Re: [modeller_usage] naming chains in pdb

[Modeller Caretaker <>]

Abdul Hameed, MohamedDiwanMo wrote:
> I have modeled a protein structure with two subunits seperately. I want 
> to label it as A chain and B chain. Is there any way to introduce it 
> automatically in the pdb file rather than manually entering A or B 
> between the residue name and residue number.

If I understand you correctly, you want to generate a single chain 
model, but rather than giving it no chain ID (the Modeller default) you 
want to call the chain 'A'. And then you want to do the same thing again 
for the other chain and call the model chain 'B'. This is 
straightforward - just override the special_patches() method, e.g.

class MyModel(automodel):
    def special_patches(self, aln):
        self.chains[0].name = 'A'

m = MyModel(env, alnfile='alignment.ali', knowns=... (etc.)

If that's not what you want to do, please clarify.

	Ben Webb, Modeller Caretaker
--
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