On 15/05/2024 11:28, Harry Powell wrote:
Hi folks
[...]
I noticed this because I was encouraged to try Moorhen and found that a HEM
(apparently written by this module) did not have the atoms connected with bonds
in the display.
Q: Is it necessary to check columns 77-78 if I really want to be sure?
I’ve read the following, but can’t see anything obvious in “official” PDB
documentation that what it says here is actually defined anywhere:
Atom names are composed of an atomic (element) symbol right-justified in
columns 13-14, and trailing identifying characters left-justified in columns
15-16. A single-character element symbol should not appear in column 13 unless
the atom name has four characters (for example, see Hydrogen Atoms). Many
programs simply left-justify all atom names starting in column 13. The
difference can be seen clearly in a short segment of hemoglobin (entry 3hhb):
Correct:
HETATM 1071 FE HEM A 1 8.128 7.371 -15.022 24.00 16.74 FE
HETATM 1072 CHA HEM A 1 8.617 7.879 -18.361 6.00 17.74 C
HETATM 1073 CHB HEM A 1 10.356 10.005 -14.319 6.00 18.92 C
HETATM 1074 CHC HEM A 1 8.307 6.456 -11.669 6.00 11.00 C
HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 C
Incorrect:
HETATM 1071 FE HEM A 1 8.128 7.371 -15.022 24.00 16.74 FE
HETATM 1072 CHA HEM A 1 8.617 7.879 -18.361 6.00 17.74 C
HETATM 1073 CHB HEM A 1 10.356 10.005 -14.319 6.00 18.92 C
HETATM 1074 CHC HEM A 1 8.307 6.456 -11.669 6.00 11.00 C
HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 C
I have a different slant on this - "is there anything that I need to do
to fix the parsing of the above file?" - or to put it another way,
"Who's wrong? Moorhen or this file?"
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.
Regards,
Paul.
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