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Usage

Command-Line Arguments

Structure Definition

  • --length <LENGTH>: Number of residues (Default: 10)
  • --sequence <SEQUENCE>: Specify sequence (e.g. "ACDEF")
  • --conformation <TYPE>: alpha, beta, ppii, extended, random
  • --structure <REGIONS>: Define mixed structure (e.g. 1-10:alpha,11-20:beta)

Physics & Refinement

  • --minimize: Run OpenMM energy minimization (Implicit Solvent)
  • --optimize: Run Monte Carlo side-chain packing
  • --refine-clashes <N>: Iteratively adjust atoms to reduce clashes

NMR Data Generation

  • --gen-nef: Generate NOE restraints (NEF format)
  • --gen-shifts: Predict chemical shifts (SPARTA-lite)
  • --gen-relax: Generate relaxation data (\(R_1, R_2, NOE\))

Examples

Basic Peptides

# Alpha helix
synth-pdb --length 20 --conformation alpha --output helix.pdb

# Beta sheet
synth-pdb --length 20 --conformation beta --output sheet.pdb

Complex Topologies

# Helix-Turn-Helix
synth-pdb --structure "1-10:alpha,11-15:random,16-25:alpha" --minimize