I have put an all new demo for electron density maps
athttp://www.umass.edu/molvis/tests/jmol_edmEverything 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.
I left my tests 1, 2, 3, and 4 up, but each index.html has a prominent note at
the top with a link to the newest update.
I found no bugs in Jmol! Kudos to Bob!! (Well, there is one minor one: after
executing a jmolLink(), Jmol temporarily responds to mouse dragging with zoom
-- everywhere in Jmol, not just on the right edge.)
-Eric
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