On Sat, May 5, 2012 at 2:23 PM, Pavel Afonine <[email protected]> wrote: > may be I'm missing something but I think all you need to do is to place (add > to PDB file) a Zn2+ into a blob of density that you believe that Zn belongs > to, and then most of refinement tools will take care of it automatically. So > I'm not seeing why you need "files for a Zn atom ...". I guess the task is > as simple as I just wrote, isn't it?
Not quite - as Roger noted, the charge would need to be set separately. (Actually, having Coot do this automatically for ions would be a very nice feature, and hopefully not difficult to add - or alternately, make this an option in the pointer atoms dialog.) This probably won't make a huge difference at most resolutions since the B-factor will soak up some of the discrepancy, but it may result in cleaner maps. -Nat
