Thank you guys, All of your suggestions were great. It worked. I can see the electron density of zinc, but now the problem is that it is not where I was expecting but at a very near but not superimposable position with the calcium.
So I am wondering what would be the best way to rectify my structure of zinc now that the anomalous difference fourier clearly shows a different site. Should I put a zinc ion in the density and re refine the structure from this phased mtz (refmac output) file? or should I go to my original molecular replacement/first model and model the zinc there and start refining? I really appreciate your suggestions and I don't know why I did not join this group earlier! thanks, Ivan
