Re: [Jmol-users] Electron Density Map Demo

[Robert H. <ha...@st...>]

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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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900