[ccp4bb]: molecule and map don't superimpose in povscript+ and pymol

[chernhoe <chernhoe@imcb.nus.edu.sg>]

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Hi, I have a slight problem with getting my electron density map to be
displayed together with my protein structure in POVSCRIPT+ and PYMOL,
although it is fine in O. In both cases, the map was displayed in
another portion of the unit cell but not in the part where the molecule
is. The only way to get the map to be properly superimposed is to get
CNS refine.inp script to calculate a new map. This map when fed into
povscript or pymol will result in the correct display of structure
within the density. I suspect this has to do with the origins/extents of
both the map and molecule. They must both be the same to get displayed
correctly. So the question is how to get a MTZ file to be converted into
a CCP4 map using FFT in the same origin as the molecule. Or conversely,
how do you put the molecule into the same origin as the calculated map??
The spacegroup in my case is P21. I've tried the following in mapman

new origin
new extents
uvw map

and also played with 'axis, symm, fftspacegroup, xyzlim' in fft to no
avail.

I like to know what is so different about the CNS calculated maps that
FFT and MAPMAN could not reproduce, yet could be read by povscript+ and
pymol?

Thanks for any help.