I know this has come up before and I can't remember what the solution was. PyMOL is drawing bonds between the protein I'm interested in, the ATP analog, and the bound metal ions, presumably because the metals are close enough to the protein and analog for bonds to be autodetected. Is there a way to turn off this behavior, other than writing a script to do it each time? In my case "unbond resnam mg, not resnam mg" does the trick, but I've had different protein chains or substrates bound together in the past.
thanks, Nat
