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Hi,

I am using the "MStats" utiliy in UPPSALA-mapman to compare the density
inside and outside of the mask of the model (basically my target is to
somehow quantify the level of noise outside the model mask). According to
the instructions, I need to do:

************
(1) MAPMAN > re m1 in.map ccp4
 ...
(2) MAPMAN > re m2 msk.mask mask
 ...
(3) MAPMAN > mstats m1 m2 0.5
****************

But the second syntax "re m2 msk.mask mask" never works. So, I replaced it
by "re m2 msk.mask ccp4". Not sure this will be ok or not, although the
3rd line "mstats m1 m2 0.5" went through. However, the output indicate the
average density inside and outside the mask are just almost the same. This
seems not to be true, since as seen in coot, the higher density always
contours around the molecule, and the noise sigma level outside of the
mask is really low.

So, I am wondering:

(1) Will "re m2 msk.mask ccp4" instead of "re m2 msk.mask mask" affect the
results?

(2) Will comparing the average density inside and outside the mask provide
a meaningful quantification of the noise level?

Sorry for the long description and thanks for any suggestions.

Best Regards, Hailiang