-mrcnn

Another implementation of mask-rcnn for detecting budding yeast cells in microscopy images