Hi Scott,
Is this possible?
# on working model bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 313" distance_ideal = 2.5 sigma = 0.2 } # on SYM mol bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285" distance_ideal = 2.5 sigma = 0.2 }
Sorry, I'm not certain where you see the potential problem. Could you explain some more? Just in case: phenix.refine support bonds to symmetry copies, via e.g. symmetry_operation=-x,y,-z inside the bond scope. I can explain more if that's what you are looking for. Ralf