I can get Rosetta to read a disulf.in file, but in the structures it produces, the disulphides are only sometimes present. I'm specifying four, but I typically only see two or three generated, and not the same ones each time. I suspect the disulphides are simply another term in the overall energy, so sometimes other energetic factors outweigh the lack of a specified disulphide. I have some related questions
1) is this normal behaviour?
2) is it possible to increase the weight on the disulphides?
3) if not, could other constraints be added - SG to SG, say - in order to encourage disulphide formation? If that's possible, what format would the .cst file take?