Eva Vanamee wrote: > I have a protein-receptor complex (P1:R1) with known structure. > I'd like to model the same receptor with another protein in complex (P2:R1). > I can easily model P2 based on P1 but I am not sure how to do it in the > complex.
I'm going to assume that you have your P1:R1 template in a single PDB file containing two chains. (If you have it stored some other way, there may still be ways to use it, but a single 2-chain PDB is probably easiest.)
In this case, it is straightforward to build a P2:R1 complex. See http://salilab.org/modeller/9v1/manual/node27.html
Feed in an alignment of P2:R1 to P1:R1 (essentially this will be your P2:P1 alignment, plus a simple 1:1 alignment for the R1 receptor). In your case, you don't need symmetry restraints, so you can remove the special_restraints and user_after_single_model methods from that example, but if you want to leave the R1 entirely unchanged, you can exclude those atoms from the optimization by defining select_atoms (see http://salilab.org/modeller/9v1/manual/node22.html ).
For the P2:R2 case, one solution would be to construct your alignment from the individual P1:P2 and R1:R2 alignments.
Ben Webb, Modeller Caretaker