`define-layer`¶

Overview¶

Summary: Define a 3-layer ML/MM system based on distance from the ML region and encode the layer assignments as B-factors in the output PDB.

mlmm define-layer partitions an enzyme system into three layers around the ML region and writes the assignments as PDB B-factors. The ML region can be specified via a model PDB, explicit atom indices, or a combination of both.

3-Layer System¶

Layer	Name	B-factor	Description
1	ML	0.0	Atoms in the ML region
2	Movable-MM	10.0	MM atoms/residues within `--radius-freeze` of ML
3	Frozen	20.0	MM atoms/residues beyond `--radius-freeze`

Layer assignment strategy¶

Residues without ML atoms: the entire residue is assigned to a single layer based on the minimum distance from any ML atom to any atom in the residue.
Residues with ML atoms: non-ML atoms in the same residue are classified individually by distance.

Minimal example¶

mlmm define-layer -i system.pdb --model-pdb ml_region.pdb -o labeled.pdb

Output checklist¶

<output>.pdb – PDB with B-factors set to 0 / 10 / 20
Console summary table of layer assignments and atom counts

Common examples¶

Using explicit atom indices (0-based).

mlmm define-layer -i system.pdb --model-indices "0,1,2,3,4" --zero-based -o labeled.pdb

Custom movable/frozen cutoff.

mlmm define-layer -i system.pdb --model-pdb ml_region.pdb \
 --radius-freeze 10.0 -o labeled.pdb

Workflow¶

ML region identification – The ML region is defined by --model-pdb (atom matching against the input PDB) or --model-indices (explicit atom indices). If --model-indices is provided, it takes precedence over --model-pdb.
Distance computation – For each non-ML atom (or residue), the minimum distance from any ML atom is computed.
Layer assignment – Non-ML atoms/residues are assigned to Movable-MM or Frozen by --radius-freeze.
Output – The output PDB has B-factors set to layer values (0, 10, 20). A summary of layer assignments is printed to the console.

CLI options¶

Option	Description	Default
`-i, --input PATH`	Input PDB file containing the full system.	Required
`--model-pdb PATH`	PDB file defining atoms in the ML region.	None
`--model-indices TEXT`	Comma-separated atom indices for the ML region (e.g. `"0,1,2,3"` or `"1-10,15,20-25"`). Takes precedence over `--model-pdb`.	None
`--radius-partial-hessian FLOAT`	Deprecated in 3-layer mode (kept for compatibility).	`0.0`
`--radius-freeze FLOAT`	Distance cutoff (Å) from ML region for Movable-MM. Atoms beyond this are Frozen.	`8.0`
`-o, --output PATH`	Output PDB file with B-factors set to layer values.	`<input>_layered.pdb`
`--one-based / --zero-based`	Interpret `--model-indices` as 1-based or 0-based.	`True` (1-based)

define-layer¶