>>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. I agree that this is a good way to think about it.
Internally, I don't use this number for anything. But script writers have (and will) use the atom numbers to identify specific atoms. > 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. Agreed. > 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 yes Miguel ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
