Our Introduction to PDB Format page covers many of the common errors. It kind of focuses on errors from hand editing of files. For PDB files generated by programs, I find that the most common errors are misaligned atom names (already covered in that page), "stale" CONECT records passed through from the input file to the output file and that no longer correspond to the atom records, and which therefore produce many incorrect bonds, and finally omission of the alternate location indicator in column 17 of the ATOM/HETATM records, resulting in duplicate atoms in the residue.

On May 15, 2026, at 7:17 AM, Steven Brawer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I will be using ChimeraX much more extensively this fall, and I think the answer to the question below might be useful (and not just for me).

Does there exist some list (or lists) of common pdb file errors? One probably can't cover all possibilities, but perhaps there are some common ones that one could find automatically by writing a python program to examine the file. (Perhaps some programs already exist.) Recently there was a case of misplaced spaces and also of duplicated lines. Presumably one could (perhaps) add a search for the correct number of atoms in each residue. What about the existence/presence of water or heavy ions? Perhaps searching for unexpected atom-atom-atom angles or bond lengths (or even separations)?

Perhaps an AI agent might be trained?

Thanks

Steve Brawer
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