I am not sure that I understand your question perfectly... You can add/remove waters "automatically" during refinement using the proper options. After refinement, then you can also (i.e. you should also) take the output mtz file and use a graphics program (with PDB and MTW file) for modelling (including addition/deletion of waters). Several programsavailable, the one I use nowadays is Coot. But perhaps this is not the question you are asking...
Fred. > Message du 16/10/10 16:29 > De : "Hussain Bhukyagps" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] How to add water molecules..?? > > Dear All, > > How to add water molecules in the structure (PDB) after all the > refinements..?? > > Thank You, > Hussey. > > >