Hi, Pavel and Peter,
Alternatively, is there a program that will build dummy atoms (zero occupancy) automatically in a map in all peaks above a certain sigma (i.e. atoms just for mask calculation).
I'm not aware of such program although it's a couple of hours to write one. I would probably even write it if I ever see a clear need for it or evidence for its usefulness. So far I don't understand why you really need it?
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. 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. Would it be easier and faster ? I understand that any solution requires your personal time (as usually, your initial time estimations multiplied by 10 :-) Best regards, Sacha