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Command-Line Reference

This guide provides a comprehensive reference for the synth-pdb command-line interface.

Basic Usage

The simplest way to use synth-pdb is to specify a sequence length:

python -m synth_pdb.main --length 20 --output my_protein.pdb

Or provide a specific amino acid sequence:

python -m synth_pdb.main --sequence "ALA-GLY-SER-THR-VAL" --output test.pdb

Core Options

Option Description Default
--length Length of the amino acid sequence (number of residues). 10
--sequence Specify an amino acid sequence (e.g., 'AGV' or 'ALA-GLY-VAL'). (Random)
--output Output PDB filename. (Generated)
--conformation Secondary structure conformation: alpha, beta, ppii, extended, random. alpha
--structure Per-region conformation specification (e.g., '1-10:alpha,11-14:typeII,15-20:beta'). -
--seed Random seed for reproducible generation. -

Validation & Refinement

Option Description
--validate Run validation checks (bond lengths, angles, Ramachandran).
--guarantee-valid Repeatedly generate until a valid structure is produced.
--max-attempts Maximum number of attempts for --guarantee-valid.
--best-of-N Generate N structures and select the one with the fewest violations.
--refine-clashes Number of iterations to minimally adjust clashing atoms.
--optimize Run Monte Carlo side-chain optimization.
--minimize Run physics-based energy minimization using OpenMM.

Scientific Features

NMR Observables

Option Description
--gen-shifts Generate synthetic Chemical Shift data (H, N, CA, CB, C).
--shift-predictor Predictor to use: shiftx2 (default) or empirical.
--gen-relax Generate synthetic NMR relaxation data (R1, R2, NOE).
--output-rdcs Generate backbone N-H Residual Dipolar Coupling (RDC) data.
--gen-couplings Generate synthetic 3J(HN-HA) scalar couplings.
--gen-nef Generate synthetic NMR data (NOE restraints) in NEF format.

MSA & Evolution

Option Description
--gen-msa Generate synthetic Multiple Sequence Alignment (MSA) via simulated evolution.
--msa-depth Number of sequences to generate for MSA (default: 100).
--evolution-temp Thermal Noise of MSA MCMC evolution (default: 1.5).

Physics & Chemistry

Option Description
--forcefield Forcefield for minimization (default: amber14-all.xml).
--solvent Solvent model: obc2, obc1, gbn, gbn2, hct, explicit.
--cap-termini Add N-terminal Acetyl (ACE) and C-terminal N-methylamide (NME) caps.
--ph pH for determining protonation states (default: 7.4).

Advanced Modes (--mode)

synth-pdb supports several specialized operation modes:

  • generate: (Default) Generate a single structure.
  • decoys: Generate an ensemble of structures (decoys).
  • docking: Prepare structures for docking (PQR format).
  • pymol: Generate PyMOL scripts for visualization.
  • dataset: Bulk generation for machine learning datasets.
  • ai: Structure interpolation and clustering.

Visualization

Use the --visualize flag to open the generated structure in a browser-based 3D viewer (powered by 3Dmol.js).

python -m synth_pdb.main --sequence "MEELQK" --visualize