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    ” Make disulfide bonds with known connectivity,
    read connectivity from a file. File format:
    Cysteine pairs listed as with cysteine, not by residue #
    -find_disulf/-fix_disulfide activate both disulfide

    The above descriptions are from the README.options_list. For example, you have 4 Cysteine in your protein, and you want to bond the first one and the third one. then you create a file include a line as following:
    1 3

    that’s it!

    > Hi there,
    > thanks. I found the flag but I have difficulties figuring out what the additional files needs to look like that specifie the cysteine pairs. Basically the documentation mentions two files that need to be added, one for the flag -fix_disulf and a resfile where the cysteines are placed using PIKAA. Additionally I need to turn on the disulfide filter I think. I don’t get the design of the resfile though because it is not clear to me how to use the PIKAA option for disulfides.
    > CS-Rosetta stands for chemical shift Rosetta. It uses NMR data in addition to sequence similarity to select the fragments that will be used by Rosetta. The step I am struggling with is a pure Rosetta issue I think, so it doesn’t matter that I am using it as part of CS-Rosetta.
    > Baerbel