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