Hi,
I have just been using MODELLER for a couple weeks now and have a question that is hopefully an easy one.
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.
I was able to work around this by following the advanced tutorial and using the multiple templates scripts (even though there is sometimes only a single template to compare the sequence to). However, I am not able to compare the correct DOPE profiles when trying
plot_profiles.py; ChainA's profile is being used when comparing to the model instead of ChainB. I would like to be able to get an idea of how good the model is and identify areas of weak reliability, so the DOPE profiles seem like a good tool.
Any help would be appreciated, as I really like the MODELLER software so far and hope to be able to make use of it.