[chimera-dev] Atom index

[Eric Pettersen]

On Friday, July 26, 2002, at 12:28 PM, Mike Liang wrote:

> Hello!
>
> I found that if I open the same molecule twice (two models of same
> structure), the atom ordering in molecule.atoms are not the same between
> the two models.  Is this correct?  What is the best way to traverse the
> corresponding atoms in both molecules?
>
> I had expected the ordering of the .atoms to be the same ordering as in
> the PDB.

Hi Mike,
	Atoms get sorted into an order that makes it faster for them to be used 
in a graph traversal (and this may vary between identical molecules due to 
memory allocation differences changing the sort order).  The 'sortedAtoms'
  attribute of Molecule will return atoms in the same order for identical 
molecules (though this still won't be in PDB order).  Hope this helps.

--Eric