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___JmolDate="$Date: 2013-12-14 11:53:49 -0600 (Sat, 14 Dec 2013) $" ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" # THIS IS THE DEVELOPMENT TRUNK # Developers: to add a description of changes you have made, # add it on a line below the "___JmolVersion=..." line. # Don't use ___ in your text, as that is the key for stripping out # the information saved in the JAR version of this file. # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. ___JmolVersion="14.1.2" JmolVersion="14.1.2_2013.12.13" new feature: JavaScript: JSmol api Jmol.evaluateVar(applet, expression) -- better than Jmol.evaluate because result is a JavaScript variable, not a string. -- DEPRECATING JSmol api Jmol.evaluate(applet, expression) 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" 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 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 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(1e10)[1] var p2 = a2.modulation(1e10)[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) new feature: modulation scale x.x new feature: caption "xxxxx" x.x -- number of seconds to run new feature: modulation 0.2 // sets t-value 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 * 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 new freature: array.mul3(pt2) -- applies mul3 to all elements of array new feature: {atomset}.modulation(type, t) -- delivers P3 (displacement modulation) -- implemented only for type="D" (optional) -- optional t is 0 by default -- if t is missing, the unmodulated displacement is returned bug fix: modulation not distinguishing between q and t; bug fix: modulated measurements not working bug fix: not skipping set defaultLattice "{NaN NaN NaN}" bug fix: isosurface map atomic orbital fails bug fix: vibrational display of modulation with distances doesn't update bug fix: vibration off causes unnecessary warning in console bug fix: draw symop broken bug fix: array.mul(matrix3f) crashes Jmol bug fix: select symop=1555 broken bug fix: set picking dragSelected not working code: refactored CifReader, separating out MMCifReader and MSCifReader code: minor renaming/refactoring of methods in SV code: adds javajs.api.JSONEncodable interface -- super-simple implementation in org.jmol.script.SV -- allows implementations of javajs to deliver custom JSON results JmolVersion="14.1.1_2013.12.04" JmolVersion="13.3.9_dev_2013.12.04" 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 bug fix: write CD removed; ChemDoodle has changed formats; use JSON instead bug fix: PDB and CIF files indicated assemblies such as PAU as large negative number bug fix: COMPARE with no rotation starts infinite loop bug fix: looping problem with delay(-1) bug fix: Mouse wheeling for Chrome in JavaScript bug fix: JavaScript popup menu fix for language changes bug fix: JavaScript core components not being processed; Jmol._debugCode not recognized bug fix: unitcell offset incorrectly for biomolecules; origin incorrect for axes. bug fix: isosurface/mo FRONTONLY broken bug fix: language localization broken in JavaScript bug fix: ADF reader not reading MO output from DIRAC Build 201304052106 bug fix: Safari reports yellow Jmol info instead of asking to accept applet -- <object> tag needed to be <applet> bug fix: CIF reader not handling _pdbx_struct_assembly_gen.assembly_id properly -- wrong atom set for load =3fsx.cif filter "ASSEMBLY 1" bug fix: [#558 Compatibility issue with ChemDoodle] JSmol error in definition of Number.toString() bug fix: mouse wheel not working properly bug fix: JavaScript J2S compiler error does not coerce int += float to integer bug fix: JavaScript WEBGL option broken bug fix: JavaScript NMRCalculation does not access resources bug fix: JavaScript stereo not implemented bug fix: MOL reader fix for multiple-model file (just 13.3.9_dev) bug fix: MOL reader error with load APPEND -- does not continue atom numbers bug fix: CIF modulation reader not reading linear combinations of cell wave vectors bug fix: CIF reading with filter "BIOMOLECULE 1" fails if only the identity operation bug fix: mmCIF reader not reading all _pdbx_struct_assembly_gen.oper_expression options bug fix: PDB CRYST entry 1.0 1.0 1.0 90 90 90 should mean "no unit cell" regardless of biomolecule filter bug fix: isosurface slab <percent> not adapting well for flat molecules such as HEM bug fix: print userfunc() may fail (userfunc() by itself is fine) bug fix: within(helix) not implemented for C-alpha-only polymers bug fix: _modelTitle not updated when a new file is loaded or zapped bug fix: {*}.symop.all not delivering symmetry operator appropriately bug fix: for triple bond in SMILES in URLs bug fix: build.xml missing PDF creation classes bug fix: [#554] for load http://sourceforge.net/p/jmol/code/18631/tree/trunk/Jmol-datafiles/xyz/3structs.xyz?format=raw; zap model!=1.1; bug fix: following Java update, adding proper path check for local signed applet bug fix: {xxx}.property_xx not saved in state (broken 8/7/2013 rev 18518) bug fix: Manifests updated for signed and unsigned applet JAR files bug fix: write <type> <filename> fails bug fix: applet scriptWait() method broken bug fix: PyMOL session may display unit cell after read from saved state bug fix: MMCIF reader fails for multiple assembly types bug fix: CIF reader "biomolecule 1" translating to "molecular" rather than "assembly" bug fix: load trajectory with multiple files not working bug fix: JS applet popup menu not closing properly upon language change bug fix: HTML checkbox id attribute not assigned code: refactoring of applet/appletjs code; org.jmol.util.GenericApplet code: refactoring, simplification of buffered readers and buffered input streams. code: JavaScript refactoring, better build_...xml code: JavaScript Integer, Long, Short, Byte, Float, Double all reworked code: disambiguation of GT._ code: Refactored all unnecessarily inner classes to top level code: isolated util/ModulationSet using api/JmolModulationSet code: All applet language localization read from plain .po files -- as for JavaScript already -- no need to compile class files for applet languages -- no language .jar files -- new jsmol/idioma directory holds .po files for both Java and HTML5 code: faster isosurface rendering adding implicit "frontonly" with select {xxx} ONLY code: faster isosurface rendering with implicit "isosurfacepropertySmoothing FALSE" in relevant (integer) cases code: JmolBinary.getBufferedReaderForResource() -- consolidates all references to URL.getContent() and Class.getResource() code: JavaScript work around for inner class problem with variable name reassignment code: work-around for eval(functionName) not working in JavaScript. code: experimenting with ambient occlusion code: Required manifests added for Java Ju51 (January, 2014). code: JmolOutputChannel moved to javajs.util.OutputChannel code: jsmol.php fixed to allow " in saveFile method code: refactoring Parser into javajs.util code: DSSP moved to org.jmol.dssx, reducing JSmol bio load by 20K code: iText package jettisoned, no longer nec, as I wrote my own PDF creator JmolVersion="13.3.7" code; JavaScript comparison, 13.2.7 with 13.3.7. module 13.2.7 13.3.7 dBytes % core.z.js* 781,122 582,590 -198,532 75 corebinary.z.js 10,958 10,852 -106 99 corebio.z.js 199,251 199,249 -2 100 coreconsole.z.js 13,421 13,421 0 100 coremenu.z.js 105,606 107,832 2,226 102 coremin.z.js 113,754 113,938 184 100 coreprop.z.js 28,601 28,918 317 101 corepymol.z.js 153,236 153,271 35 100 corescript.z.js* 430,832 339,062 -91,770 79 corescript2.z.js 159,078 159,078 coresmiles.z.js 90,317 90,317 0 100 corestate.z.js 60,478 49,667 -10,811 82 coresurface.z.js 271,642 271,535 -107 100 coresym.z.js 129,456 129,529 73 100 coretext.z.js 46,033 46,033 corezip.z.js 163,080 92,476 -70,604 57 *core+scripting 1,211,954 921,652 -290,302 76 TOTAL 2,551,754 2,387,768 -163,986 94 JmolApplet0.jar 1,034,203 1,044,111 JmolApplet.jar 2,757,469 2,766,400 JmolVersion="13.3.7_dev_2013.10.01" bug fix: Crystal reader not applying lattice translations bug fix: translations incomplete bug fix: state saving of echo "bottom left" instead does "top left" bug fix: multiple-file crystal structures may fail to load if there is a lattice shift bug fix: space group not being calculated automatically for user-defined space groups bug fix: measures broken code: further consolidation: -- uncompressed(former) gzipped -- JSmol.min.nojq.js 134K 38K -- core.z.js 1583K(1781K) 363K -- corescript.z.js 339K (436K) 83K -- TOTAL 2056K(2217K) 484K (7% reduction) -- JmolApplet0.jar 1038K 1005K JmolVersion="13.3.7_dev_2013.09.30" JmolVersion="13.3.6" bug fix: angle measurements can end with "//nanometers" bug fix: first pending measurement loses label JmolVersion="13.3.6_dev_2013.09.27" new feature: adds remote logging for applet and app via http:// and via function for applet using jmolApplet0._applet.viewer.setLogfile(function(data) {......}) new feature compare {1.1} {2.1} BONDS "smiles" -- does flexible fit based on dihedrals. -- does internal rotation even if ROTATION TRANSLATION are not given (considered a possible bug) -- concatenation of: list = compare({1.1},{2.1},"smiles","BONDS") rotate branch @list 1 compare {1.1} {2.1} SMARTS "smiles" rotate translate so, for example: load files "$tyrosine" "$lysergamide" select 1.1; color bonds red select 2.1; color bonds yellow sm = "c1ccccc1CCN" compare {1.1} {2.1} BONDS @sm rotate translate new feature: show BEST ROTATION / show BEST VOLUME (better than undocumented show rotation best, show rotation volume) new feature: set animationMode "ONCE" "LOOP" "PALINDROME" new feature: show animationMode; x = animationMode new feature: CAPTURE command, including ROCK and SPIN -- application and signed applet only (no JS) -- creates animated GIF -- uses ANIMATION FPS to determine play-back rate. CAPTURE "filename" -- starts capturing -- uses ANIMATION MODE to determine looping -- both PALINDROME and LOOP create looping; ONCE (default) does not CAPTURE "filename" ROCK x|y|z degrees -- does a clean rocking of the molecule about one of the three major axes -- axis and degrees optional; y 5 assumed -- based on: rotate Y 10 10;delay 2.0; rotate Y -10 -10; delay 2.0;rotate Y -10 -10; delay 2.0;rotate Y 10 10;delay 2.0 -- uses LOOP mode CAPTURE "filename" SPIN x|y|z -- does a full spin of the molecule about one of the three major axes -- axis optional; y assumed -- based on: rotate Y 360 30;delay 15.0; -- uses LOOP mode CAPTURE off/on -- temporarily disables/enables capturing CAPTURE "" or just CAPTURE -- end capturing new feature: set drawFontSize // defaults to 14.0 FEATURE CHANGE: added bindings: "drag" and "up" -- may affect power users who use BIND command new: _center CTRL+SHIFT+LEFT+click new: _reset SHIFT+LEFT+double+click mouse actions include one (each) of: SINGLE DOUBLE LEFT MIDDLE RIGHT WHEEL DOWN DRAG UP CLICK for example: SINGLE-RIGHT-CLICK DOUBLE-LEFT-DRAG defaults are SINGLE, LEFT, and CLICK sequence is always: down (drag,drag,drag...) up (click) (only if no drag) Any of these actions may be tapped using bind "<some mouse action>" "<jmol action or script>" Note that adding "+:" to an action bind "<some mouse action" "+:<script...>" does not replace the Jmol action, just supplements it. $ show mouse _assignNew LEFT+click assign/new atom or bond (requires set picking assignAtom_??/assignBond_?) _center CTRL+SHIFT+LEFT+click center _clickFrank LEFT+click pop up recent context menu (click on Jmol frank) _pickConnect LEFT+click connect atoms (requires set picking CONNECT) _deleteAtom LEFT+click delete atom (requires set picking DELETE ATOM) _deleteBond LEFT+click delete bond (requires set picking DELETE BOND) _depth CTRL+SHIFT+LEFT+double+drag adjust depth (back plane; requires SLAB ON) _dragAtom LEFT+drag move atom (requires set picking DRAGATOM) _dragDrawObject SHIFT+LEFT+drag move whole DRAW object (requires set picking DRAW) _dragDrawPoint ALT+LEFT+drag move specific DRAW point (requires set picking DRAW) _dragLabel SHIFT+LEFT+drag move label (requires set picking LABEL) _dragMinimize LEFT+drag move atom and minimize molecule (requires set picking DRAGMINIMIZE) _dragMinimizeMolecule LEFT+drag move and minimize molecule (requires set picking DRAGMINIMIZEMOLECULE) _dragSelected ALT+SHIFT+LEFT+drag move selected atoms (requires set DRAGSELECTED) _dragZ SHIFT+LEFT+drag drag atoms in Z direction (requires set DRAGSELECTED) _navTranslate LEFT+drag translate navigation point (requires set NAVIGATIONMODE and set picking NAVIGATE) _pickAtom LEFT+click pick an atom _pickIsosurface LEFT+click pick an ISOSURFACE point (requires set DRAWPICKING _pickLabel LEFT+click pick a label to toggle it hidden/displayed (requires set picking LABEL) _pickMeasure LEFT+click pick an atom to include it in a measurement (after starting a measurement or after set picking DISTANCE/ANGLE/TORSION) _pickNavigate CTRL+SHIFT+LEFT+click pick a point or atom to navigate to (requires set NAVIGATIONMODE) _pickPoint LEFT+click pick a DRAW point (for measurements) (requires set DRAWPICKING _popupMenu CTRL+LEFT+down, RIGHT+down pop up the full context menu _reset SHIFT+LEFT+double+click, MIDDLE+double+click reset (when clicked off the model) _rotate LEFT+drag rotate _rotateBranch SHIFT+LEFT+drag rotate branch around bond (requires set picking ROTATEBOND) _rotateSelected ALT+LEFT+drag rotate selected atoms (requires set DRAGSELECTED) _rotateZ ALT+LEFT+drag, SHIFT+RIGHT+drag rotate Z _rotateZorZoom SHIFT+LEFT+drag, MIDDLE+drag rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse) _select LEFT+double+click select an atom (requires set pickingStyle EXTENDEDSELECT) _selectToggleOr LEFT+click if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires set pickingStyle DRAG) _setMeasure LEFT+double+click pick an atom to initiate or conclude a measurement _slab CTRL+SHIFT+LEFT+drag adjust slab (front plane; requires SLAB ON) _slabAndDepth CTRL+ALT+SHIFT+LEFT+drag move slab/depth window (both planes; requires SLAB ON) _slideZoom LEFT+drag zoom (along right edge of window) _spinDrawObjectCCW LEFT+drag click on two points to spin around axis counterclockwise (requires set picking SPIN) _spinDrawObjectCW SHIFT+LEFT+drag click on two points to spin around axis clockwise (requires set picking SPIN) _stopMotion LEFT+double+click stop motion (requires set waitForMoveTo FALSE) _swipe LEFT+drag spin model (swipe and release button and stop motion simultaneously) _translate CTRL+ALT+LEFT+drag, CTRL+RIGHT+drag, SHIFT+LEFT+double+drag, MIDDLE+double+drag translate _wheelZoom WHEEL zoom bug fix: JSON NIO port SYNC broken bug fix: print getProperty("image", "width=200;height=300;type=png") not working bug fix: write IMAGE "t.png" not working bug fix: rotate -10 -10 not working bug fix: mouse bindings not distinguishing DOWN/CLICK/DRAG/UP properly bug fix: mouse bindings _center and _reset not working bug fix: show MOUSE not including user-defined mouse bindings bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: JSmol/HTML5 not allowing WRITE xxx.pdb, xxx.mol, etc bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching code: overhaul of image creation methods code: careful attention to core functions yields results in 5% reduction in core download size: -- uncompressed(former) gzipped -- JSmol.min.nojq.js 134K 38K -- core.z.js 1586K(1781K) 364K -- corescript.z.js 378K (436K) 95K -- TOTAL 2098K(2217K) 497K (5% reduction) -- JmolApplet0.jar 1038K 1005K -- Thus, the "real" transfer size -- based on server-side gzipping -- is half the size of Jmol/Java. code: continued refactoring of ScriptEvaluator to ScriptExt code: refactoring to isolate LabelToken and Labels from core JavaScript load code: refactoring, simplification of image output and export -- folders created: org.jmol.image, org.jmol.dialog -- JpgEncoder, Jpg64Encoder, PngEncoder brought to org.jmol.image and made subclasses of ImageEncoder -- PpmEncoder fixed -- ImageEncoder stripped of all unnecessary ImageConsumer/producer business -- org.jmol.export.image.ImageCreator and parts of org.jmol.viewer.stateCreator reorganized into org.jmol.OutputManager, org.jmol.OutputManagerAwt, and org.jmol.OutputManagerJS -- clipboard functions moved into org.jmol.awt and org.jmol.awtjs2d -- org.jmol.io.JmolOutputChannel now serves for just about all output needs. code: major simplification and consolidation of file I/O methods, including exporters, using JmolOutputChannel class. code: only FileOutputStream reference is one reference in org.jmol.awt. code: code merge between 13.2 and 13.3 18 Sept 2013 code: major clean-up of ActionManager JmolVersion="13.3.5" JmolVersion="13.3.5_dev_2013.09.06" new feature: show NMR taps into NMRDB directly -- for now, application only bug fix: CRYSTAL reader not allowing vibration for conventional cell bug fix: JavaScript binary for Safari and Opera new feature: strutureModifiedCallback bug fix: ID @id vector fails JmolVersion="13.3.4" bug fix: select 1-5 broken JmolVersion="13.3.4_dev_2013.08.21" bug fix: JANA2006 reader not processing occupancies -- read now forced to "PACKED" in order to calculate site multiplicity bug fix: CIF reader not reading _CCDC_GEOM_BOND_TYPE record bug fix: File dialog problems with paths having space bug fix: GAMESS reader not reading energies bug fix: TRY failure in a load command followed by a successful load having a loadScript will pop past the second TRY and crash Jmol new feature: _logfile holds full path to logfile code: Incommensurate modulated structure CIF and M50/40 file loading validation -- includes d=1 and d=2 -- Fourier, sawtooth, crenel bug fix: translation not read from state new feature: set platformSpeed [0 to 10] -- basically an expanded "set wireframe OFF" with more options -- only effected during model rotation (including mouse dragging, spin, vibration, and animation) -- default value is 10 (all features; no compromises) -- value >= enables 8 antialiasDisplay (and thus, all features) 7 translucency 6 meshes (contact, draw, isosurface, MO, pmesh, lcaocartoon, CGO) 5 cartoons, rockets, trace, ribbon 4 geosurfaces 3 ellipsoids 2 wireframe and balls 1 none of the above (same as "set wireframeRotation off") 0 [reserved for "auto"] FEATURE CHANGE: set wireframeRotation expanded new feature: show ROTATION BEST -- operates on currently selected atoms -- reports "{quaternion}" new feature: quaternion("best") -- delivers actual quaternion new feature: show ROTATION VOLUME -- calculates approximate best box (from 1495 quaternion-based alternatives) -- reports "<volume> {dx dy dz}" -- where <volume> is the volume, -- and {dx dy dz} are the dimensions, where dx > dy > dz new feature: rotate BEST new feature: rotate SELECTED BEST new feature: pop-up menu selection "view...best" bug fix: CIF reader does not find Hall name for space groups bug fix: binding names not included in SHOW MOUSE bug fix: "single" touch can fire double-click bug fix: {x}.tensor() command fails when no atom tensors bug fix: isosurface slab not allowing two different slabs for two diffrent isosurfaces bug fix: set wireframeRotation not working ("inMotion" flag not properly read in Viewer). bug fix: screen repaints were being requested far too frequently *indicates when a refresh is made (external apps and applets only) external apps only via loadInline(List)* createModelSetAndReturnError openDOM, openReader, openFile, openFiles via loadModelFromFileRepaint* createModelSetAndReturnError loadInLine(String) via loadInLineScriptRepaint* FileDropper (string drop) via openStringInline* via openStringInlineParamsAppend createModelSetAndReturnError external apps, applet only, via loadInline(String[])* via openStringsInlineParamsAppend createModelSetAndReturnError script LOAD via loadModelFromFile createModelSetAndReturnError script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) via openStringInlineParamsAppend createModelSetAndReturnError script LOAD DATA via loadFileFull and loadInlineScript openStringsInlineParamsAppend createModelSetAndReturnError new feature: incommensurate modulation of ADPs. new feature: Jana2006 M40/M50 file reading bug fix: set loglevel 6 (debugHigh) not working bug fix: {*}.tensor("", "id") not implemented bug fix: {*}.tensor("") not implemented bug fix: {*}.tensor("adp") fails bug fix: {*}.symmetry fails when space group is P1 bug fix: atom tensors lost when merging bug fix: Jsmol menu and console broken in 2013.08.07 when jQuery calls were all moved into JSmolCore.js bug fix: float parser broken in dev_2013.08.07 code: reorganization of ScriptEvaluator into two sections, one optional new feature: COMPARE {atoms} [coords] new feature: COMPARE {atoms} ATOMS {subset1} [coords1] {subset2} [coords2] ... new feature: MODULATION command -- for modulated structures -- operates on currently selected set of atoms -- MODULATION ON -- MODULATION OFF -- MODULATION t -- sets modulation "t" of selected atoms -- MODULATION PLAY t1 t2 -- animates a once-through sequence of t from t1 to t2 -- MODULATION FPS x.x // may be < 1 -- sets speed of animation bug fix: zoom setting lost in state code: incommensurate crystal work -- Uiso, preliminary Uij and subsystems code: incommensurate crystal work -- occupancy Crenel, displacive sawtooths bug fix: shapeInfo not reporting visibility of isosurface code: pdb, cif readers separated into separate packages; p2n, pqr readers with pdb now new feature: Jana2006 reader -- reader for http://jana.fzu.cz/ new feature: CIF reader reads incommensurate modulated structures -- FILTER options include: -- NOSPECIAL (include special atoms for debugging -- MODAVERAGE (do not read modulation -- MODAXES=xyz (select only specific axes -- x, y, and/or z) -- NOSYM (no symmetry read) code: Even faster float parsing bug fix: filter lost after CENTROID or PACKED load option bug fix: set rangeSelected not functional new feature: msCIF file reading of incommensurate modulation data as vibration new feature: msCIF file filter "MODAXES=xxx" where xxx = X,XY,XYZ,YZ,etc. new feature: msCIF file filter "MODAVE" gives average structure with vibration vectors. bug fix: minimization can fail after MMFF switches to UFF. bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif JSmol: Jmol form moved to end of body JSmol: All $(xx) references moved to JmolCore.js JmolVersion="13.3.3_dev_2013.07.27" code: reconfigured JSmol build no longer needs jsmol/make directory. bug fix: Gaussian cube format changed and not recognized (extra "1" in third line). bug fix: PDB header don't do trim(); bug fix: isosuface ID @x ... becomes isosurface ID "@x" bug fix: color chain broken bug fix: rockets with color chain bug fix: filter ":X" broken bug fix: O not 2- in PDB adding hydrogens bug fix: NWChem reader error TODO: mouse exit then release doesn't trigger release TODO: ingenol/jsmetest.htm? TODO: minimization set position calculation optimization? TODO: documentation (see below, including % units on measure distance) TODO: isosurface SLAB TRANSLUCENT 0.x color -- inherits color of isosurface when color parameter is absent -- TODO - properly save in JVXL file TODO: PyMOL uniqueAtomSettings for transparency -- will require by-vertex translucent option bug fix: JSmol 2-sided surface color problem due to Java2Script miscoding of Number.shortValue() bug fix: PyMOLMeshReader code clean-up. JmolVersion="13.3.2_dev_2013.07.21" bug fix: PyMOL mesh reader broken for EDS files JmolVersion="13.3.1_dev_2013.07.20" bug fix: MMCIF_PDBX structures not being read bug fix: allow PyMOL PSE files reading as part of a set of files, not just by itself bug fix: quaternion plots not synched with originating structure bug fix: 1skt.cif loses secondary structure (MMCIF_PDBX reader needed) new feature: calculate formalCharge bug fix: set showTiming not functional bug fix: set pdbAddHydrogens does not set formal charge on O(1-) or "O" of H2O (2-) bug fix: PNGJ files not properly caching, and PSE files with DOCACHE option JmolVersion="13.3.0" JmolVersion="13.1.19_dev_2013.07.18" new feature: set exportScale x.x -- adjusts export scale -- only implemented for VRML and X3D exporters new feature: unitcell center {atomset} new feature: unitcell center {fx fy fz} new feature: {*}.ms, {*}.cs %[ms] %[cs] magnetic shielding and chemical shift new feature: label <color red>xxx</color> new feature: set shift_H xxx (ppm) new feature: getProperty("nmrInfo") new feature: NMR analysis tools: -- x = measure({a} {b} "isc_hz") -- J coupling -- x = measure({a} {b} "dc_khz") -- dipolar constant -- MEASURE {a} {b} "2://dc_hz" -- dipolar constant -- MEASURE {a} {b} "2:%3.2VALUE//dc_khz" -- dipolar constant -- MEASURE {a} {b} "2://khz" -- defaults to dc_khz -- MEASURE {a} {b} "2://hz" -- defaults to isc_hz -- MEASURE {a} {b} "2://isc_1hz" new feature: {xxx}.tensor(type,what) -- type = "temp", "ms", "efg", etc. -- returns a list of data. isc-type returns a list of lists [index1, index2, value] -- what = "j" (isc-type only) "chi" (efg only) "dc" (dipolar coupling constant; type ignored) "eigenvalues" float[v1,v2,v3] "eigenvectors" P3[V1,V2,V3] "value" Float (v3) "asymMatrix" Matrix3f "symMatrix" Matrix3f "isotropy" Float v_iso=(v1 + v2 + v3)/3 "anisotropy" Float v3 - (v1 + v2)/2 "asymmetry" Float (v2 - v1)/(v3 - v_iso) "eulerzxz" float[] "eulerzyz" float[] "quaternion" Quaternion "indices" float[modelIndex,atomIndex1,atomIndex2] "string" selected readable data "type" anything else -- all key/value pairs new feature: bind "+:<script...>" -- added "+:" indicates to NOT unbind Jmol action new feature: ellipsoid OPTIONS "xxxx" -- "xxxx" is a quoted string of options separated by semicolon: "arcs;arrows;axes;ball;dots;fill;wireframe" with optional "no" in front of each new feature: SET ECHO POINT {atom or point} -- allows 2D and 3D echos to have pointers to atoms or points bug fix: set shift_XX not saved in state bug fix: JSmol menu not disappearing upon touch outside menu bug fix: PyMOL surface map reading error bug fix: magres measurement of dipole coupling constants do not reach just min-distance set bug fix: "cs" for Cs symmetry broken in chemicalshift bug fix: cartoons with too small nonzero size will not render anything code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar coupling constant display. code: org.jmol.quantum.NMRCalculation implements org.jmol.api.JmolNMRCalculation: public float getQuadrupolarConstant(Tensor efg); public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor t); public float getDipolarConstantHz(Atom a1, Atom a2); public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField); public JmolList<Tensor> getInteractionTensorList(String type, BS bs); public BS getUniqueTensorSet(BS bs); public JmolList<Object> getTensorInfo(String tensorType, String infoType, BS bs); public Map<String, Float> getMinDistances(MeasurementData md); public boolean getState(SB sb); public Object getInfo(String sym); JmolVersion="13.1.17_dev_2013.06.27" new feature: CASTEP reader filter option q=all new feature: set picking DRAGLIGAND -- won't move the protein new feature: CIF reader upgrade to allow multicharacter chain specs. -- See 1bgl_1bgm.cif -- automatically switches to chainCaseSensitive if multi-character or lower-case chains are read in a CIF file. -- note that in certain cases quotation marks will be needed: select chain=0123 NOT OK select :0123 NOT OK select chain="0123" OK select :"0123" OK select :"A*" or :"A'" or :'A"' or :"A\"" TODO: document these: new feature: {atomset1}.distance.min({atomset2}) -- returns an array -- minimum distance of each atom in atomset1 to any atom in atomset2 new feature: {atomset1}.distance.max({atomset2}) -- returns an array -- maximum distance of each atom in atomset1 to any atom in atomset2 note: much of the next compare/branch business was built into a new COMPARE command for Jmol 13.3.6 new feature: list = compare({atomset1} {atomset2} "ccCCN" "BONDS") -- determines the dihedrals that match atomset1 to atomset2 -- returns arrays of length 6n, list[6n] which lists six numbers for each dihedral in the comparison set, including i1 i2 i3 i4 set1value set2value, where i1-i4 are atom indices, and set1value and set2value are the dihedral angles in sets 1 and 2, respectively. -- feeds into the rotate BRANCH @list command new feature: BRANCH @list -- takes a list of 6n numbers from compare function -- rotates all dihedrals in the selected atom set to target values concurrently // application: flexible substructure fit using a SMARTS search load files "$tyrosine" "$lysergamide" select 1.1; color bonds red select 2.1; color bonds yellow sm = "c1ccccc1CCN" list = compare({1.1},{2.1},sm,"BONDS") rotate branch @list 1 compare {1.1} {2.1} SMARTS @sm rotate translate // at this point the two models match almost perfectly among these key atoms. new feature: {1.1}.find("ccCCN", "BONDS") -- finds the first match in the structure to the given SMARTS string -- returns an n-length array of 4-length arrays, list[n][4] -- each list[i] is a set of four atoms in bond-connected order -- full list comprises all dihedrals in the found set of atoms. new feature: set translucent -- default TRUE : translucent objects are fully translucent -- FALSE: translucent objects are opaque to other translucent objects bug fix: CrystalReader broken by recent change to simpleReplace() bug fix: PyMOL movie start frame bug fix: PyMOL putty broken bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands bug fix: pdbAddHydrogens may miss H in first group of a chain bug fix: set defaultDrawArrowScale broken bug fix: "ligand" should include all _g=0 (nonPDB atoms) bug fix: applet getpropertyAsArray("bondInfo") fails bug fix: JSmol script/scriptWait nuance with moveto. -- when using scriptWait with HTML5, there can be no threading bug fix: invertSelected on trajectory causes nullPointerException bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES option nonfunctional bug fix: JavaScript not returning arrays properly from Jmol.getPropertyXXXX() -- very important to have {} after j2sNative directive! bug fix: COMPARE could rotate to less-good fit with SMARTS search bug fix: draw ARROW ATOM/BOND broken bug fix: animation MORPH broken for non-PyMOL files -- load trajectory ({0 6}) 1cdr.pdb -- animation MORPH 10 -- animation ON -- load trajectory "test1.pdb" "test2.pdb" -- animation MORPH 30 -- animation ON bug fix: draw ARROW ATOM/BOND broken bug fix: draw ARROW with offset disallows set picking draw adjustments bug fix: concurrent loading of two cif files by two different applets fails bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx INTERSECT yyy) -- needs revision to create DATA option; can be huge and very long to process state file bug fix: load :2-butanone fails bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different data structure bug fix: jvxl reader ignores jvxlVertexColorData bug fix: ellipsoid rendering problems code: MagRes/CASTEP reader upgrades code: color/translucent/opaque clean up in ScriptEvaluator ============================================================================= JmolVersion="13.1.16_a" new feature: set defaults PyMOL -- zoomHeight TRUE -- measurementUnits ANGSTROMS new feature: color BALLS -- distinct from color ATOMS because it doesn't get inherited -- for PyMOL compatability with sphere_color TODO: document these: new feature: restore SCENE "xxxx" nSec new feature: Scene menu -- PyMOL scene names, in order new feature: added parameters to moveTo allows setting cameraDepth, cameraX, and cameraY new feature: moveTo <nseconds> PYMOL [18-element standard PyMOL view matrix] -- used for PSE file loading -- to be used also for scenes [0-8] are 3x3 rotation matrix (row/column inverted) [9,10] are x,y translations (y negative) [11] is distance from camera to center (negative) [12-14] are rotation center coords [15-16] are slab and depth distance from camera (0 to ignore) [17] is field of view; positive for orthographic projection new feature: cache CLEAR -- same as cache REMOVE ALL new feature: load xxx.pse FILTER "DOCACHE" -- specifically for editing large PSE files when included in a state -- caches streamlined file that is still readable by PyMOL (needs testing!) (no electron density map data, for instance -- see HupA_2.pse) -- caches all isosurfaces, creating JVXL equivalents -- should be followed with WRITE xxx.pngj or WRITE xxx.jmol or WRITE xxx.zip -- for example: before: 04/07/2013 07:46 AM 11,929,507 HupA_2.pse $ zap;load "HupA_2.pse" filter 'DOcache' $ write t.zip after: Listing archive: t.zip Physical Size = 395174 Date Time Attr Size Compressed Name ------------------- ----- ------------ ------------ ------------------------ 2013-05-17 06:46:36 ..... 1092432 219718 HupA_2.pse 2013-05-17 06:46:36 ..... 1473760 6589 isosurface_level2 2013-05-17 06:46:36 ..... 25495 11624 state.spt 2013-05-17 06:46:36 ..... 134 119 JmolManifest.txt 2013-05-17 06:46:36 ..... 0 2 Jmol_version_13.1.16_dev_2013.05.17__2013-05-15_07.09 2013-05-17 06:46:36 ..... 158082 156316 preview.png ------------------- ----- ------------ ------------ ------------------------ 2749903 394368 6 files, 0 folders new feature: anim FRAMES [1, 3, 9, 9, 9, 3, 1] -- arbitrary PyMOL-like model list new feature: FRAME n -- same as MODEL n, unless we have PyMOL-like frames -- if have frames, then FRAME 2 goes to the second frame (model 3 in this case) -- MODEL n still always goes to a specific model. -- all relative options -- FIRST LAST PREV NEXT -- refer to frames if there are frames even if the MODEL command is given. new feature: pyMOL PSE state options: LOAD "FOO.PSE" state FILTER "xxxx" -- [state not present; default] load all PyMOL states (one PyMOL state == one Jmol model) -- state = 0 (load only the current PyMOL state) -- state > 0 (load just a specific PyMOL state) -- FILTER "nosurface" -- load PyMOL file without surfaces new feature: getProperty BONDINFO {atomset1} {atomset2} new feature: measurements with IDs and radius/diameter: -- measure ID "xxx" ... -- measure ID "xxx" RADIUS x.y (or DIAMETER x.y) -- renders as dots new feature: set zoomHeight -- FALSE by default -- set TRUE for PyMOL-like resizing (scale only set by height adjustment) new feature: isosurface color density (decimal) - variable decimal point size new feature: PyMOL CGOs as CGO command - needs testing - CGO ID "xxx" [ cgo data (float array) ] - includes basic CGO methods BEGIN GL_POINTS GL_LINES GL_LINESTRIP GL_TRIANGLE GL_TRIANGLE_STRIP GL_TRIANGLE_FAN VERTEX END COLOR NORMAL SIMPLE_LINE SAUSAGE TRICOLOR_TRIANGLE popup: added menu for MEP range -0.1 0.1 PyMOL: uniqueBondSettings working PyMOL: better scene restore; PyMOL: adds SASURFACE option (surface_solvent ON), with "carving" (ProFusion_ABL.pse, scene F6) PyMOL: abstraction of scene setting from reader PyMOL: first phase of reader development complete (working with Jaime Prilusky) -- 104 test models http://ispcsrv3.weizmann.ac.il/a2jmolb/browse -- implementation of standard objects, including: -- atoms with labels -- bonds -- standard PyMOL rendering, including: -- lines -- sticks -- nonbonded (stars) -- nb_spheres -- cartoons of various types (not plank) -- rockets -- ribbon (backbone/trace) -- putty (trace) -- dots -- measures -- simple CGO objects -- molecular surfaces -- electron density as points and meshes -- custom colors -- fog and slab -- morphing movies -- JVXL caching of isosurfaces PyMOL: measurement font/offsets enabled -- adds measure ID "xxx" FONT scale face style -- adds measure ID "xxx" OFFSET [mode, sx, sy, sz, ax, ay, az] -- adds measure ID "xxx" OFFSET {sx, sy, sz} PyMOL: perspective fix for translated center -- H115W.PinM.PSE PyMOL: preliminary scene implementation -- view only -- use RESTORE ORIENTATION xxxxx code: Text.java, Object2d.java moved from shapes to modelset bug fix: COMPARE move of group saved in state may not be correct when restored bug fix: write command doesn't accept parameter sequence IMAGE PNGJ ... (broken in 13.1.14) bug fix: load APPEND with PDB file loses structure (broken in 13.1.15) bug fix: restore command broken bug fix: JavaScript: adding SYNC bug fix: antialiasing or resizing stray lines problem solved (introduced in 11.0, 08/2006!) bug fix: "display add" by itself should not do anything bug fix: Hall translation initialization problem bug fix: JavaScript reading of old-style JVXL files bug fix: Gaussian reader not splitting MO set by model bug fix: polyhedron reading from state bug fix: connect delete not saved in state bug fix: rockets not working for alpha polymer (also in 13.0.16) bug fix: GXL added to carbohydrates bug fix: show state/anim turns "anim" into "animation" bug fix: MoldenReader orbitals are not in energy order; use FILTER "NOSORT" to prevent sorting by energy bug fix: simultaneous spin/animation broken in 13.1.13 bug fix: MoldenReader fix for file blank lines and g,h,i orbitals - also for 13.0.16 bug fix: COMPARE does not allow nSeconds at beginning, as described in documentation bug fix: isosurface VOLUME/AREA SET n cannot return to full array reporting; SET -1 added. bug fix: isosurface VOLUME/AREA always returns an array, possibly of length 0 bug fix: isosurface molecular/solvent can give inappropriate inner surfaces bug fix: show selected includes deleted atoms ============================================================================= JmolVersion="13.1.15" FEATURE CHANGE: default JPEG quality set to 100 (was 75, which looks crappy) new feature: select command parameter completion using [TAB] includes variables new feature: PyMOL-like label offset options: set labelOffset [sx, sy, sz] set labelOffset [mode, sx, sy, sz, ax, ay, az] where sx,sy,sz are screen coord offsets -- in Angstroms -- applied after view rotation -- sy > 0 LOWERS label ax,ay,az are xyz position (in Angstroms; applied before view rotation) mode == 1 indicates xyz position is an offset to the atom position mode != 1 indicates xyz position is absolute defaults: mode == 1; ax = ay = az = 0 new feature: CASTEP energy reading new feature: XCrysDen file reader new feature: VASP POSCAR reader new feature: set cartoonLadders -- no bases, like PyMOL new feature: model CREATE n -- allows "empty" model creation without atoms -- n = number of models to create -- defaults to 1 new feature: "all frames" toolbar button starts/stops PyMOL movies: if(_isMovie){if (_animating) {animation off}else{animation play}} else {frame *} new feature: Jmol/JmolData application -I flag accepts input from System.in and command piping: type t.spt | jmol -I start Jmol with this script Note: if you use a pipe, be sure to make "exitJmol" the last command of the script Add -o for output to System.out. Without the pipe, we are going to control Jmol from a Jmol> prompt on the command line console jmol -Io see messages on input console ...messages from Jmol Jmol> background red;load 1crn.pdb;.... ...messages from Jmol Jmol> exitJmol Add -n for headless operation (will not exit automatically). type t.spt | jmol -Ion Note: if you use a pipe, be sure to make "exitJmol" the last command of the script Add -i for silent operation (no writing to System.output). new feature: dots IGNORE {atom set} ON; new feature: Jmol or JmolData with -g0x0 and load filter "DORESIZE" will automatically resize the image to what is given in the PyMOL file as its default size: JmolData -ns "load t.pse filter 'DORESIZE'" -g0x0 -w "PNGJ:t.png" bug fix: isosurface map property may not reference correct atom bug fix: set isosurfacekey may not work with slabbing bug fix: deleting atoms does not remove bioshape rendering bug fix: isosurface in multi-model context saved in state with wrong model number bug fix: PyMOL label fix, including fonts bug fix: PyMOL rockets, nucleic acid rendering bug fix: write JPG not working in JavaScript bug fix: isosurface ... map property colors not cleared entirely before next mapping bug fix: MSMS reader broken bug fix: labels lost upon z-shading bug fix: isosurface property temperature default smoothing broken in 13.1.13. bug fix: {xxx}.cartoon = {xxx}.temperature.all fails to use correct values (also backbone, trace, etc.) bug fix: isosurface translucent level not re-zeroed properly bug fix: IDTF exporter with translucency fails bug fix: commands f.sort() and f.reverse() fail. bug fix: {;...;} syntax does not work in 13.1 bug fix: select dots > 0 does not work bug fix: JmolData broken code: PyMOL work; CGO command and class CGO extends DRAW preliminary only; preliminary putty; fix for putty+sticks issue code: PyMOL reader localSettings code: PyMOL putty hack for Cover1.pse removed; colix index error fixed code: PyMOL slab and depth; better field of view; even better zslab/zdepth code: PyMOL reader "backbone" (really a trace -- fixed width?) code: PyMOL reader isosurface solvent code: PyMOL reader and full surfaces, mixed bigEndian/littleEndian Pickle reading code: PyMOL reader: cartoon_ladder_mode approximation as cartoons code: PyMOL reader: includes cartoon type 1,4,7 -> trace code: String JmolViewer.runScript(String script) runs script immediately and returns output buffer code: continued work on PyMOL PSE file reader code: simplification of JmolViewer interface and access to global parameters: // several; methods were deprecated and removed in 13.1.15. All are accessible via "getXxxx" methods: abstract public float getFloat(int tok); abstract public int getInt(int tok); abstract public boolean getBoolean(int tok); //abstract public int getAnimationFps(); see getInt(T.animationFps) //abstract public boolean getShowHydrogens(); see getBoolean(T.showhydrogens) //abstract public boolean getShowMeasurements(); see getBoolean(T.showmeasurements) //abstract public boolean getAxesOrientationRasmol(); see getBoolean(T.axesorientationrasmol) //abstract public int getPercentVdwAtom(); see getInt(T.percentvdwatom) //abstract public boolean getAutoBond(); see getBoolean(T.autobond)) //abstract public boolean showModelSetDownload(); deprecated -- was just "true" ============================================================================= JmolVersion="13.1.14" new feature: JVXL vertex-only data encoding "none" allows hand-coding of JVXL files new feature: isosurface efvet reader data "0" is "indicated colors" -- isosurface "test.efvet" 0 JavaScript: WebGL fix involving Collections.list calling ArrayList.add() JavaScript: disambiguation of Mesh() JavaScript: changing to utf-8 String nonbinary reading of .po files JavaScript: localization working code: cleaning up of Escape and checks for array types code: JavaScript does not need a visible canvas to create images -- could allow for "headless" JS operation bug fix: isosurface boundbox plane .... bug fix: isosurface boundbox {pt1} {pt2} plane ... bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state bug fix: JavaScript minimization fix bug fix: sync socket connections not working bug fix: "navigate percent" broken bug fix: isosurface area/volume broken bug fix: JavaScript WRITE IMAGE with HTML5 does not allow change of width or height bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", bug fix: getProperty fileInfo fixed and documented bug fix: assign atom does not update selections for elements bug fix: FileDropper broken bug fix: LcaoCartoon "-sp3d" not working bug fix: PyMOL PSE files not accessible by Jmol app File...Open or drag/drop bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" bug fix: starting applet console takes two clicks bug fix: JavaScript SMILES bug (String.replaceAll() does not work bug fix: JavaScript LOOP command not implemented ============================================================================= JmolVersion="13.1.13" FEATURE CHANGE: multiple applets no longer share the same lighting space new feature: animation DISPLAY {atomset} - applies a filter to a running animation to display only a certain set of atoms. - for example: load test.pse animation display {act_site} // defined in test.pse new feature: animation MORPH n - where n is a number of frames to be inserted between trajectories - requires previous LOAD TRAJECTORY or the loading of a PyMOL PSE file having a movie (automatically a trajectory) - Jmol will do a linear morph as the animation runs. - for example: load test.pse animation morph 3 - could be used for a linear morph between just two structures: load trajectory "test1.pdb" "test2.pdb" animation morph 32 // animation will run 33 frames new feature: frame -x.y - negative decimals indicate a linear morph is requested between two trajectory frames. - for example: load test.pse frame -3.5 new feature: set celShading TRUE -- produces cel shading effect - see http://en.wikipedia.org/wiki/Cel_shading - introduced by N David Brown new Feature: Experimenting with ellipsoid {atom set} and ellipsoid $isosurfaceID new feature: PyMOL PSE reader enhancements -- labels, simple surfaces, measures new feature: isosurface xxxx MAP property COLOR -- allows inheritance of color from underlying atom (as in PyMOL) new feature: UHBD grid file reader new feature: DelPhi grid file reader new feature: load =xxx/ where xxx is a database code that can be set up in the future by a user. -- currently including mp MaterialsProject http://www.materialsproject.org/materials/%FILE/cif -- along with ligand, nci, nmr, pdb, pubchem -- see JmolConstants.databases for the full list. -- note that nci can take an additional tag such as /names after the name, and pubchem can take one before it: load =mp/1 load =nci/caffeine load =pubchem/caffeine load =pubchem/cid/2345 print(load('=nci/caffeine/names')) bug fix: set picking IDENT when picking is already ident can cancel a pending measurement bug fix: applet does not refresh when mouse exits with pending measurement bug fix: labels within fog should be hidden bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) bug fix: property_xxx does not work (since 10/3/12, 13.1.7) bug fix: The "show history" command is supposed to clear out the "show history" command itself, but only if it is a top-level command (from the console), but it does more than that if it is part of script("show history"). Probably true with all recent versions of Jmol. bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH, etc.) broken bug fix: JavaScript: zoomTo [seconds > 0]... and restore rotation|orientation [name] [seconds > 0] not waiting code: Refactoring class names to reduce JSmol JavaScript footprint ScriptVariable --> SV Token --> T BitSet --> BS BitSetUtil --> BSUtil Colix --> C Point3f --> P3 Point3fi --> P3i StringXBuilder --> SB Vector3f --> V3 JmolConstants --> JC code: shader functions removed from Colix; Shader class made nonstatic code: refactored to allow scriptless JavaScript. (reduces initial core code load size by 25%, to 2.5Mb) ============================================================================= version="13.1.12" new feature: PDB reading of X-PLOR using hybrid-36 and NAMD files using hex -- see https://www.schrodinger.com/AcrobatFile.php?type=supportdocs&type2=&ident=530 -- see http://cci.lbl.gov/cctbx_sources/iotbx/pdb/hybrid_36.py new feature: load xxx.pdb filter "TYPE i,n" -- loads custom text fields into the "atomType" property of an atom upon customized PDB file loading where i is the number of the column (starting with 1) and n is the number of columns -- text is trimmed -- e.g. load xxx.pdb filter "TYPE 73,4" loads four characters starting at column 73 as "atomType" (segID) -- to convert to a numerical value, convert that to .property_foo: load xxx.pdb filter "type 22,4"; {*}.property_seqNo = {*}.atomType new feature: PDB filter "TYPE 73,4=xxx" -- loads four characters starting at column 73 (1-based) as "atomType" -- loads only those atoms with atom types starting with "xxx" new feature: axes labels "a" "b" "c" "xxx" where "xxx" is the label for the origin bug fix: PDB file reading of remediated 1A7Y and 1E9W error due to too many CONECT bonds -- now reads HEADER columns 63-66 for 4-digit PDB ID. -- only if this ID is absent will the number of CONECT bonds be checked in decision to autobond bug fix/update: revision of the pages that make the About menu (application) in each language. -- Some changes that had been formerly applied to the English page are now in all. (Removal of copyright date in text) -- All About_xx.html files are now encoded and saved in UTF-8 w/o BOM, except Chinese which is in GB2312/GB18030. -- Extended characters in tr and zh that had become corrupt across revisions were restored from old ones. -- Several html header tags updated or added (html5 doctype, charset, lang) -- Hopefully all will display correctly after these changes! JavaScript: fix for SMILES matcher and compare({*},{*},"isomer") -- j2s reminder: Can't use Java new int[n][]; must use org.jmol.util.ArrayUtil.newInt2(n) JavaScript: going to Float64Array for all noninteger arrays -- all numbers double Note that this could cause differences with Jmol, but I think we will have to live with that. The problem was with (new Float32Array([13.48]))[0] != 13.48. So instead of trying to force floats, it seems to make more sense to me to force doubles, using Float64Array instead of Float32Array. Thanks given to Ira Hanson for clearing this up for me. JavaScript: JSmol writes PNG, PNGJ, JMOL, ZIP files from a web page JavaScript: JSmol writes text files from a web page ============================================================================= version="13.1.11" new feature: Jmol app "recent files" recognizes if file was drag-dropped or opened via "File Open" new feature: color cartoons red blue -- front/back colors -- preliminary - only for hermiteLevel = 0, not cartoonFancy -- a bit rough at the edges -- not in state bug fix: 13.1 does not calculate partial charges (mark/reset fault in reading resource files) bug fix: MOPAC2012 files not recognized bug fix: patch 3581394 - small fixes for cartoon meshes bug fix: 13.1.8 does not display translucent bonds when only bonds are translucent JavaScript: flat cartoons for WebGL using mesh JavaScript: adds XML model file readers -- tested: VASP, XODYDATA, CML, Chem3D, MolPro, XSD code: refactoring for JavaScript popup/modelkit menus code: GT optimization, refactoring code: Naga sockets upgrade to Naga-3_0. (MolecularPlayground and jsonKiosk) ============================================================================= version="13.1.10" FEATURE CHANGE: set perspectiveMode removed -- nonlinear version 10 perspective mode no longer supported bug fix: !quit was not stopping animation and vibration bug fix: slowed zoomTo in Java version of 13.1.9 bug fix: PDB occupancies for first atoms may be 0.0 instead of 1.0 (broken in 11.7) bug fix: select *W does not work bug fix: setEllipsoid... options not implemented for nonthermal ellipsoids in 13.0 or 13.1 bug f
Source: README-14.1.2.properties, updated 2013-12-15

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