Hens,
I took a look at the atom numbering in RasMol. The heart of the Chime code is based upon RasMol ... so they will be the same.
Here is what I found out about the atom numbering: with .pdb files the atom number is the number in the file with .mol files the atom numbering starts with 1 with .xyz files the atom numbering starts with 0
I am *not* happy about this :-(
This is a tough area because the semantics are fuzzy. Particularly where the number is implicit (as in mol, xyz) or has gaps (e.g. PDB). It may help to think of these "numbers" as labels. Again it is dangerous to try to map to the *internal* numbering in another program because it might get updated when you are looking. It is particular problematic when the numbering changes when an atom is added/deleted.
In general I would try to use these "numbers" only for input/output or when they have to be visually displayed to a human. If it's feasible I would create additional data storage for these number rather than trying to keep them in sync. Having to remember when to add +1, etc. is fragile
P.
Will advise.
Miguel
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