Leaving aside medians/means and legs-number-of
I assume you have the EM problem that the actual "zero" level of the
electron density is unreasonably high, so that apparently you have much
too much density. You need to substract something off all the grid
points, then reset all negatives to zero to get a better representation?
If you want to create a mask from your map at a given density level you
can use MAPMASK three times over.
1) Use the keyword SCALE to subtract the 4SIG level from your map.
2) Create a mask for all density > 0 using the keyword MASK CUT 0,
2) Output a masked map including only those grid points present in the
MASK.
(Of course the "sigma" level will have changed in the new map..)
That should give more sensible SFS
Eleanor
Jin K. Yang wrote:
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Hi all..
As Dr. Eleanor Dodson pointed out in the paper (Using electron-microscopy
images as a model for molecular replacement, Acta Cryst (2001) D57, 1405-1409),
EM density doesn't represent the presice scale of the particle. So we need to
try different scales of the EM image for MR search.
In addition to this scale problem, I feel I need to try different sigma levels
in my case.
My EM density shows more features at higher sigma-cutoff level, say 4 sigma.
My case is the 3:3 complex of the two proteins which are already solved
separately before.
I think the density shown at 4 sigma level looks reasonable enught to
accomodate all protein modules.
And my EM collaborator says "The sigma level doesn't matter because it is
reconstituted from negative staining. So, we can use the higher sigma level density,
which is more featurous, for the atomic models to be fit in. "
I don't know about the EM, but it might be the technical consequence from the
negative staining.
So, I want to generate a new map whose 1-sigma level density is actually the
4-sigma level density of the original one, and to get the structure factor from
the new map and to try MR.
But, I cannot find a way to manipulate the map in this way. Is there anybody
who knows how to do it?
Does this sound reasonable ?
Jin Kuk Yang
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