Skip to content

Rosetta Fast Relax

Runs ProteinMPNN-FastRelax cycles on sequences and structures to make proteins more stable and realistic.

Quick Start

  1. Prepare your input FASTA and PDB files with matching IDs.
  2. Set the desired number of relax cycles.
  3. Run the node to obtain relaxed protein structures.

Setup Guide

1. Prepare Input Data

  1. Ensure your FASTA contains sequence records with IDs matching the PDB structure IDs.
  2. Ensure your PDB input contains structures with IDs matching the FASTA records.

2. Configure Node Parameters

  1. Set the number of relax cycles (relax_cycles).
  2. Choose whether to enable debug mode (debug).

Basic Usage

Relaxing Protein Structures

  • Use to improve stability and realism of predicted protein structures.
  • Batch process multiple sequence-structure pairs by matching IDs.
  • Useful after structure prediction or design steps.

Configuration

Required Inputs

Field Description Type Example
fasta Sequences to run through the model. IDs must match structure IDs. FASTA ">design_1\nMKT..."
pdb Structures to run through the model. IDs must match sequence IDs. PDB "{design_1: ...}"
relax_cycles Number of relax cycles to perform on each structure. INT 3
debug If true, errors will crash the script; if false, will skip failed poses. BOOLEAN true

Optional Inputs

None

Outputs

Field Description Type Example
structure.pdb Relaxed structures. PDB "{design_1: ...}"

Best Practices

Input Preparation

  • Ensure FASTA and PDB IDs match exactly for correct pairing.
  • Use validated, high-quality input structures for best results.

Parameter Tuning

  • Start with a low number of relax cycles for speed; increase for higher accuracy.
  • Enable debug mode during development to catch errors early.

Troubleshooting

Common Issues

  • Mismatched IDs: Ensure FASTA and PDB record IDs correspond exactly.
  • Node crashes on error: Set debug to false to skip failed poses instead of crashing.

Need Help?