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.



Justin C. Havird, PhD
Department of Biology
Colorado State University
Room E106 Anatomy/Zoology Building
Fort Collins, CO 80523
Lab telephone: 970-491-2058
Fax: 970-491-0649
Email: Justin.Havird@colostate.edu
Justin's Research Website: http://jchavird.wix.com/jchavird
Sloan Lab Website: https://sites.google.com/site/danielbsloan/