Keep talking, Rich. I don't quite have it.
I have a file of numbers. An isosurface is produced not by contouring but by
finding the surface that intersects that cube of numbers at a specific
"cutoff" value.
> dmin dmax dmean (density min max mean)
> >
> > rms
>
>1 sigma = 1 esd = 1 rmsd*rmsd
>
>
esd is what? Sorry, I really need this from the beginning. Is that the value
I read from the file?
What I'd like to know is what the "rms" in the file is referring to:
FileManager opening 3hyd_map.ccp4
MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891
MRC header: rms: 0.74718976
Is that really the square root of the average of the squares of the numbers?
I guess it could be....
FileManager opening 1blu.ccp4
MRC header: dmin,dmax,dmean: -2.0043933,4.9972544,-0.0151823275
MRC header: rms: 0.46335652
FileManager opening mrc.map
MRC header: dmin,dmax,dmean: -144.45335,251.23714,2.3224847
MRC header: rms: 24.480686
FileManager opening mrc2.map
MRC header: dmin,dmax,dmean: 0.0,1.0,0.34194112
MRC header: rms: 0.099831074
As you can see, these number are all over the map. As I said, my current
hack of
cutoff = dmean + 2 * rms
seems to work acceptably, but I would like to do whatever people think
really should be done. We need some sort of default, of course, and it
obviously can't be a specific number. So I'm hoping that this "sigma"
business is identifiable from dmean and/or rms.
I note that when I have Jmol calculate the rms as
sqrt ( SUM(x^2) / n )
and the rms deviation as
sqrt ((sum(x^2) - mean^2)/n)
I do NOT get this number.....
Bob
> i.e. the rmsd is the square root of the esd
>
> so to contour the map at 2.5 sigma: square the rmsd and multiply by 2.5
> and plot lines from dmin to dmax at that interval.
>
> Rich
>
>
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------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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