The old BNL PDB format documents are available at
https://www.wwpdb.org/documentation/file-format
I looked at the Feb 1992 document to be certain that my memory was
correct [I am 6 days shy of 82 and am reassured that my recollection
was,in fact, correct] for information about the representation of
hydrogen naming as we had to violate the rule of two characters
right-adjusted for the chemical symbol and two following location
characters left-adjusted as we would have needed three location
characters for hydrogens. I then looked at 2MB5 which was deposited in
1989 and has hydrogens. At BNL we would have put, e.g., 1HD1, 2HD1,
3HD1 for leucine hydrogens and the current version of the entry has
HD11, HD12, HD13. And the redone representation of HEM is totally
confusing to me,
Given the revisions made by the RCSB PDB it makes sense to use the
element type and not the atom name.
Frances Bernstein
On 2024-05-15 11:34, Harry Powell wrote:
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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