I think Peter touches the point that we discussed previously, and this is one more reason to think about it in practical terms : it would be nice if phenix has an alternative option NOT to build a mask from the model but to read it outside. For example, it may be an EM envelope, or a mask built by any automated procedure.
I still don't see why it is necessary / important. Also, if you know a better way of mask calculation (or alternative way that sometimes may be better), then I would rather implement that then spend time on an option to allow a user-made mask.
An intermediate option is that indeed phenix gives a procedure to fill an external mask by dummy atoms with occ=0 and then you add them to you "regular" model and build the mask by your usual procedure.
If I see a case where it really makes positive difference I will think of implementing it -:) Pavel.