Is that in the file somewhere? What I have is
dmin dmax dmean (density min max mean)
rms
Now, I DON'T think the "rms" is really "rms" -- I think it's rms deviation,
but I could be wrong about that. What seems to work as a reasonable default
is
dmean + 2*rms
But that could be a complete misuse of the numbers.
OK, Brian -- we want an answer from you, then! How do we do this? :)
On Tue, Jan 19, 2010 at 1:26 PM, <[email protected]> wrote:
> The "sigma" is the esd (estimated standard deviation) for the value of the
> electron density at any grid point. So if the electron density calculations
> provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour
> lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc.
>
> Rich
>
> On Tue, 19 Jan 2010 13:08:10 -0600, Robert Hanson <[email protected]>
> wrote:
> > Great to hear that, Eric. I would be very interested in seeing on that
> > last
> > page a comparison of loading the ccp4 file and a JVXL version of it.
> >
> > Main question is: "What's a sigma?"
> >
> > On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <[email protected]>
> wrote:
> >
> >> I have put an all new demo for electron density maps at
> >> http://www.umass.edu/molvis/tests/jmol_edm
> >> Everything works!! (as far as I can tell ... now I need to learn more
> >> from
> >> the crystallographers here before I can take it further).
> >>
> >> As for the default sigma value for the contours, I have talked to 3
> >> crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at
> >> 1.5
> >> sigma. You can see the comparison between 1.0 and 1.5 at the above demo
> >> page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The
> >> higher values are probably used for difference maps, not for full maps.
> >> So
> >> when the cutoff value is not specified, I think Jmol should default to
> >> 1.0
> >> sigma.
> [snip]
>
>
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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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