Congrats Bob! I'll try to make the best of this - especially the changes to
the Java applet!
Cheers,
Simone
2013/12/5 Greg Edwards <[email protected]>
> 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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