Perfect, this works!
Thanks! Jan
On 09/04/2014 08:24 PM, Modeller Caretaker wrote: > On 9/4/14, 9:33 AM, Jan Kosinski wrote: >> class MyModel(automodel): >> num_map = None >> >> def fix_numbering(self): >> for old_resi, new_resi in zip(self.residues, self.num_map): >> old_resi.num = str(new_resi) >> >> def user_after_single_model(self): >> self.fix_numbering() > ... >> and it would be fine, but I get the residue numbers in wrong columns of >> the PDB: > > Modeller residue numbers are actually 5-character strings (they > include the 1-character PDB insertion code at the end). When you > assign to .num there's some logic to pad the numbers so they look > right when they get written out to PDB, but there's a small bug in > Modeller here specifically for 4-digit residue numbers. I've just > fixed this, so it'll be in the next Modeller release. For now you can > work around it by explicitly padding yourself (with a blank insertion > code), e.g. by replacing > old_resi.num = str(new_resi) > with > old_resi.num = "%4d " % new_resi > > Ben Webb, Modeller Caretaker