>
> > • Alignment of one-letter atom name such as C starts at column 14, while
> > two-letter atom name such as FE starts at column 13.
>
> indicating a rule does exist.
There are programs that don't read/write the element from columns
77-78, so this rule still matters, but using it is less reliable, as
Robbie wrote. After I wrote a function that reads pdb files for gemmi,
over the next few years I received feedback about cases in which the
element columns are absent and the element determined from the atom
name is incorrect. The problem is primarily with 4-character atom
names that can't be aligned, because they use all the four columns
anyway. I added such comments to the code [1] when trying to get it
right:
// Atom names HXXX are ambiguous, but Hg, He, Hf, Ho and Hs (almost)
// never have 4-character names, so H is assumed.
// Similarly Deuterium (DXXX), but here alternatives are Dy, Db and Ds.
// Only Dysprosium is present in the PDB - in a single entry as of 2022.
// Old versions of the PDB format had hydrogen names such as "1HB ".
// Some MD files use similar names for other elements ("1C4A" -> C).
// ... or it can be "C210"
[1]
https://github.com/project-gemmi/gemmi/blob/148f37b7c6561c55553a255a6a4dd75d6bae888e/include/gemmi/pdb.hpp#L302
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