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This a side effect of the idiocy of setting a contour level as a multiple
of the so-called "sigma" level (a battle that some of us have fought &
lost for many years). This is actually the RMS deviation over the volume
of the map box, so if this includes a larger volume of solvent the RMS
value will be smaller, ie it is a funciton of the box size!. Maps from
refinement programs (when there is a model) are on an absolute scale in
e/A^3 and it makes sense to set contour levels in these units, which are
independent of the box size.
Phil
>
> Hi,
> I'm attempting to use maprot to rotate a map (in order to get the map
> covering one molecule in alignment w\ another), and noticed that it seems
> to change the contour level of the output map (the new map contoured at 2
> sigma seems to be equivalent to the original at 1 sigma).
>
> Based on the example for density cutting, I'm using (cut&paste from csh
> script):
>
> maprot wrkin ${inmap} cutout ${outmap} <<eof
> mode to
> cell xtal ${cell}
> grid xtal 100 160 120
> symmetry ${symnum}
> average
> rotate polar 180.0 0.0 180.0
> translate 0 0 70.0273
> eof
>
> The same effect shows up with the identity transformation (rotate polar 0
> 0 0 ; translate 0 0 0 ). My best guess is that it's doing some type of
> averaging (although removing the average keyword results in error message
> "maprot: rcards - wrong number of operaters entered").
>
> Does anyone have any suggestions as to what I'm doing wrong, or
> alternative ways of doing this (other than just looking at the transformed
> map contoured at 2 sigma)?
>
> Thanks,
>
> Pete
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>
