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 |