FDTBX - Computational Tools for Simulation of X-ray Fiber Diffraction Patterns from Atomic Coordinates
Year: 2026
Type: preprint
Abstract: FDTBX - Computational Tools for Simulation of X-ray Fiber Diffraction Patterns from Atomic Coordinates. V2.1.0 - 24th of August 2026. ABOUT fdtbx is an open-source Python module for simulating X-ray fiber diffraction patterns from atomic coordinate models. Fiber diffraction underpins landmarkwork in structural biology, polymer science, and materials science — the DNA double helix, protein alpha-helices and beta-sheets, and fibrous materials such ascellulose, collagen, and synthetic polymers. Because these paracrystalline samples give broad, weak, and overlapping reflections, analysis relies onmodel-based refinement: simulating patterns from candidate models and comparing them with experiment. fdtbx provides that simulation engine, with anarchitecture built for readability, extensibility, and multicore computation. What it does Given an atomic model, fdtbx generates realistic fiber diffraction patterns in detector space while accounting for the disorder effects that dominate realspecimens. It is built on Fourier-transform diffraction theory. Structure factors are computed via cctbx, and every broadening or attenuation effect enters through the convolution theorem before the pattern is mapped from reciprocal to detector coordinates. Modeled effects include: - Finite crystallite size - order-independent peak broadening (~1/L).- Orientational disorder - crystallite misalignment smears reflections into arcs.- Paracrystalline disorder - Hosemann g-factor formalism, giving order-dependent broadening and intensity loss.- Thermal disorder - an independent Debye-Waller attenuation factor. Applications Structural biology (fibrous proteins, amyloids, supramolecular assemblies), polymer science, and nanotechnology - offered as an open, reproducible tool in afield where access to specialized software has often been limiting. Quick start (Jupyter) create venv and install in editable mode with dev extrasconda create -n fdtbx-devcanda activate fdtbx-devconda install mamba -c conda-forgemamba install -f environment.ymljupyter lab or if you want to install to an existing env: Edit environment.yml and add the name of your env under name name: fdtbx-dev Then run: mamba install -f environment.ymljupyter lab In a notebook cell (example in the notebooks folder) import fdtbxfdtbx.__version__ # LicenseMIT © 2026 Pawel Sikorski
Source: arXiv (Cornell University)
Author: Sikorski, Pawel
Institution: Norwegian University of Science and Technology
Language: English
Subfield: Structural Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204106929