Re: [modeller_usage] Different behavior about mislabeled HETATMs since 9v9

On 10/25/11 7:28 PM, Yingjie Lin wrote: > This problem occurs when dealing with a PDB file containing > mislabeled HETATMs (some heteroatoms labeled as ATOM). When MODELLER > reads in such a PDB file with model.read() and then writes in out > with model.write(), 9v7 automatically corrects the labeling, however > 9v9 and 9v10 do not. > > I wonder whether that's an intended change or a bug.

This is an intended change. MODELLER attempts to leave your PDBs as it finds them. Previous versions did not "correct" the labeling, but rather labeled everything that was not a standard amino acid as HETATM.

Ben Webb, Modeller Caretaker