relax is not a score. It moves nearby backbone while holding the theozyme still, then the real objectives run on that structure.
Flexibile backbone design can be added to the design process to allow for more natural design of the active site. This is optional and can be added to the design process at two points:
| when | what it does | how you opt in |
|---|---|---|
| Placement | Small nudge of host loops so other catalytic CBs can land | on by default (--sat-mode shift); --no-accommodate to skip |
| Evolution | Relax after each mutate, before the other models score | put relax in --models |
If you use it during evolution, keep it second (right after
seq_model). Model order is load-bearing: later scores must see the
relaxed PDB.
The theozyme residues stay fixed. emit_objective: false in the config
means relax does not appear on the Pareto front or get factored into the fitness scoring.
Generic:
python run.py -c configs/your_run.yml \
--models seq_model relax <your other scores>Leave relax out of --models for a fixed backbone. Which method moves the backbone is a config detail (models.relax.backend); you do not pick it on the command line.
| file | role |
|---|---|
models/relax.py |
evolution-time relax (not a score) |
theozyme/prepare_placements.py |
placement-time loop nudge |