Dear Michael
This is very helpful. But just one clarification: If domain B is “undesired” to be removed from protein X (=A+B), then mask for “Particle subtraction” should be made by executing: Vop subtract #maskX #maskA = Mask (X=A+B) - Mask (A) = Mask (B). Is this correct? Your command is: vop subtract #maskX #maskB, which leads to mask A.
Best
Yuro