It says in aforementioned docs:
"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.
"
and no, hopefully they don't mean that, since their example shows plenty
of 2-letter and 3-letter atom names starting at column 14 in the Example
section below which directly contradicts that statement.
They mean one-letter and two-letter element names, where possible, but
as previously discussed there are many atom names that don't fit that
model. Plus, since they define element names elsewhere they perhaps
don't want to conflate this data.
PDB's own format definition is both incorrect and confusing.
Sadly I couldn't find PDB format v2 definitions, to see if the
description changed.
Phil
(Column names starting at 1, I'm having a brief moment of Fortran nostalgia)
On 5/15/24 2:16 PM, Paul Emsley wrote:
On 15/05/2024 18:45, Filipe Maia wrote:
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It is, I think you would agree, unconventional to put a CA label for a
main-chain carbon at positions 13 and 14 (I have never seen such a
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this
case, putting "CHA" in positions 13-15 is unconventional (again, I
have
never seen such a thing) - but is it wrong? The official PDB
documentation, according to my reading at least, is not clear.
As Harry pointed out the documentation at
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM says in the "Details" that it's incorrect.
Maybe I am being dense, sorry, but could you be more clear about what
you mean here?
Paul.
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