Unfortunately, in manual & tutorial there’s no information about how disulphide bonds can be defined in PyRosetta, although without this feature many modeling tasks become impossible.
Can anyone please inform me about how this can be done?
Disulfide bonds are currently handled automatically using several disulfide scoring components (i.e. dslf_ss_dst) that favor the formation of disulfide bonds and penalize breaking of disulfide bonds. Are your disulfide bonds breaking during the simulation?
I am currently embarking on the same task. I think what batch2k meant was defining specific disulfides in a protein, aka AA 25 to AA 45. I am trying to use pose.conformation().bond_length() as a way to tell if the correct disulfides have been created. If the wrong one(s) were created during a perturbation step, the pose will revert back to its original form. And eventually, the correct disulfides should emerge. We shall see.