Hi Paul,
it seems the atom order for the main chain of proteins is part of the
standard: http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
states that
ATOM records for proteins are listed from amino to carboxyl
terminus.
But what does that mean for the side-chain? I can't find anything in
there ... apart from the shown example:
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85
ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34
ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65
ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88
ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41
ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64
ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11
ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58
ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25
which seems to suggest for proteins: first main-chain atoms ordered
from amino to carboxyl terminus, followed by side-chain. Which seems
to contradict the specification above: if I walk along atoms in an
amino acid from amino to carboxyl terminus, I encounter the side-chain
when I hit the CA atom. So then I would be inclined to use
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85
ATOM 147 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88
ATOM 148 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41
ATOM 149 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64
ATOM 150 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11
ATOM 151 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58
ATOM 152 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25
ATOM 153 C VAL A 25 30.447 15.105 58.363 1.00 12.34
ATOM 154 O VAL A 25 29.520 15.059 59.174 1.00 15.65
But neither of these two possibilities seem to be explicitely
stated. Maybe coot could remember the ordering used on the input PDB
file and stick with it?
Cheers
Clemens
On Mon, Dec 10, 2007 at 04:25:28PM +0000, Paul Emsley wrote:
> You are right to complain that Coot reorders your atoms - the atom
> ordering is part of the PDB standard.
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