Non-Canonical Amino Acid Residue Mapping
May 27, 2026 ยท View on GitHub
PDB structures often contain modified amino acid residues (e.g., selenomethionine MSE,
phosphoserine SEP). P2Rank maps these to standard amino acids for feature calculation.
The -aa_mapping parameter controls which mappings are used.
Modes
| Mode | Description | Mappings |
|---|---|---|
minimal | Default, backward-compatible (MSE->MET, MEN->ASN only) | 2 |
pdbfixer | Extended set from pdbfixer (source code) | 87 |
/path/to/file.csv | Custom user-provided mapping file | User-defined |
Residue codes not in the active mapping pass through unchanged.
minimal preserves original P2Rank behavior.
pdbfixer covers comprehensive set of phosphorylated, methylated, and acetylated residues, selenocysteine,
histidine protonation variants, D-amino acids, and other modifications.
Derived from pdbfixer (commit 94cfa4c, extracted February 2026), with minor modifications
(see src/main/resources/mappings/README.md for details).
Usage
# Default (minimal)
prank predict -f protein.pdb
# Extended pdbfixer mappings
prank predict -f protein.pdb -aa_mapping pdbfixer
# Custom mapping file
prank predict -f protein.pdb -aa_mapping /path/to/my-mappings.csv
Custom Mapping Files
Any value other than minimal or pdbfixer is treated as a file path.
Important
A custom file replaces all built-in mappings (it does not extend them).
To add entries on top of the pdbfixer set, copy the bundled aa-mapping-pdbfixer.csv
and append your entries.
Format - two-column CSV:
# Custom mappings
MSE,MET
LLP,LYS
SEC,CYS
Format notes:
- Lines starting with
#and empty lines are ignored - Codes are case-insensitive
- Whitespace around codes and commas is trimmed
- Duplicate source codes: warned, first mapping wins
- File not found or not readable: P2Rank exits with an error