TL;DR
Side-by-side or overlay comparison for completed structures and Interface jobs.
Use it / Skip it
Scores alone are not enough; Compare helps inspect whether two candidates bind the same patch, clash differently, or preserve an expected pose.
Use when
You need head-to-head visual review between candidate structures, competitor complexes, or Interface jobs.
Don't use for
Do not use it before structures exist. Generate them through Interface or Fold first.
Inputs
- Structures
- PDB uploads or completed Interface jobs depending on the compare mode.
- Reference
- For overlay mode, the first selected job is the reference antigen.
Outputs
- Visual comparison
- Dual viewer or overlay scene.
- Metric context
- ipTM, contacts, epitope/paratope counts where available.
Walkthrough
1. Choose completed jobs or upload structures
Choose completed jobs or upload structures.
2. For overlay, select a reference first
For overlay, select a reference first.
3. Load comparison and inspect pose, epitope overlap, and contact differences
Load comparison and inspect pose, epitope overlap, and contact differences.
4. Return to Interface job detail for exact exports
Return to Interface job detail for exact exports.
Under the hood
- Overlay mode loads completed Interface jobs and their PDB artifacts.
- Alignment uses antigen atoms and reports alignment failures when geometry is insufficient.
Worked example
Pitfalls
- Overlay requires enough antigen atoms to align.
- A similar pose does not guarantee identical specificity.
- Failed or running jobs cannot be compared structurally.