Thanks, that really helps. Unfortunately, that won't work. I don't know if
it's just different fields using the same data files, but the files I have
that are from electron diffraction simply display nothing when you use that
cutoff. Still, it might be useful to implement something like a sigma option
then at least.
Bob
The rmsd isn't calculated from the dmin/dmax values but comes from a
> separate calculation which generates the map itself.
>
> When calculating the electron density value an associated calculation
> determines the likely error in that value and that error is the
> estimated standard deviation (errors are assumed to be distributed
> following a normal distribution curve). The rmsd value is simply the
> square root of the esd value.
>
> So for a point in the cell the calculation of the electron density might
> be, say, 3 electrons per cubic angstrom. To a crystallographer this
> number means more if the error associated with it is also known. So an
> additional calculation is run which will give a best guess for the error
> in those map values. Say that is 0.78 electrons. Thus for any value of
> the electron density we have an estimated error (standard deviation) of
> plus or minus 0.78 electrons.
>
> For the example you site above: the max. electron density in the map
> volume is 4.9988 e/A^3 with an rmsd of 0.747. Or to express it as an esd
> (i.e. sigma): 5.0 e/A^3 +/- 0.6 (the square of 0.747). Similarly, the
> minimum density is -1.2 e/A^3 +/- 0.6.
>
> I'm not sure how you want to generate the isosurface but if you are just
> giving it a single cutoff value then use 0.6 as a 1 sigma cutoff
> isosurface or 1.2 for a two sigma cutoff isosurface, etc.
>
> 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
------------------------------------------------------------------------------
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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