synth-xtal is a lightweight Python library for simulating X-ray Crystallography diffraction data (structure factors and MTZ files) from input atomic models (PDB/mmCIF files).
Extracted from the synth-pdb ecosystem, it provides a physically grounded, education-focused engine for reciprocal space simulation.
-
Virtual Crystallography: Generate ideal
$F_{calc}$ and$\phi_{calc}$ structure factors from structural models. -
Automated Cell Generation: Transparently computes optimal bounding unit cells in
$P 1$ for standalone peptides/proteins lacking periodic symmetry constraints.
- Standard Integrations: Built directly on top of
gemmiandreciprocalspaceshipfor native FFT acceleration and robust MTZ writing. - Multi-Model Support: Seamlessly handles NMR ensembles or MD trajectories by accurately averaging grid densities to simulate alternative conformations.
- Educational Clarity: Simple, well-commented implementation of crystallographic density mapping — easy to audit and extend.
- Diffraction Simulation: Direct generation of complex structure factors from atomic coordinates using
gemmi.DensityCalculatorX. - Ensemble Averaging: Calculates coherent scattering intensities over an ensemble of structural models.
- Pythonic Data Structures: Outputs are formatted to
reciprocalspaceship.DataSetobjects for seamless downstream integration with standard ML/data-science tools (Pandas).
# Basic installation
pip install synth-xtal
# Installation for contributors/developers
pip install "synth-xtal[dev,test,docs]"synth-xtal provides a simple CLI for rapid simulation:
# Basic simulation (outputs to MTZ format)
synth-xtal input.pdb -o simulated.mtz
# Simulation at a specific high-resolution limit (e.g., 1.5 Å)
synth-xtal input.pdb -o simulated.mtz --resolution 1.5
# Simulation with a custom padding margin for automatically generated unit cells
synth-xtal input.pdb -o simulated.mtz --margin 15.0input: Path to PDB or mmCIF file.-o,--output: Save structure factor data to an.mtzfile (Required).-d,--resolution: High resolution limit in Ångströms (default: 2.0).--margin: Margin in Ångströms for the unit cell bounding box if the input lacks a defined unit cell (default: 10.0).
from synth_xtal.simulator import simulate_diffraction
# Calculate MTZ from a PDB or mmCIF file
simulate_diffraction(
input_pdb="protein.cif",
output_mtz="simulated_data.mtz",
d_min=2.0
)Try out synth-xtal interactively in Google Colab:
- 01. Crystallography Basics:
- 02. Experimental Validation (4LZT):
- 03. Virtual Crystallography Lab:
synth-xtal was heavily inspired by the educational goals of the larger synth-pdb ecosystem and relies critically on:
- gemmi - for core density calculations and FFT operations.
- reciprocalspaceship - for MTZ manipulation and Pandas integration.