It would also be good to check the monomer library (expanded with any
user-supplied dictionaries). Cases where an element in columns 77-78 exists
and it does not agree with the component definition should probably be
flagged up.
Cheers,
Paul
On Wed, 15 May 2024 at 12:39, Marcin Wojdyr <woj...@gmail.com> wrote:
> >
> > > • 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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