For some weeks now I have been thinking about bug 1309731: “ModelBuilder3D overwrites Atom IDs”. The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception. Somewhere in October, however, I found that Taverna could not create 3D models and convert these into reasonable CML because the Atom ID’s were messed up. So the question is, where did the ModelBuilder3D do this?