If you want to be 'by the book' on it, you should follow IUPAC rules for
atomic numbering of chemical compounds. Unless you're an organic chemist,
these rules are pretty hard to follow, so most people number at will.
If you're dealing with a 'known' series of compounds, such as analogous
inhibi
Dear Joe,
Atom labels are, in principle, arbitrary. The molecule doesn't case
what we call its atoms. To make the PDB more useful, it is handy if
all the people working with a particular compound use the same names for
their atoms. If you find that someone has already deposited a structure
