Jmol 14.0.2 and 14.1.2 have been released. They are identical except for
version number, since I needed to merge them this time.
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.2/
The rather short eclectic set of bug fixes include:
bug fix: select symop=1555 broken
bug fix: set picking dragSelected not working
bug fix: isosurface map atomic orbital fails
bug fix: state reading not skipping set defaultLattice "{NaN NaN NaN}"
bug fix: vibration off causes unnecessary warning in console
bug fix: draw symop broken
bug fix: array.mul(matrix3f) crashes Jmol
bug fix: vibrational display of modulation with distances doesn't update
bug fix: modulation not distinguishing between q and t;
bug fix: modulated measurements not working
NEW FEATURES
Several new features common to both: (I prefer to add new features only to
the trunk, but it was important to synchronize these two versions for other
reasons, so both have these.
Probably the most important new feature is that for JavaScript,
*Jmol.evaluate() is deprecated. (It's still there, but I don't recommend
using it; no need to update current pages.) Long live Jmol.evaluateVar()! *
The big difference is that Jmol.evaluate() could only return three variable
types: integer, float, and string. Jmol.evaluateVar() will return those as
well as arrays and booleans. I didn't want to change the definition of
Jmol.evaluate() in case some people are parsing those strings that are
coming from arrays. Thus, the new function name. Jmol.evaluateVar is MUCH
more convenient when working with more complex information.
Jmol.evaluate(jmolApplet0)
by itself returns the set of ALL variables.
This next feature I just found to be very handy:
new feature: select ON/OFF atom-set
-- turns selection halos on or off as well as doing the selection
-- convenience only
-- for example:
select on _O2
select off *
It's common to want to know what the most recent atoms picked were. The
*pickedList* variable now tracks that as an array.
new feature: pickedList -- ordered array of recently picked atoms
-- can be used the same as the PICKED variable,
but that is ordered sequentially, not temporally
-- twice clicking off structure clears the list
-- @{pickedList[0]} last-picked atom
-- @{pickedList[-1]} next-to-last-picked atom
-- @{pickedList[-1][0]} last two picked atoms
This perhaps seemingly odd function can be quite useful, actually:
new feature: pt1.mul3(pt2)
-- returns {pt1.x*pt2.x, pt1.y*pt2.y, pt1.z*pt2.z}
-- if both are not points, reverts to simple multiplication
A few new features make array handling easier:
new freature: array.mul3(pt2)
-- applies mul3 to all elements of array
new feature: array.pop(), array.push()
-- similar to JavaScript
-- for example:
a=[];a.push("testing");print a.pop()
// create a distance t-plot
at = [] // t points
am = [] // distance measurements
var p1 = a.modulation()[1]
var p2 = a2.modulation()[1]
for (var i = 0; i <= 50; i++) {
var t = i / 50.0;
at.push(t);
var b1 = a.modulation(t)[1];
var b2 = b.modulation(t)[1];
var m = distance((p1 + b1).xyz, (p2 + b2).xyz);
am.push(m);
}
d = at.add("\t", am)
The CAPTURE command creates animated GIF files. A new feature
allows capturing a very specific number of seconds worth of animation.
This is particularly useful for capturing a simple vibration. I think
there's a
slight bug in that you need to specify a time just shy of the period. I will
try to fix that when I can. You can see it in operation at
http://chemapps.stolaf.edu/jmol/jsmol/images.htm
new feature: caption "filename.gif" x.x -- number of seconds to run
These next two features primarily support the new Jmol.evaluateVar() method:
new feature: getProperty("JSON", ....)
-- returns JSON code for property
-- allows JavaScript: x = Jmol.getPropertyAsArray("variableInfo","some
expression")
new feature: getProperty variableInfo <expression>
-- allows retrieval of variables in Java or JSON format
-- evaluates expression
-- defaults to "all"
The rest of these features have to do with modulated structures
(
http://www.ccp14.ac.uk/ccp/web-mirrors/crys-methods/Project/modulate/modulate.html)
and reading msCIF files:
new feature: modulation scale x.x
new feature: modulation 0.2 // sets t-value
new feature: {atomset}.modulation(type, t)
-- returns a 3-vector (displacement modulation)
-- implemented only for type="D" (optional)
-- optional t is 0 by default
-- if t is missing, the unmodulated displacement is returned
new feature: modulation adjustable by q and t, up to d=3
// modulation on/off (all atoms)
// moduation {atom set} on/off
// modulation int q-offset
// modulation x.x t-offset
// modulation {t1 t2 t3}
// modulation {q1 q2 q3} TRUE
*Bob*
--
Robert M. Hanson
Larson-Anderson 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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