Nicholas,
My experience from comparing conventional (FFT-based) and maximum-entropy- related maps is that the main source of differences between the two maps has more to do with missing data (especially low resolution overloaded reflections) and putative outliers (for difference Patterson maps), but in certain cases (with very accurate or inaccurate data) standard deviations do matter.
I'm curious - which programs have you used for maximum-entropy for map calculation?
Pete
