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[modeller_usage] building a model with zn ions

Hi all,
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.
Thank you.


Research student,
National university of singapore.