Re: [modeller_usage] renumbering residues

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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