anu priya wrote: > My target protein has two zinc atoms. I aslo obtain the binding sites of > these metals in my target sequence. > how do i incorporate these zn ions in to my modelled structure? > Is it appropriate to include zn ions after modelling or is it neccessary > to include it before modelling? > Also please give me a procedure to do this like example script files or > alignment files or any alternative methods.

Did you look at the example at http://salilab.org/modeller/9v7/manual/node18.html ? It does essentially what you want to do (just with Fe-S clusters rather than Zn).

Ben Webb, Modeller Caretaker