Hi Robbie
I’m not actually using PDB files of proteins - I’m using the PDB format files
in PDBeChem, because at the moment I’m interested in doing stuff with
ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what
I’d expect, but I’m prepared to work around that.
Harry
> On 15 May 2024, at 16:24, Robbie Joosten <robbie_joos...@hotmail.com> wrote:
>
> Hi Harry,
>
> It might be better now, but there used to positively charged aspartates in
> the PDB. You have a better chance taking charges out of the CCD for your
> atoms of interest. I'm not saying all charges in the CCD are correct, but
> they are much more reliable. If you find errors, please report them to the
> proper authority. See it, say it, sorted.
>
> Cheers,
> Robbie
>
> On 15 May 2024 14:41, Harry Powell
> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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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