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Can I thread a two chained structure in RosettaCM?

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Can I thread a two chained structure in RosettaCM?
#1

Most Rosetta CM tutorials show a one chain example for threading. If my structure has two chains, is it possible to align and thread my two chained sequence and template in a one run.

What should the grishin alignment format for the two chains look like?

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Mon, 2018-01-08 09:41
ahmadkhalifa

I would appreciate any help. 

Mon, 2018-01-15 10:59
ahmadkhalifa

The grishin alignment file is just used for threading, and considers each residue in turn. I don't believe you need to have any special chain separation designation in it -- simply align up your template and target sequences in-order, as one long string.

The critical thing when modeling multiple chains is to have the appropriate chain break annotated in your fasta file. This is simply a slash ('/'), placed between the last amion acid of one chain, and the first aa of the next. If you feed this slash-designated fasta file to both the partial_threading and the rosetta_scripts portions of the RosettaCM run, I think it should work how you want it to.

Mon, 2018-01-15 14:23
rmoretti