add-elem-info

mlmm add-elem-info adds or repairs PDB element symbols (columns 77-78). It infers elements from fixed-column atom names and residue context, and replaces only the element field on ATOM/HETATM records. Use it before downstream tools when element columns are missing or unreliable; --overwrite also replaces existing element fields.

Examples

Command form:

mlmm add-elem-info -i INPUT [-o OUTPUT] [--inplace] [--overwrite]

Add or repair element columns into the non-destructive default output:

mlmm add-elem-info -i 1abc.pdb

This writes 1abc_add_elem.pdb. To replace the input explicitly:

mlmm add-elem-info -i 1abc.pdb --inplace

Write the result to a separate output file:

mlmm add-elem-info -i 1abc.pdb -o 1abc_fixed.pdb

Re-infer and overwrite existing element fields:

mlmm add-elem-info -i 1abc.pdb --overwrite

Workflow

  1. Read raw PDB records and classify atoms with the residue definitions used in extract.py (AMINO_ACIDS, WATER_RES, ION).

  2. For each atom, guess the element by combining the atom name, residue name, and whether the record is HETATM:

  • Ion residues: Prefers residue-derived elements; polyatomic ions (e.g., NH4, H3O+) are assigned per atom (H/N/O).

  • Proteins, nucleic acids, water: Maps H/D to H; water atoms to O/H; first-letter mapping for P/N/O/S; recognizes Se; carbon labels (CA/CB/CG/…) to C.

  • Ligands/cofactors: Uses atom-name prefixes (C*/P*, excluding CL) and two-letter/one-letter normalization; recognizes halogens (Cl/Br/I/F).

  1. Replace only columns 77–78 on ATOM/HETATM records and preserve all other columns and records:

  • No -o/--out given: writes <input>_add_elem.pdb.

  • --inplace without -o/--out: replaces the input file.

  • -o/--out given: writes to the specified path.

  1. Print a summary reporting total atoms, newly assigned, kept existing, overwritten (when --overwrite), per-element counts, and up to 50 unresolved atoms (model/chain/residue/atom/serial).

Outputs

  • PDB file with element columns (77-78) populated or corrected

  • Console report with totals for processed/assigned atoms, per-element counts, and up to 50 unresolved atoms

CLI options

Option

Description

Default

-i, --input PATH

Input PDB file.

Required

-o, --out PATH

Output PDB path; takes precedence over --inplace.

None → <input>_add_elem.pdb

--inplace/--no-inplace

Replace the input file when -o/--out is omitted.

False

--overwrite/--no-overwrite

Re-infer and overwrite element fields even if already present (by default, existing values are preserved).

False

Every input line is preserved byte-for-byte except columns 77–78 of ATOM/HETATM records selected for repair. HEADER, REMARK, CONECT, ANISOU, and legacy charge columns are retained.

The full flag list is in the generated command reference.

See Also