Citing Reciprocal Space Station packages

If you’re making use of any RSS packages, amazing! Please cite them as follows:

ABISMAL

Abismal: Approximate Bayesian Inference for Scaling and Merging at Advanced Lightsources. Doris Mai, Doeke R Hekstra, Frédéric Poitevin, Kevin M Dalton. Structural Dynamics, 2025

Careless

Sensitive detection of structural dynamics using a statistical framework for comparative crystallography. Doeke R. Hekstra, Harrison K. Wang, Margaret A. Klureza, Jack B. Greisman, Kevin M. Dalton. Science Advances, 2025

A unifying Bayesian framework for merging X-ray diffraction data. Kevin M. Dalton, Jack B. Greisman, Doeke R. Hekstra. Nature Communications, 2022

Please cite both papers when using careless with the Double Wilson prior.

EmbedOpt

Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization. Minhuan Li, Jiequn Han, Pilar Cossio, Luhuan Wu. arXiv (preprint), 2026

Laue-DIALS

Laue-DIALS: open-source software for polychromatic X-ray diffraction data. Rick A. Hewitt, Kevin M. Dalton, Derek A. Mendez, Harrison K. Wang, Margaret A. Klureza, Dennis E. Brookner, Jack B. Greisman, David McDonagh, Vukica Šrajer, Nicholas K. Sauter, Aaron S. Brewster, Doeke R. Hekstra. Structural Dynamics, 2024

MatchMaps

MatchMaps: non-isomorphous difference maps for X-ray crystallography. Dennis E. Brookner and Doeke R. Hekstra. Journal of Applied Crystallography, 2024

METEOR

Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals. Alisia Fadini, Virginia Apostolopoulou, Thomas J. Lane, Jasper J. van Thor. Communications Biology, 2025

reciprocalspaceship

reciprocalspaceship: a Python library for crystallographic data analysis. Jack B. Greisman, Kevin M. Dalton, Doeke R. Hekstra. Journal of Applied Crystallography, 2021

ROCKET

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network. Alisia Fadini, Minhuan Li, Airlie J. McCoy, Suresh Banjara, Hiroki Okumura, Eve Napier, Pietro Fontana, Amir R. Khan, Luca Jovine, Thomas C. Terwilliger, Randy J. Read, Doeke R. Hekstra & Mohammed AlQuraishi. Nature Methods, 2026

SFCalculator

SFCalculator: connecting deep generative models and crystallography. Minhuan Li, Kevin M. Dalton, Doeke R. Hekstra. bioRxiv (preprint), 2025

VALDO

Improving Signal-to-Noise Ratio of Drug Fragment Screening with Variational Autoencoder. Phyllis Zhang, Minhuan Li, Daniel Keedy, Tamar Skaist Mehlman, Doeke Hekstra. Structural Dynamics (meeting abstract), 2025

RSS in other publications

The following publications explore, expand upon, or apply RSS packages. If there’s a paper we’re missing, or you’ve recently published a paper using an RSS package, please let us know!

• TorchRef: An open-source PyTorch Framework for Crystallographic Refinement. Hans-Peter Seidel, Jörg Standfuss, Tobias Weinert. bioRxiv (preprint), 2026

• CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography. Minseo Kim, Huanghao Mai, Jay Shenoy, Alec Follmer, Gordon Wetzstein, Frédéric Poitevin. arXiv (preprint), 2026

• Inferring structure factors of weakly populated excited states in perturbative crystallography experiments. Andrew K. Choe, Harrison K. Wang, Doeke R. Hekstra. bioRxiv (preprint), 2026

• Assessing the applicability of Bayesian inference for merging small molecule microED data. Huanghao Mai, Ariana Peck, Kevin M. Dalton, Lygia Silva de Moraes, Jessica E. Burch, Frédéric Poitevin, Hosea M. Nelson. chemRxiv (preprint), 2024

• Resolving DJ-1 glyoxalase catalysis using mix-and-inject serial crystallography at a synchrotron. Kara A. Zielinski and Cole Dolamore, Kevin M. Dalton, Nathan Smith, John Termini, Robert Henning, Vukica Srajer, Doeke R. Hekstra, Lois Pollack, Mark A. Wilson. bioRxiv (preprint), 2024

• Scaling and merging time-resolved pink-beam diffraction with variational inference. Kara A. Zielinski, Cole Dolamore, Harrison K. Wang, Robert W. Henning, Mark A. Wilson, Lois Pollack, Vukica Srajer, Doeke R. Hekstra, Kevin M. Dalton. Structural Dynamics, 2024

• Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism. Jack B. Greisman, Kevin M. Dalton, Dennis E. Brookner, Margaret A. Klureza, Candice J. Sheehan, In-Sik Kim, Robert W. Henning, Silvia Russi, Doeke R. Hekstra. PNAS, 2024

• Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Doeke R. Hekstra. Annu. Rev. Biophys., 2023

• Correcting systematic errors in diffraction data with modern scaling algorithms. Luis A. Aldama and Kevin M. Dalton, Doeke R. Hekstra. Acta Crystallographica D, 2023

• Online Inference of Structure Factor Amplitudes for Serial X-ray Crystallography. Kevin M. Dalton and Doeke R. Hekstra. Machine Learning for Structural Biology Workshop, NeurIPS 2022

• Native SAD phasing at room temperature. Jack B. Greisman, Kevin M. Dalton, Candice J. Sheehan, Margaret A. Klureza, Igor Kurinov, Doeke R. Hekstra. Acta Crystallographica D, 2022

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