Hi Laura, Chimera's PDB support was written with macromolecules in mind and adheres as closely as possible to the PDB standard. This means that it outputs amino and nucleic acid atoms within a residue in the same order that the PDB uses, regardless of original input order. Not much thought was given to the order of "other" residue atoms, and they basically come out in random order -- which is obviously bad in your case. I'm going to open a bug report on this, with you on the recipient so that you will know when the behavior is fixed. Until then, the only way to preserve ordering is to output in some other format, e.g. Mol2, which may or may not be acceptable for what you're doing. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu