With luck in about a week a new exhibit on nanotechnology will roll out at
the Epcot Center in Florida. One of the three centerpieces is called "Touch
a Molecule" and involves absolutely cutting edge Jmol. We have....
infinite tours through silicon and quartz crystals and liquid water
featuring:
-- set navigationMode (takes you right into the structure)
-- set navZ nnn (speed of navigation, both forward and backward)
-- set navigationPeriodic (makes for a never-ending experience)
-- new set zShadePower (nonlinear fog for a very spooky effect)
-- new set slabByAtom (no half-slabbed atoms)
-- new set slabByMolecule (no partial molecules)
hemoglobin oxygenation animation featuring:
-- new XML JVXL mesh compression for animating surfaces
-- new isosurface SLAB option does a clean removal of a
section of an isosurface based on any defined plane
-- new set waitForMoveTo FALSE allows starting a moveTo
operation and letting it run like spinning so that code can
continue, and buttons can continue to be operated.
-- new moveto STOP option to stop that.
-- new mouse binding DOUBLE-CLICK LEFT bound to the
_stopMotion action allows user to stop the moveTo
operations running in the no-wait mode.
-- new PDB reader option lets you just have a sequential set of "frames"
kind of like the old XYZ file option but for proteins, that can be
read as a trajectory, saving immense amounts of memory.
rhinovirus (4rhv) full capsid ( FILTER "biomolecule 1;*.CA")
animation featuring two buttons "Blow Apart" and "Reassemble"
and highlighting:
-- new set pickingStyle drag; set drag selected allowing direct
dragging of pieces of a structure. This is WAY cool. You can
drag the pieces out while Jmol is putting them back in. Guess
who will win in the long run? I could imagine this to be a standard
feature -- letting you move whole sections of a protein out and have
look into them, then from the "exploded view" letting Jmol
return them to their original location for you. Sort of like
taking the engine of a car apart and having an expert mechanic
who takes over and does the dirty work for you in the end.
-- new set picking select chain and set picking select polymer
(this is important when symmetry is present, because there might be
12 chains all with the same designation, but they are separate
molecular fragments (separate "polymers")
-- new set preserveState FALSE option to save memory for large
systems
-- new TIMEOUT command allows an operation similar to JavaScript's
setTimeOut method, but all within Jmol. THIS IS VERY COOL!
I think it opens the door to all sorts of game-like scenarios.
all involve
-- use of actual PNG images as the source of the Jmol state
-- new Jmol.js option that allows running JavaScript instead of
directly starting a Jmol script
-- new LOG command allowing script to write information directly
to files (sort of like the C++ "printf" command, but easier to use).
-- new set allowMultiTouch option for multi-touch screens
-- new JmolMultiTouchDriver.exe for the NewWindow screen (HP TouchSmart)
-- new set logCommands option to log command history to a file
-- new set logGestures option to log flick, pan, and zoom gestures
-- 10-50% speed enhancement in script processing.
What a month! Alas, my break is over -- time to go back to work....
Bob
--
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
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