Protein Structure

Common Patterns

# Check which structure tools are really installed
command -v colabfold_batch pymol chimera chimerax foldseek mmseqs fpocket

# Use the local RFdiffusion repo for generative design
cd /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion
./test_rfdiffusion.sh

# Inspect the local Evo 2 repo for sequence-model-based analysis
cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2
python examples/run_evo2.py

Recommended Workflow

1. Verify the required predictor or viewer is actually present before promising a structure workflow.
2. If you need generative backbone or binder design, start from the local RFdiffusion repo.
3. If you need sequence-model scoring or embeddings on DNA-scale inputs, evaluate whether Evo 2 is the right supporting asset.
4. Install missing prediction/visualization tools explicitly before planning around ColabFold, PyMOL, or Chimera-based steps.

Guardrails

• colabfold_batch, pymol, chimera, chimerax, foldseek, mmseqs, and fpocket are not currently on PATH in this workspace.
• RFdiffusion is present locally, but its Docker image is not prebuilt yet.
• The local Evo 2 repo exists, but direct import evo2 currently fails because vortex is missing.
• Do not present RFdiffusion as a native fold-prediction replacement; it is primarily a generative structure-design workflow.