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