Hi Allister,
1) How do I specifically prevent a disulfide bond from being defined between two sulfurs that are close together (I tried manipulating the "disulfide_distance_cutoff" variable but this doesn't seem to stop a disulfide being formed).
If you set, e.g. disulfide_distance_cutoff=0.1 you shouldn't get any disulfide bonds anymore. I just tried it on a small structure and it worked as expected.
2) How can I soften the restraint on the disulfide bond length for specific cysteine residues.
With the current phenix.refine you cannot edit the automatically determined disulfide bonds (sorry). However, you can use disulfide_distance_cutoff=0.1 to turn off the automatic bonds. Then use geometry_restraints.edits (see documentation at http://phenix-online.org/documentation/refinement.htm) to define the disulfides manually one by one, with the ideal distances and sigmas you want to use. Use a log file from a previous phenix.refine run to obtain the list of all disulfides. Ralf