Re: [modeller_usage] Modelling a heterodimeric structure using heterodimeric template

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

On 8/17/12 6:59 AM, Rakshambikai R wrote:
> I am modelling a heterodimeric structure from a heterodimeric template. I tried
> modelling it using separate chains but I am facing difficulty in building the
> complex. Is it possible to build a model using the complex structure as a whole
> (I did see a mention of using "/" as a chain separater in your archives for a
> homodimer)?

Yes. Look at the example in the manual:
http://salilab.org/modeller/9.10/manual/node28.html

A heterodimer would be exactly the same, except that you don't include 
the symmetry restraint.

> If so, how do I specify the regions to be modelled?

It's exactly the same as for single chain models. Your alignment file 
tells Modeller the range of residues to read from the PDB file. Modeller 
reads PDB files line by line, so most likely you'll want to tell it to 
start at the first residue in chain A and stop at the last residue in 
chain B, just like the example in the manual.

	Ben Webb, Modeller Caretaker
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