Re: [modeller_usage] homodimer problem

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

On 04/10/2011 10:07 PM, rjayashree13-science AT yahoo.co.in wrote:
> My template is a homodimer and I want to model my target also as a
> hmodimer.
> The sequence of the chain A of homodimer in the PDB file is like:
> MKQA.............G.
> The sequence of the chain B of homodimer in the PDB file is like:
> MKQA.............GK.

If the sequences are different, then it isn't a homodimer...

> But if
> there is a slight difference in the two chains, like in this case the K
> residue is extra, then what should I do?

Either model it as a heterodimer (in which case you wouldn't add the 
Modeller symmetry restraints) or align that extra K residue with a gap 
in your model sequence (or add a gap to the end of the template A chain 
and align it with a K in your model sequence), so that the two chains 
are identical in the model.

	Ben Webb, Modeller Caretaker
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