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The other thing you might have noticed is if you contour low enough
(probably already at 2 sigma) and allow the map to be big enough you
will have a sphere of density around your molecule sitting in the middle
- you can (should) get rid of those EM artifacts by masking out your
molecule at whatever sigma level suits you.
Juergen
Eleanor Dodson wrote:
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
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-418
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4542
FAX: +1-206-685-7002
