Re: [modeller_usage] Protein:Protein complex PIR format

[Modeller Caretaker <>]

On 7/15/14, 4:41 PM, Parker de Waal wrote:
> After looking through the mailing list I have been able to find
> numerous discussions about protein:protein complex homology modeling,
> however I have been unable to find any examples for proper PIR
> formatting and was wondering if someone would be willing to help.

You don't have to do anything special. Assuming your input complex is in 
a single PDB file containing two chains, this is just the same as 
modeling a heterodimer, which is just the same as regular modeling 
except that your alignment file contains two chains separated by a / 
character:
http://salilab.org/modeller/9.13/manual/node28.html

> I would like to perform modeling for unknown complex A2:B1 where
> A1:B1  is known and while holding B1 completely frozen.

In that case you need to select only the first of the two chains for 
modeling by adapting the script at
http://salilab.org/modeller/9.13/manual/node23.html

Your select_atoms method would look like
    def select_atoms(self):
        # Select first chain
        return selection(self.chains[0])

> Would the following PIR
> snippet below work for such modeling or is more information required on
> the second line

The latter - you need to tell Modeller the name of the PDB file 
containing your known complex (and the subset of residues to read from 
it), as shown at
http://salilab.org/modeller/9.13/manual/node488.html

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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