Hey Batch. I know this is a little late, but I went my own way for a while trying to develop an abinitio folder, and had some of the same luck. While I did some interesting things, I was told to stick with what works; and so I am trying to design the abinitio program found in rosetta, within pyrosetta.
Sounds easier then it is, but I have made some strides. This is the paper that describes the low res, abinitio program (as used in all CASP experiments from 04 to present):
Rohl, et all; Protein Structure Prediction using Rosetta, methods in enzymology vol 383, 2004.
I have been able to implement every step correctly except the Gunn approach to fragment insertion (last step). I may be able to program it, but I am doubtful. As soon as I am done, I will post it here.
The other paper that further defines how Rosetta is used within the CASP experiments is as follows:
Bradley, et al; ‘Toward High-Resolution de Novo Structure Prediction for Small Proteins’, Science 2005, vol 309 pgs 1868 – 1871
This is a little stranger, as it uses homologies in a unique way, but I am fairly sure this was done in CASP8.
Wish you well.