If you take a look at
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
you will see the following:
77 - 78 LString(2) element Element symbol, right-justified.
Going by atom name will get you in trouble. As you stated calcium vs
Calpha. The element symbol comes from the chemical component dictionary.
Ezra
On 5/15/24 6:28 AM, Harry Powell wrote:
Hi folks
I’m sure that this has been answered many times before (I’m sure that when I
was young I even read it here…), and I *know* that we should all be using
mmCIF, but I’m using PDB format files generated by a popular Python module and
I wanted to check the output against a definitive format definition (if that’s
not tautology).
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.
I’m particularly interested in metal atoms here, and want to be 100% sure that
I’ve found a calcium, say, and not a C-alpha.
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’m sure that someone here will say “why don’t you look at *****, it’s
obvious”, in which case - many thanks!
help
Harry
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