Re: [modeller_usage] Newbie question - Selecting chains and plotting DOPE profiles

[Modeller Caretaker <>]

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
--
             http://www.salilab.org/modeller/
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