add-elem-info (repair PDB element columns)

add-elem-info fills in or corrects the element symbols (columns 77–78) of the ATOM and HETATM records in a PDB file.

What it is for

  • PDB files without element columns: structures from modeling tools or molecular dynamics (MD) that leave columns 77–78 blank.

  • Wrong element symbols: re-infer every column with --overwrite-elem.

  • Preparing input for other commands: run add-elem-info before a standalone command such as extract.

Examples

1. Write <input>_add_elem.pdb

Fill the element columns and write the result next to the input.

pdb2reaction add-elem-info -i 1abc.pdb

The console prints [OK] Wrote: 1abc_add_elem.pdb and the counts total atoms, assigned/updated, and kept existing. With no [WARN] line, every atom has an element.

2. Choose the output file

pdb2reaction add-elem-info -i 1abc.pdb -o 1abc_fixed.pdb

3. Overwrite the input

Replace the input file itself.

pdb2reaction add-elem-info -i 1abc.pdb --overwrite

How it works

  1. Reading the records: add-elem-info reads every line, follows MODEL blocks, and looks only at ATOM and HETATM records.

  2. Keeping valid symbols: An element field that already holds a valid symbol (or EP for a water virtual site) is kept. Blank or unrecognized fields are repaired; --overwrite-elem re-infers every field.

  3. Inferring the element: The element comes from the four-character atom name (columns 13–16) and the residue name. Ion residues give the element of the ion; amino acids, nucleic acids, and water follow the usual naming. Other ligands use the column where the atom name starts: NA from column 14 is N, and from column 13 is Na. This also covers LEaP halogens such as CL1 from column 14 and hydrogen names such as HG11.

  4. Writing and the summary: Only columns 77–78 of the repaired records change, and the console prints a summary.

Output files

  • The repaired PDB: <input>_add_elem.pdb by default, the path given with -o, or the input file itself with --overwrite and no -o.

  • Console summary: total atoms, assigned/updated (atoms whose element column changed), kept existing, and assignment breakdown (counts per element). Atoms that could not be assigned are left unchanged and listed after [WARN] Could not confidently assign N atoms; left unchanged., up to 50 of them. Type the element symbol of each listed atom into columns 77–78 by hand, right-aligned; --overwrite-elem uses the same rules and will not assign them.

Main options

Option

Type

Default

Description

-i, --input

path

(required)

Input PDB file

-o, --output

path

None

Output PDB file; without it, <input>_add_elem.pdb

--overwrite/--no-overwrite

flag

False

Overwrite the input file when -o is not given

--overwrite-elem/--no-overwrite-elem

flag

False

Re-infer element columns that already hold a valid symbol

See the generated CLI reference for every option.

Notes

  • What changes: only columns 77–78 of the ATOM and HETATM records being repaired. Every other line, including HEADER, REMARK, CONECT, ANISOU, and the charge columns (79–80), is written unchanged.

  • Special names: deuterium labels become H, selenium (SE*) is recognized as Se, and halogens are recognized automatically.

  • Two different flags: --overwrite-elem decides which element columns are re-inferred; --overwrite decides only where the file is written.

  • Writing to the input path: when -o names the input file, including through a symbolic link, --overwrite is required; without it the run stops with an error.

  • Exit codes: see Exit codes.

See also

  • extract — extract the active-site model from the repaired PDB

  • all — the full workflow, which repairs blank element fields on its own

  • Troubleshooting — what to do when a run fails