Hi Ed, it is true - you cannot avoid serial numbers being appended to the output.prefix. At least as far as I know. Pavel. On 1/20/10 8:38 PM, Ed Pozharski wrote: > Do I understand correctly that there is no way to force refine to skip > the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb? > > >