Nico has released new versions of Jmol.
11.4.RC3 fixes a set of mostly obscure bugs:
version=11.4.RC3
# bug fix: antialias of images not functionally independent of antialias
for display
# bug fix: label offset doubled for multiline labels with
left/right/center alignment not specified
# bug fix: default label offsets mangled by default Front/Group
# bug fix: PDB files with missing amino acid carbonyl O cause exception
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11.5.4 introduces several new features:
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# new feature: Spartan input files read as Odyssey format
Jmol will now read .spinput files using the already-present Odyssey file
format reader.
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# new feature: set delayMaximumMs nnn
sets the maximum delay that scripts will use, primarily for testing
scripts. This one is for Eric.
set delayMaximumMs 100
sets the maximum delay to 100 ms. In this way you can more efficiently
test scripts that have longer delays built into them.
------------------
# new feature: set fontScaling TRUE/FALSE
OK, this is big. It still needs extensive testing. I'm sure there are a
few bugs here.
After using
set fontScaling TRUE
when you then introduce a label or 3D echo, the current zoom is used as
a basis for the font size. When the zoom is changed (or the window size
is changed), the font sizes follow.
Note that this only affects fonts for atom labels and 3D echos.
In addition, now when you create a JPG image, Jmol will adjust the fonts
of axes, unit cells, captions, titles, and such so that the produced
image looks (nearly) the same as the original model. I say "nearly"
because when you scale fonts they are not going to be exactly the same.
But they should be very close.
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# new feature: font [type] [size] [face] [weight] [scaleReference
(Angstroms per pixel)]
You can set the reference scale for a scalable font in Angstroms per
pixel. So if an echo font has a size of 20, and you designate the scale
reference as 0.1, then that text will be about 2.0 Angstroms high at any
zoom level. For atom labels, there is an additional setting that does
not require specifying all the font information:
set labelScaleReference x.x
So you could, for example, have:
select (atomno=3)
label "Atom 3"
font label 20
set labelScaleReference 0.05
Note that the offset from the atom also scales; we should talk about
whether we want that or not.
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# new feature: getProperty("appletInfo") includes a key "registry"
You can get a listing of all active applets using
var info = jmolEvaluate('getProperty("appletInfo", "registry")')
and you can run through the listing using
var Info = jmolGetPropertyAsArray("appletInfo")
from which you can use JavaScript "for ... in" to get the list of applets.
Or you can use Java methods directly, if you know some Java:
javascript:alert(jmolGetPropertyAsJavaObject("appletInfo").get("registry").keySet().toArray())
for example. The following JavaScript retrieves the registry as a Java
Hashtable:
var registry = jmolGetPropertyAsJavaObject("appletInfo").get("registry")
and the following code then retrieves a Java array of applet names:
var AppletNames = registry.keySet().toArray()
and the following uses the registry to send a command to the first
applet in the registry:
registry.get(AppletNames[0]).script("background white")
Notice that the registry contains references to the actual applets, not
just a name. You have to be careful using this sort of thing. I don't
recommend using global variables, as when a page closes, it may or may
not properly dispose of those, and you could have memory-leak problems.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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