Hi MODELLER,
I found different behavior between 9v7 and 9v9 (also 9v10)about mislabeled HETATMs. I haven't tried 9v8 so I don't know how it would behave.
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.
- Yingjie
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
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Modeller Caretaker -
Yingjie Lin