Ezequiel, since you mentioned you tried Phenix too:
in Phenix you can remove a particular disulfide bond by using a parameter, for example: disulfide_bond_exclusions_selection_string="(chain A and resseq 1 and name SG) or (chain B and resseq 10 and name SG)" This works in the command line and GUI. Please let me know (off-list) if you any help with this. Pavel On Sun, Jun 1, 2014 at 10:08 PM, Eze Chivi <[email protected]> wrote: > Hello, when I refine my structure, I see negative density around the > disulfide bond. I have 7 copies per ASU, and I can see this density in many > of them. In some cases, I see positive density also (negative in the center > of the straight line linking S atoms, and positive in both sides). What can > I try to solve it? Is it due to radiation damage? Alternative conformation > (partial oxidation)? Incorrect disulfide geometry parameters? My resolution > is 2.1 A, R/Rfree are around 0.220/0.243, and similar results with refmac5, > phenix and PDBREDO. Please find two example pictures in attachment. > Thanks for your help! > > > Ezequiel >
