Are crystallographic omit maps only used with molecular replacement? (This is in the context of macromolecular X-ray crystallography.)
From Lamb et al. 2015:

Model bias is the result of how maps are calculated: because the
phase estimates [of the structure factor] for the calculation come from the model, maps will
tend to show electron density for an atom in the model whether it is
truly there or not. A simple omit map is normally a difference (Fo −
Fc) map calculated after omitting specific atoms from a model, like a li-
gand or a functionally important loop.

From this the purpose of an omit map is rather clear.
But what I don't understand is when omit maps are used w.r.t. the source of the phases. From what I can tell, if the phases have been determined experimentally (e.g., using MAD), there cannot be any extraneous electron densities in the atomic structure model. This drives me to the conclusion that omit maps are used when the source of the phases is molecular replacement (I presume this is what the &quot;model&quot; alludes to).
Is this correct? Are omit maps only used with molecular replacement?
Edit: I am also confused with regards to how an omit map actually works. If the phases are what determine the final electron density irrespective of the amplitudes used, how does deleting a part of the atomic model, getting the phases from that and recalculating a new map (with these phases and the experimental amplitudes) actually help?
Edit 2 (from comments): I got the impression that if we don't have the phases (say for a part of a model), it just wouldn't get built even if we have the amplitudes for that part, right? Or is it that in this case (of omitting a part), there would be an electron density (because the amplitudes are still there), just that it would be featureless?!
I would be very glad to receive some clarifications and/or pointers.
Experimental phasing and molecular replacement provide initial phases used to start model building. Later on (refinement, validation) phases are calculated from the model.

If the phases are what determine the final electron density irrespective of the amplitudes used

Both amplitudes and phases are used to determine the electron density.
If you calculate the phases omitting part of the model, the electron density in this place won't be biased by that part of the model. (It may be biased by the absence of the model in this place).