[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] renumbering residues



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
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage