Bob,
Thanks. This has been said before but it can't be said too often. Thanks
for all the work you put into this and the friendly spirit in which you
take the stream of bug reports, not to mention the mess of browsers, Java
and JavaScript revs, the platforms with random mixture of these, and all
the rest.
Hope the Jmol conference goes well. Fly yourself First Class !
Cheers
Greg E
On 5 December 2013 06:16, Robert Hanson <[email protected]> wrote:
> Happy to report the release of Jmol 14.0
>
> new feature: Jmol._j2sLoadMonitorOpacity (default 55)
>
> new feature: load() function, as in print load("xxx"), limited local file
> reading in applet:
> -- no root-directory files
> -- no files without extension
> -- no files with any "/." in path
>
> new feature: JAR files securely signed
>
> new feature: applet JAR files include JNLPs (Java Network Launch
> Protocols) for local file loading
>
> new feature: JSmol URL options _USE= _JAR= _J2S= overrides for Info data
>
> new feature: (was present but undocumented) print quaternion([array of
> quaternions])
> -- returns spherical mean a la Buss and Fillmore (
> http://www.math.ucsd.edu/~sbuss/ResearchWeb/spheremean/)
>
> new feature: print quaternion([array of quaternions], true)
> -- returns standard deviation for spherical mean a la Buss and Fillmore (
> http://www.math.ucsd.edu/~sbuss/ResearchWeb/spheremean/)
> -- units are angular degrees
>
> new feature: named quaternion modulus values
> -- print quaternion(1,0,0,0)%"matrix"
> -- options include w x y z normal eulerzxz eulerzyz vector theta axisx
> axisy axisz axisangle matrix
>
> new feature: set celShadingPower
> -- sets strength of cel shading
> -- integer values
> -- default 10 is a thick line
> -- 5 is a fine line
> -- 0 turns cel shading off
> -- negative value removes interior shading -- outline only
> -- operates on pixel based on normal to light source (power > 0) or user
> (power < 0)
> -- sets color to background contrast (black or white) when
> normal_z < 1 - 2^-(|celShadingPower|/10)
>
> new feature: mmCIF reading reports _citation.title in Jmol scripting
> console
>
> new feature: minimize SELECT {atomset} ONLY
> -- ONLY option excludes all other atoms
>
> new feature: minimize {atomset}
> -- implicit SELECT and ONLY
>
> new feature: "extensions" directories in JSmol for contributed JS and SPT
> scripts
> -- jsmol/js/ext
> -- jsmol/spt/ext
>
> new feature: load ... filter "ADDHYDROGENS"
> -- local set pdbAddHydrogens just for one load command
>
> new feature: compare {1.1} {2.1} BONDS SMILES
>
> new feature: list = compare({atomset1} {atomset2} "SMILES" "BONDS")
> new feature: list = compare({atomset1} {atomset2} SmartsString "BONDS")
>
> new feature: write JSON xxx.json
>
> new feature: [#210] JSON {"mol":...} reader
> -- example (penicillin; no actual line breaks)
> {"mol":{
> "_is2D":false,
> "_scale":{"x":1,"y":1,"z":1},
>
> "a":[{"x":3.9236999,"y":-0.9222,"z":0.1835},{"x":3.2479,"y":-3.2106004,"z":0.3821},{"x":5.1731,"y":-1.3284999,"z":-0.24640003},{"x":4.4973,"y":-3.6169,"z":-0.0478},{"x":5.4598002,"y":-2.6759,"z":-0.3623},{"x":1.599,"y":-1.4203,"z":0.9663},{"x":-4.2137,"y":0.8188001,"z":2.5929},{"x":-5.7525997,"y":0.1604,"z":0.70350003},{"l":"H","x":-0.92130005,"y":-0.6858,"z":0.8503},{"x":2.961,"y":-1.8632,"z":0.49760002},{"l":"O","x":-4.989,"y":2.5026002,"z":-1.2333001},{"l":"O","x":-1.2756001,"y":1.6640999,"z":-1.9360001},{"l":"O","x":1.104,"y":-1.4738001,"z":-1.3405999},{"l":"O","x":-4.604,"y":3.4702,"z":0.7158},{"x":-4.4305005,"y":2.47,"z":-0.1623},{"x":0.68810004,"y":-1.2541,"z":-0.2227},{"x":-3.5391,"y":1.3063,"z":0.1875},{"x":-1.4742,"y":-0.7,"z":-1.1997},{"x":-1.8847001,"y":0.7218999,"z":-1.4753001},{"l":"H","x":-5.185,"y":4.1949,"z":0.44660002},{"l":"N","x":-0.5887,"y":-0.86149997,"z":-0.043799996},{"x":-2.9578,"y":-0.84800005,"z":-0.8823999},{"x":-4.298,"y":0.3443,"z":1.1408},{"l":"S","x":-3.3189998,"y":-1.1949,"z":0.8809},{"l":"N","x":-3.159,"y":0.59889996,"z":-1.0386},{"l":"H","x":-2.6423,"y":1.6747,"z":0.6855},{"l":"H","x":-3.5207,"y":-1.4693998,"z":-1.5789001},{"l":"H","x":-4.6569,"y":1.8111,"z":2.6771998},{"l":"H","x":-4.7551003,"y":0.123500004,"z":3.2344003},{"l":"H","x":-3.1692,"y":0.86,"z":2.9017},{"l":"H","x":-5.7794,"y":-0.2569,"z":-0.3031},{"l":"H","x":-6.2558002,"y":-0.5187,"z":1.3918},{"l":"H","x":-6.2588997,"y":1.1256,"z":0.71029997},{"l":"H","x":-1.1443,"y":-1.2523,"z":-2.0796},{"l":"H","x":1.1846,"y":-2.1707997,"z":1.6393999},{"l":"H","x":1.6871,"y":-0.46960002,"z":1.4921},{"l":"H","x":3.7012,"y":0.1303,"z":0.2784},{"l":"H","x":2.4957001,"y":-3.9457002,"z":0.62750006},{"l":"H","x":5.9251003,"y":-0.5933,"z":-0.4921},{"l":"H","x":4.7215,"y":-4.6695,"z":-0.13759999},{"l":"H","x":6.4357004,"y":-2.9933,"z":-0.6989}],
>
> "b":[{"b":10,"e":14,"o":2},{"b":13,"e":14},{"b":14,"e":16},{"b":16,"e":24},{"b":16,"e":22},{"b":21,"e":24},{"b":18,"e":24},{"b":6,"e":22},{"b":7,"e":22},{"b":22,"e":23},{"b":21,"e":23},{"b":17,"e":21},{"b":17,"e":18},{"b":11,"e":18,"o":2},{"b":17,"e":20},{"b":15,"e":20},{"b":5,"e":15},{"b":12,"e":15,"o":2},{"b":5,"e":9},{"b":0,"e":9,"o":2},{"b":1,"e":9},{"b":0,"e":2},{"b":1,"e":3,"o":2},{"b":2,"e":4,"o":2},{"b":3,"e":4},{"b":13,"e":19},{"b":16,"e":25},{"b":21,"e":26},{"b":6,"e":27},{"b":6,"e":28},{"b":6,"e":29},{"b":7,"e":30},{"b":7,"e":31},{"b":7,"e":32},{"b":17,"e":33},{"b":8,"e":20},{"b":5,"e":34},{"b":5,"e":35},{"b":0,"e":36},{"b":1,"e":37},{"b":2,"e":38},{"b":3,"e":39},{"b":4,"e":40}]
> }}
> -- is2D will trigger minimization
> -- scale indicates overall scaling present in the "a" records
>
> new feature: set particleRadius
> -- global radius for atoms over the max radius value (16.0)
> -- defaults to 20.0
>
> new feature: CIF and PDB filters "BYCHAIN" and "BYSYMOP" for virus
> particulation
> -- creates just one atom per chain or per symop
> -- size can be scaled larger than the max of 16 Angstroms using, for
> example:
> set particleRadius 30;
> spacefill 30; // any number over 16 here uses particleRadius
> instead
>
> new feature: symop() function allows symmetry from biomolecule filter for
> PDB and mmCIF
>
> new feature: isosurface SYMMETRY
> -- applies symmetry operators to isosurface
> -- more efficient rendering and creation
> -- default selection is {symop=1} only
> -- default coloring is to color by symop based on propertyColorScheme
> -- example:
> load 1stp filter "biomolecule 1"
> color property symop
> isosurface sa resolution 0.8 symmetry sasurface 0
>
> new feature: new atom property: chainNo
> -- sequentially from 1 for each model;
> -- chainNo == 0 means "no chain" or chain = '<space>'
>
> new feature: new propertyColorScheme "friendly"
> -- color-blindness-friendly color scheme
> -- used at RCSD
> -- example:
>
> set propertyColorScheme "friendly"
> color {chainNo > 0} property chainNo
>
> new feature: JSpecView completely Java-free; includes 2D nmr and PDF
> printing of spectra
>
> new feature: WRITE PDF <width> <height> <quality> "xxx.pdf" quality > 1
> requests landscape mode
> -- uses efficient custom PDF creation classes
> -- sizes image to fit if too large
>
> new feature: JSpecView adds PDF and 2D NMR for JavaScript
>
> new feature: load "==xxx" FILTER "NOIDEAL"
> -- chemical component load from PDB using the "nonideal" coordinate set
>
>
> --
> 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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>
--
Greg Edwards,
Port Jackson Bioinformatics
[email protected]
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