BoltzMaker

New campaign wizard

Builds a boltz_input.md from plain fields — matches exactly what BoltzMaker.py new's terminal wizard asks for. Newer fields (Apo structure, Family type, Group, Role) aren't covered here yet — hand-edit the file afterward, or see the project's GitHub for the full grammar.

Settings

Predict binding affinity too (slower, adds Kd/pIC50 estimates)

The summary table ranks on pIC50; without this its ranking column is empty. Rank on pIC50 rather than binder probability, which has measured near-zero correlation with it.

Keep ligands on their own protein — a ligand with no pocket set still has to bind its receptor somewhere, rather than a co-folded partner

Off, ligands can dock onto a co-folded partner instead of your protein — in one campaign 6 of 27 did. It picks the protein, not the site. Not Boltz's force flag: every pocket constraint sets that anyway, and this decides whether a target with no pocket is restrained at all.

Pocket distance (Å)

How close the ligand must sit to the pocket residues. Tight matters: on one test the same residues at 8 Å left the ligand 9.5 Å from its crystal pose, and at 4 Å reproduced it to 2.6 Å. Set the holo reference per ligand below — a pocket belongs to the ligand, not the protein.

Targets per prediction process (optional)

Restarts boltz predict every N targets. On Apple unified memory the allocator never gives everything back, so a long campaign starves itself; only process exit frees it. 0 disables recycling.

BoltzMaker

New campaign wizard

Settings

Proteins (at least one required)

Partners (optional — co-folded chains the proteins above can reference)

Constraints (optional — reference a protein short name from above)

Ligands (at least one required)