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Re: [modeller_usage] naming chains in pdb

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