Hi
This is very, very useful and hits on the four-letter name problem that I am
encountering - thank you. Saves me trying to produce a new design for a
circular object with an axle…
For the files that I am trying to use, columns 77-78 are present (actually,
columns 79-80 are there so I can read the atomic charge as well, which is
useful for my purposes) so I’m hoping that this will be reliable.
Harry
> On 15 May 2024, at 12:38, 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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