Contig
(Can only pass a contig string.) Indexed motif specification, e.g., "A1-80,10,/0,B5-12". Residues whose position/order in the final sequence is specified.
Unindex
(Can only pass a contig string or dictionary.) Unindexed motif components, the specified residues can be anywhere in the final sequence. See Unindexing Specifics for more information. Which residues should have their index be inferred by the model instead of prespecified
Length
Total design length constraint; "min-max" or int for specified length.
Ligand
Ligand(s) by chemical component name (from RSCB PDB) or index. These are ligands built in to the source mmCIF file, using the identifiers specified there
CIF parser args
Optional args to CIF loader. See CIF parser options for more information.
In this form: Enter a JSON object. The local cache_dir option is not available, and extra_fields is accepted only alongside an mmCIF structure because the PDB reader ignores it.
Extra
Extra metadata (e.g., logs). Current options include sampled_contig.
Dialect
2 — current
1 — legacy
2=new (default), 1=legacy, Learn more about the legacy parsing system by looking at input_parsing.py.
Select fixed atoms
Atoms with fixed coordinates. See the Select Fixed Atoms subsection for more information. Dictionary that indicated which atoms should be fixed (can use ALL, BKBN, or TIP for all atoms in the residue, backbone atoms only and tip atoms only
In this form: Name a ligand by its chemical component code, such as NAI, rather than by chain and residue number. A ligand written into a chain that also holds polymer residues is moved onto a chain of its own while the structure is parsed, so a chain-and-number reference to it no longer matches.
Select unfixed sequence
Where sequence can change. Default is True - all input regions have fixed sequences. Contig string input specifies components to unfix the sequence for. Dictionary inputs are allowed but not recommended.
Select buried
Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.
Select partially buried
Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.
Select exposed
Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.
Select hbond donor
Atom-wise donor/acceptor flags. Atom-wise selection of hydrogen bond donors and acceptors, respectively. Only dictionary inputs allowed. See RFdiffusion3 — Nucleic acid binder design examples for an example.
Select hbond acceptor
Atom-wise donor/acceptor flags. Atom-wise selection of hydrogen bond donors and acceptors, respectively. Only dictionary inputs allowed. See RFdiffusion3 — Nucleic acid binder design examples for an example.
Select hotspots
Atom-level or residue-level hotspots. Hotspots will typically be at most 4.5 Å to any heavy atom in the designed structure. Typically used for designing binders.
Redesign motif sidechains
Fixed backbone, redesigned sidechains for motifs (input structures).
Symmetry
See Overview of Symmetry in RFD3.
In this form: Enter SymmetryConfig as JSON, for example {"id": "C3", "is_symmetric_motif": true}.
Ori token
[x,y,z] origin override to control COM (center of mass) placement of designed structure.
Infer ori strategy
Model default
com
hotspots
"com" or "hotspots". The center of mass of the diffused region will typically be within 5Å of the ORI token. Using hotspots will place the ORI token 10Å outward from the center of mass of the specified hotspots. Using com will place the token at the center of mass of the input structure.
pLDDT enhanced
Default True. Enables pLDDT (predicted Local Distance Difference Test) enhancement.
Is non loopy
Model default
True — fewer loops
False — more loops
Default None. If True/False, produces output structures with fewer/more loops.
Partial t (angstroms)
Noise (Å) for partial diffusion, enables partial diffusion (sets the noise level.) Recommended values are 5.0-15.0 Å. See Partial Diffusion for more information.
Allow ligand on existing chain
Allow the shared ligand chains used by some official input structures. This is enabled in presets that require it.
In this form: Accepting such a structure logs a warning that the shared chain is being separated, which is expected. The ligands end up on a chain of their own, so select them by chemical component code.