On 09/12/2012 01:13 PM, Joshua Adelman wrote: > I've looked through the mailing list archives and online documentation, > but I'm having some trouble wrapping my head around the proper way to > accomplish the following. I have two PDB files of a protein in different > conformations, where in one of the two PDBs, a short stretch of residues > are missing, but in the other the complete coordinates in that region > are known. Both PDBs have different missing residues throughout their > chain, but I'm only interested at this time in modeling that small > section that's present in one and not in the other.
This is a very simple case of multiple template modeling, very similar to question 1 in the FAQ: http://salilab.org/modeller/9.11/FAQ.html#1
Simply add a third sequence 'C' to your alignment (the sequence you want to model) and align it with both A and B, then use regular automodel with knowns=('A', 'B') and sequence='C'.
Ben Webb, Modeller Caretaker