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 <hans...@stolaf.edu> 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 <martze...@yahoo.com> 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] ------------------------------------------------------------------------------ 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 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
