Just for info, I've tested the animated gif creation with 60+ msCIF structures in the IUCr archive and am extremely pleased to report that both representation of the modulation and gif creation worked very nicely in all cases.
Anyone interested in modulated structures might like to take a look at the gifs and jmol links at http://publcif.iucr.org/cifmoldb/mscif/ (the gifs are simply 'default' views - I've yet to really play with the new functionality) Many thanks to Bob for this excellent work Cheers Simon Quoting Robert Hanson <[email protected]>: > 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 > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
