Starr Hazard wrote: > mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', > file=code+'.profile', > normalize_profile=True, smoothing_window=15) > > are producing output files with a question mark in the name string. > > ABC31_HUMAN.BL09950001.pdb?.profile
If this is from your earlier script, you're getting 'code' from the following bit of Python: code = in_file.readline() Note that readline() does not remove the line-end character(s), and that's probably confusing Modeller. Try putting in code = code.rstrip('\r\n') after you read the line from your file.
> The question mark renders cp, mv and rename incapable of doing anything > with the file.
You can just quote the filename, or escape the ? with a \ character, to make cp, mv and friends work with it.
Ben Webb, Modeller Caretaker