I have a rough model of my target Protein in which I want to dock a (small) polypeptide.
I have some information about the protein structure via Cross-Linking experiments and want to apply them while generating the decoys.
Lets say I know that there is a distance of 10A between the C-Alphas of amino acid 1 and 15
Can I pass this information somehow, or do I have to check each decoy that the distance between my amino acids is in an acceptable range?
Ahh, I should tell you that I am totaly new to rosetta and just read the tutorial and manual, I could have missed the one or other hint about that.