synth-cryo-em 0.1.0

Synthetic Cryo-EM map generator from PDB models

synth-cryo-em

A lightweight Pythonic utility to convert atomic models (PDB/CIF) into synthetic 3D Cryo-EM maps with realistic noise, CTF effects, and varying resolutions.

🌟 Features

• Voxelize atomic models with accurate resolution simulation.
• Simulate Physics: Apply Contrast Transfer Functions (CTF) and envelope functions.
• Noise Modeling: Add adjustable Gaussian noise to simulate low-SNR experimental data.
• Standard Format: Export results to MRC files compatible with RELION, ChimeraX, and other tools.

🚀 Quick Start

Installation

pip install synth-cryo-em

Basic Generation

synth-cryo-em structure.pdb output.mrc --resolution 4.0

Realistic Simulation

synth-cryo-em structure.pdb output.mrc --resolution 3.5 --apply-physics --snr 5

📚 Documentation

For detailed guides and API reference, visit the Documentation Site.

🛠️ Development

To install for development and documentation:

pip install -e ".[test,docs]"

Run tests:

pytest tests/

Build docs locally:

mkdocs serve