On 10/22/2014 02:05 PM, Justin Havird wrote: > I am trying to model proteins of the cytochrome oxidase (COX) complex > from a variety of organisms. I followed the "basic tutorial" online and > got great results for the first subunit in the complex (COX1). But, when > I tried the same thing for COX2, the align2d.py script aligns my > sequence against ChainA in the complex instead of ChainB, so I end up > with something that looks like COX1 instead of COX2. This happens even > though I change the "aln.append_model" line in align2d.py to > align_codes='1v54B', instead of 1v54A.
It's hard to tell exactly what your problem is without seeing your script and alignment, but it sounds like you're not specifying model_segment when you read in your complex, so Modeller's reading in both chains, not just one.
Ben Webb, Modeller Caretaker