Usage Guide

Installation

pip install .

Basic Usage

To generate a simple density map from a PDB file:

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

Simulating Realistic Physics

To add CTF effects and noise:

synth-cryo-em structure.pdb output.mrc \
  --resolution 3.5 \
  --apply-physics \
  --defocus 2.0 \
  --bfactor 150 \
  --snr 5

Options

Option	Description	Default
--resolution / -r	Target resolution in Angstroms	4.0
--spacing / -s	Grid spacing (pixel size) in Angstroms	resolution / 3
--snr	Signal-to-Noise Ratio for Gaussian noise	None
--defocus	Defocus in micrometers	2.0
--voltage	Acceleration voltage in kV	300.0
--cs	Spherical aberration in mm	2.7
--bfactor	Envelope function B-factor	0.0
--apply-physics	Enable CTF effects	False

Map Validation

The package also includes synth-cryo-em-validate, a tool to compare two Cryo-EM maps and compute their Cross-Correlation Coefficient (CCC) and Fourier Shell Correlation (FSC) curves.

synth-cryo-em-validate map1.mrc map2.mrc --output fsc_results.csv

Validation Options

Option	Description	Default
--output / -o	Path to save FSC data (CSV)	None