___JmolDate="$Date: 2013-12-29 18:37:43 -0600 (Sun, 29 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="14.0.3"
(synced with 14.1.3 2013.12.29)
new feature: filter "MODCELL=x"
-- incommensurate composite readers Jana2006 and CIF
-- sets base cell to specified subsystem
new feature: MSCIF reader now allowing up to d=10; was d=6
new feature: escape pressed cancels pending measurement
new feature: {xxx}.getProperty("yyy")
-- only for FIRST atom
-- returns getProperty("atomInfo.yyy", {xxx})[1] (not xxx.yyy.all)
new feature: unitcell {atomset}
-- unit cell based on first atom of atom set.
-- canceled by any unitcell {none}
or other unitcell command other than on/off and width
new feature: altloc set for msCIF _atom_site_subsystem_code
-- sets % and also configuration
-- prevents covalent bonding between subsystems
new feature: select ON ; select OFF
-- same as selectionHalos ON/OFF
-- deprecates selectionHalos command
new feature: atomSet1.distance.min(atomSet2, TRUE)
new feature: atomSet1.distance.min(point, TRUE)
new feature: atomSet1.distance.max(atomSet2, TRUE)
new feature: atomSet1.distance.max(point, TRUE)
-- returns single closest/furthest atom in atomSet1 from point or atomSet2
bug fix: incommensurate composite structures not packed into unit cell properly
bug fix: incommensurate composite structures - wrong unit cell for d > 1
bug fix: if load "" fails, last file name is lost
bug fix: print a (operator) b not processing string parameter B consistently across operators
bug fix: composite structures reading for JANA2006 M50/M40 files
bug fix: capture time slightly off; needs 50 ms addition. This may vary with rendering speeds.
bug fix: CIF reader goes into molecular mode even if geom_bond block is all "? ? ? ? ?"
bug fix: n-d incommensurate modulated composite structures (preliminary testing)
bug fix: getProperty atomInfo broken for modulated atoms
bug fix: x.distance.min(y) broken
code: generic javajs.util.Matrix class added based on Jama code for inversion using L/U decomposition
JmolVersion="14.0.2"
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="14.0.1"
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 fix: nonthermal ellipsoids broken in 13.1.
JavaScript: !quit and navigation enabled
JavaScript: script queue enabled
JavaScript: move thread implemented; needs navigation threads
code: JmolApplet0_Navigate.jar and JmolApplet0_Parallel.jar added
code: Navigator separated from TransformManager11
code: TransformManager10 removed
code: TransformManager11 combined with TransformManager
=============================================================================
version=13.1.9
new feature: MO or (ISOSURFACE MO) DENSITY
-- electron density
-- same as MO [1] SQUARED
new feature: MO HOMO|LUMO|NEXT|PREV|[c1 n2 c2 n2...] SQUARED
-- Squares wave functions as it combines them.
-- That is, displays the collective electron density (if occupied)
-- if [...] is not given, groups orbitals by energy
-- examples:
load c6h6.smol;mo homo squared // displays symmetric squared sum of two degenerate orbitals
load co2.smol; mo homo squared // displays cylindrical electron density
mo next squared // lumo, provided homo was just displayed
bug fix: Molden reader tweaks
bug fix: Jmol application toolbar picking tool should not select none
bug fix: ellipsoid rendering fails
bug fix: translucent echo oddities in Jmol 13.1.8
bug fix: lost volume rendering in 13.1.8
bug fix: CASTEP density reader fails to reset origin to 0 0 0 in mapping
bug fix: UTF files with BOM (byte order marker) present not read correctly
bug fix: UTF files within GZIP or ZIP files not read correctly
bug fix: set picking draw no longer works in Jmol 13.0 or 13.1
bug fix: translucent echo backgrounds lost in 13.1.8
bug fix: select resno=@{n+3} fails in 12.2, 13.0, and 13.1
bug fix: isosurface AtomicOrbital broken in 13.1.8
JavaScript: removing ambiguity in AtomObject in setColix(short, int, int) and (int, short, int)
JavaScript: binary Spartan SMOL reader enabled
- nice IEEE calculator: http://www.merlyn.demon.co.uk/js-exact.htm#DW4
JavaScript: delay, hover, animation, vibration, moveto, spin, timeout
JavaScript: full binary loading for JavaScript -- tested only in Firefox, but specifically
designed for Chrome's insistence that synchronized AJAX processes must not be binary
JavaScript: base64 translation of encoded binary strings from JS file reading
prefix: ";base64," initiates decoding.
JavaScript: com.json JSON package removed due to licensing issues
JavaScript: JSmol -- all references to InputStream.read(byte[]) --> InputStream.read(byte[], 0, len)
to speed file reading processing
JavaScript: JSmol -- float[].clone(), int[].clone() not supported in Java2Script
JavaScript: java.text.DateFormat not supported in Java2Script
JavaScript: Note -- org.jmol.adapter.smarter.Atom is not fully cloned
(anisoBorU and ellipsoid are not copied
and their values must be considered "final")
code: adding quotes to above properties allows them to be used in JavaScript; j2sNative in JmolConstants.java
code: refactoring org.jmol.util into org.jmol.io and org.jmol.io2
=============================================================================
version=13.1.8
new feature: much better text rendering using 3-bit translucency
bug fix: boundbox $pmeshID, center $pmeshID, and zoomto $pmeshID not implemented
bug fix: stronger (bold) frame labels
bug fix: no automatic change to bold for antialiasDisplay or PovRAY
bug fix: try/catch not working when embedded in another context
bug fix: JmolData not producing output for PRINT commands
bug fix: JmolData setting haveDisplay true, then failing to get mouse manager
bug fix: MRC file reader not setting default cutoff correctly
bug fix: (13.1 only) MRC/DNS6 file readers fail
bug fix: MRC surface file reader with symmetry error
bug fix: (13.1 only) minimization broken
code: clearing font cache upon zap.
code: HTML5-only JavaScript full text working
code: HTML5-only JavaScript version working
=============================================================================
version=13.1.7
FEATURE CHANGE: getProperty isosurfaceInfo no longer returns vertex data
new feature: getProperty isosurfaceData returns vertex data
new feature: set cartoonFancy -- creates elliptical ribbon for cartoons
-- if ribbonAspectRatio is its default value of 16, it is reset to 4 while cartoonFancy = true.
bug fix: (13.1 only) reading of states with select BONDS fails to select bonds broken in 13.1.6
bug fix: (13.1 only) centered/right-aligned text only aligned after first line
bug fix: export WRL missing various objects requiring transformMatrixInv
bug fix: export may be missing protein cartoon turn
bug fix: set ribbonAspectRatio improperly widens ribbon
bug fix: zShadePower should not be static (affecting all applets/Jmol application frames)
bug fix: write OBJ xxx.obj not working (but write xxx.obj is fine)
bug fix: cartoons (with hermiteLevel > 1) adjusted to have smooth
normals between segments (Alexander Rose)
also, hermiteLevel >= 6 now gives ellipse cross-section
recommended settings: set hermiteLevel 6;set ribbonAspectRatio 4
bug fix: JmolControls.js had broken radio buttons
bug fix: DRAW {x y z} "title" can fail in multimodel cases with translucency
=============================================================================
version=13.1.6
new feature: showTiming
new feature: CIF reader reads assembly information
-- load =1vif.cif filter "ASSEMBLY 1"
-- load =1vif.cif filter "ASSEMBLY 1;$A" # just label_asym_id A
-- load =1vif.cif filter "ASSEMBLY 1;!$C" # just label_asym_id values not C
new feature: LOAD "xxx.cif" APPEND "appendedData" @x
-- specifically for CIF files, reads a CIF file, appending string in variable
-- intentionally not documented.
-- feature particularly for RCSB (John Westbrook), so, for example:
Var x = load("test.txt")
load "1vif-early.cif" append "appendedData" @x FILTER "assembly 1;$A"
-- or in one line:
load "1vif-early.cif" append "appendedData" @{load("test.txt")} FILTER "assembly 1;$A"
-- where, perhaps, x =
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2,3,4
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.symmetry_operation
1 x,y,z
2 y,x,-z+1
3 -x+1,-y+1,z
4 -y+1,-x+1,-z+1
#
new feature: LOAD "xxx.cif" APPEND DATA "appendedData" .... end "appendedData"
-- specifically for CIF files, reads a CIF file, appending string in lines of script
-- intentionally not documented
-- most important for saving the state:
load "1vif-early.cif" append data "appendedData"
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2,3,4
_pdbx_struct_assembly_gen.asym_id_list A,B,C
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.symmetry_operation
1 x,y,z
2 y,x,-z+1
3 -x+1,-y+1,z
4 -y+1,-x+1,-z+1
#
end "appendedData" FILTER "assembly 1;$A"
-- option reserved to allow different data names for different purposes
-- not general yet -- specific to CIF reader.
bug fix: PDB 4B2Q, with faulty (incomplete) REMARK 350 not read
code: successfully refactored for JavaScript
(see http://chemapps.stolaf.edu/jmol/jsmol-10-1/jsmol2.htm)
-- note that all code development is done in Jmol, then
Java src code is transferred to JSmol project
-- adding:
javax.util.BitSet
javax.util.StringXBuilder
-- streamlining:
javax.vecmath...
-- removed all references to StringBuffer
-- StringXBuilder allows optimization of performance in JavaScript
-- workaround for Java2Script compiler bug setting "char x;" to 0
-- Java2Script compiler is not distinguishing int[] from float[] when creating the array
-- StringXBuilder takes care of adding ".0" to floats and doubles, but
we need to be on the lookout for not places where we are constructing
a string where the difference between an int and a float is significant.
-- optimize class hierarchy return by cataloging classes
as org_jmol_xxxx in addition to org.jmol.xxxx
-- tie in graphics on JavaScript side
-- add fonts
-- add "billboard" objects such as labels, 3D echos, etc.
-- add 2D echos
-- ultimately write an asynchronous version of JSmol
code: org.jmol.jvxl.readers classes accessed reflexively (for JavaScript optimization)
code: JSmol classes incorporated into Jmol code -- org.jmol.awtjs, org.jmol.appletjs, org.jmol.exportjs
code: refactored for JavaScript (mostly removing ambiguity in method names)
=============================================================================
version=13.1.5
bug fix: CASTEP PHONON files not loading
code: refactored for JavaScript
=============================================================================
version=13.1.4
new feature: ISOSURFACE PLANE ... MAP ... LATTICE {i j k} [volume data]
-- allows periodic volume data to be mapped to a plane
based on a specified translational lattice
-- for example: isosurface plane x=2 map LATTICE {1 2 2} "data.dat"
new feature: POLYHEDRA {atom1} to {atoms_including_atom1}
-- polyhedra with or without central atom, but with a reference atom
bug fix: translate selected x ... bug
bug fix: ISOSURFACE saving in state broken 7/30/12 in 13.0.RC3
bug fix: simple isosurface PLANE not saved in state
bug fix: isosurface command with MAP from state when saved to state may fail
bug fix: 13.1.2 offsets label positions incorrectly
code: refactored for JavaScript
=============================================================================
version=13.1.3
bug fix: 13.1.2 breaks loading of ZIP files
bug fix: CUBE reader reading atom Z numbers as partial charge
bug fix: 13.1.2 breaks LOAD ?
=============================================================================
version=13.1.2
new feature: cache ADD "filename"
-- adds a file into the memory cache as a set of bytes
new feature: cache REMOVE "filename"|ALL
-- removes a file from the cache
new feature: show cache
-- displays the cache as an array
new feature: cache() function
-- returns the cache as an associative array {filename: nBytes, filename: nbytes,...}
new feature: write INLINE "xxxx" "filename"
for example: write INLINE "testing" "myfile.txt"
for example: write INLINE @{load("$caffeine")} "caffeine.mol"
new feature: set defaultDropScript for drag-drop and File|Open
bug fix: translate x 0 does not recenter the model in the window
bug fix: PDB polymers of length 1 allow size to be set and appear {visible} but are not
bug fix: OPEN dialog doesn't allow for no PDB cartoons.
bug fix: open dialog for 1-residue PDB files does not show atoms.
bug fix: pngj storage of Spartan directory zip files or Spartan directories cannot be read
because the PNGJ files created do not contain the necessary files from the directory
code: (JmolViewer) public void cacheFile(String fileName, byte[] bytes)
-- allows a mechanism for applets or embedding apps to deliver file content as bytes
-- for applets, first getPropertyAsJavaObject("Viewer")
code: refactored for Java2Script due to inner class bug there.
=============================================================================
version=13.0.1
APPLET:
-- a new OOP JavaScript interface (Jmol-JSO)
allowing nonJava options such as ChemDoodle and GLmol
as well as JME/JSpecView connectivity
-- JmolData full "headless" operation for server-side processing
BIOPHYSICS:
-- COMPARE command
FILE READING:
-- reading of JCAMP-DX files having structure/spectra assignment data
using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
-- Gaussian log reading of Natural Transition Orbitals
-- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers
FILE WRITING:
-- write PNGJ files encapsulate all model file data into one PNG file
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
-- write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations
ISOSURFACES:
-- isosurface caching
-- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)
MINIMIZATION:
-- MMFF94/UFF minimization and energy calculation
MOLECULAR DATA:
-- show CHEMICAL
-- show NMR
MOLECULAR PLAYGROUND:
-- MolecularPlayground -- remote status and remote control
SOLID-STATE PHYSICS:
-- solid state physics support
SPECTROSCOPY:
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation
STRUCTURE SEARCHING:
-- extended Jmol SMARTS searching
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
=============================================================================
version=13.0.RC7_dev
bug fix: isosurface CAVITY not saved in state
=============================================================================
version=13.0.RC6
bug fix: isosurface CAVITY not saved in state
bug fix: Gaussian reader not reading "AO basis set in the form of general basis input" properly ("Gen" keyword)
bug fix: Gaussian reader not reading "7D 0" correctly
bug fix: Trajectories still broken for PDB files
code: all import foo.*; removed, specified
=============================================================================
version=13.0.RC5
bug fix: broke trajectories in 13.0.RC4
=============================================================================
version=13.0.RC4
new feature: write SCENE PNG|PNGJ "xxxx.spt" option to create PNG or PNGJ files (same file, just different extension)
new feature: "menu" as sole contents of a script pops up the context menu
-- joins category of special commands, including "exit" "pause" and "quit"
bug fix: load append TRAJECTORY (upper case) fails
bug fix: load append trajectory "$mannose" fails (loads two models)
bug fix: load trajectory "maleic.cif" fails with cryptic error message (not appropriate for trajectory loading)
bug fix: undocumented and inaccurate CALCULATE VOLUME removed
=============================================================================
version=13.0.RC3
new feature: automatic PNGJ file caching for immensely faster loading
new feature: write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
new feature: isosurface CACHE <surface creation parameters> ....
-- parameter CACHE along with isosurface creation or alone instructs Jmol to
immediately create JVXL data for the specified surface and to load that data instead.
The surface remains in memory (in this version of Jmol) can can be used again
using cache://isosurface_<ID> where <ID> is the isosurface ID such as "isosurface1".
-- The command ISOSURFACE CACHE alone will cache the current isosurface
-- If the cache is no longer needed, then RESET CACHE will release the memory used to hold the JVXL data for the isosurface
-- The result should be essentially equivalent to the original command.
(It is recommended that the original be a relatively simple command, because not all nuances
of an isosurface may be stored in the JVXL data.)
-- THIS OPTION IS NOT COMPATIBLE WITH SAVING THE STATE AS AN SPT FILE.
-- Instead, one needs to save the state in PNGJ or JMOL format, where the cached isosurface
can be reloaded from a file saved in the PNGJ or JMOL zip directory
bug fix: load a model, then load append TRAJECTORY -- will fail
bug fix: load APPEND xxx where xxx is FILE, INLINE, SMILES, TRAJECTORY, MODEL
all save incorrect LOAD command in state
bug fix: shelx reader (.res) not assigning space group name or applying normalization
=============================================================================
version=13.0.RC2
bug fix: isosurface molecular producing artifacts
bug fix: isosurface select {...} molecular not excluding all other atoms for troughs
new feature: Gaussian log reading of Natural Transition Orbitals
new feature: isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)
bug fix: isosurface moved by atom connection not saved correctly in state
bug fix: isosurface SET n not read properly from JVXL file.
ant fix: changing the way Jmol.properties is handled vis-a-vis # and underscores
bug fix: isosurface SOLVENT producing artifacts --- needed minimum resolution
bug fix: isosurface with selected set not delivering just those vertices for within distance calc
bug fix: isosurface CONNECT in documentation but never implemented
bug fix: isosurface SET n not saved in state or JVXL file.
bug fix: Gaussian reader fails for 2-digit basis orbital names such as "12XX"
bug fix: PNGJ creation not handling same-file or same-name issues.
bug fix: isosurface SOLVENT producing cavity-like artifacts
bug fix: SCENE writing with toggle (pause scene 2 ... pause scene 2) in error
bug fix: SCENE min spt script needs wrapping by pathForAllFiles
bug fix: isosurface MINSET or SET not compatible with SLAB
bug fix: show $d1 where d1 is a DRAW object broken
bug fix: calculate hydrogens incorrect for proteins
=============================================================================
version=13.0.RC1
-- a new OOP JavaScript interface allowing nonJava options and JME/JSpecView connectivity
-- MMFF94/UFF minimization and energy calculation
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation
-- reading of JCAMP-DX files having structure/spectra assignment data
##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations
-- write PNGJ files encapsulate all model file data into one PNG file
-- extended Jmol SMARTS searching
-- show CHEMICAL
-- show NMR
-- solid state physics support
-- MolecularPlayground -- remote status and remote control
-- COMPARE command
-- JmolData full "headless" operation for server-side processing
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
-- isosurface caching
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
=============================================================================
version=12.3.33 (13.0.RC1)
new feature: full JSpecView support for NMR
-- integration, peak listing, measurements
-- printing with peak measurements
new feature: measure(a b "minArray")
-- measures minimum distance from atom set a to atom set b atom by atom
-- return array with number of elements corresponding to the number of selected atoms
-- for example: {1.1}.property_distTo12 = measure({1.1}, {1.2} "minArray"); color property_distTo12
new feature: {x}.property_d = [....]
-- allows for [....] to have length of the number of atoms in {x}
in which case the values are assigned on a 1:1 basis
new feature: PDB reader reads gromacs-created "pdb_wide_format" files
and also automatically reads PQR based on gromacs REMARK
bug fix: select within(1.0, withinallmodels, 1.1) and 1.2 causes exception
bug fix: script xxx(yyy).spt broken
=============================================================================
version=12.3.32
FEATURE CHANGE: LOAD "myfile.xxx" with no additional parameters
where xxx is "png" or "pngj" or "spt"
now assumes these are scripts and runs SCRIPT "myfile.spt" instead
new feature: write SCENE "xxxx.spt"
-- creates pngj files
-- using "xxxx.png" will STILL USE "xxxx.spt" but will create PNGJ files with ".png" extensions
-- scene creation with linked PNGJ files
-- xxxx.spt should include "pause scene n" commands, which are then
used to separate the script into separate scenes. "n" must be an integer.
-- Two files are created for each scene (pngj unles:
xxxx_scene_n.min.pngj very small; does not contain anything more than
an image, JmolManifest.spt, and scene.spt
xxxx_scene_n.all.pngj adds all necessary files, plus script.spt
-- Either of these files can be used, but if x.min.pngj is used,
then x.all.pngj needs to be present as well in the same directory.
new feature: drawHover displays ID for isosurface and reports to hoverCallback
new feature: load "$$xxxxx" loads 2D version, not 3D (used for JmolData connection with JME)
-- basically, use of two $ signs results in drop of "&get3d=True" from NCI call
bug fix: compiler not synchronized; allows jmolEvaluate() to fail if two threads access it simultaneously
bug fix: getproperty isosurface after a "no-surface" isosurface call like load $water;isosurface sasurface fails
bug fix: color for hbonds/ssbonds backbone incorrect
=============================================================================
version=12.3.31
bug fix: isosurface plane ... within ... map ... fails
bug fix: write broken in 12.3.30
=============================================================================
version=12.3.30
new feature: atom properties sx, sy, sz, and sxyz -- screen coordinates
new feature: app flag -r restricts file access
-- like -R, but allows reading of ".spt" files
new feature: load("http://.....?POST?_PNGJBIN_")
-- accompanies load("http://....?POST?_PNG_") and load("http://....?POST?_PNGJ_")
-- sends PNGJ image to server as byte array instead of as application/octet-stream
instead of Base64-encoded string and application/x-www-form-urlencoded
-- return value is whatever server is set up to send
new feature: select within(distance, $drawID)
bug fix: isosurface plane... map property temperature not working
bug fix: PNG files written by Jmol from 12.3.7 - 12.3.29 have incorrect
checksum. Browsers do not seem to care, but Java does
when loading a background image in Jmol!
bug fix: background image NONE fails
bug fix: if(...) statement (no braces) broken in 12.3.21
=============================================================================
version=12.3.29
new feature: (JmolCore.js/JmolApplet.js/JmolCD.js/JmolApi.js)
-- changes "useChemDoodleOnly" to "disableJmol"
in preparation for non-ChemDoodle plug-ins similar to JmolCD.js
-- allows for default values for Info
-- adds Info.src
-- similar to src in an <image src="xxx.png" /> tag
-- turned into LOAD "xxx.png"
-- more efficient coding
new feature: set MESHSCALE (default 1) also allows isosurface/mo mesh scaling
-- was DOTSCALE in 12.3.26, but that is not appropriate
new feature: Mopac archive reader, including internal coord. defs
-- use FILTER "NOCENTER" to NOT center atoms in unit cell
-- use CENTROID for complete molecules with centroids within unit cell
-- use PACKED CENTROID for complete molecules with any atoms within unit cell
-- properties stored in auxiliaryInfo
use getProperty auxiliaryInfo or x = getProperty("auxiliaryInfo".foo) to retrieve
new feature: set pathForAllFiles "..."
-- all files, local or remote, will be taken from the indicated path
-- the indicated path may be a zip file entry (ending with "|")
-- automatically reset to '' in case of an unrecoverable error in execution
-- used for creating JMOL files containing user scripts instead of a state
-- disallows all writing and image creation
-- scripts including prompts to read wildcard files (for example, "load ?")
will still prompt for those and read them properly
new feature: write SCRIPT ["scriptFileName", "filename2","filename3",...] PNGJ|JMOL...
-- syntax is WRITE SCRIPT followed by an array of file names
then whatever else is necessary to create the PNGJ or JMOL file
-- for example: write script ["wind.spt"] test.jmol
-- Creates a single PNGJ or JMOL file that instead of containing the state
contains the script and additional files listed by the user.
The first script is run, and it is presumed that the other files are
needed for full execution of that script.
-- Allows for creating PNGJ and JMOL files that run as animations, not just final states.
-- Jmol will automatically add any files current to the state,
but other files not indicated by the state (script files especially)
required for the script to run need to be indicated by the user.
-- When the script is executed, pathForAllFiles is set to the zip file
itself. Thus, even scripts containing references such as "script2.spt" or "=xxxx"
can be run, provided the user supplies script2.spt xxxx.pdb.gz as one of the required filenames.
-- Note that if a file is saved locally using LOAD =xxxx AS t.pdb, Jmol will automatically use
the local file reference to t.pdb, not the RCSB reference.
-- If the file is loaded using only LOAD =xxxx, then Jmol will reload the
remote file and store it in the PNGJ/JMOL file as xxxx.pdb.gz.
bug fix: Jmol 12.3.28 breaks writing JMOL/PNGJ files
-- Jmol 12.3.28 release DELETED
bug fix: modelkit mode creating atoms after load "@x" fails
bug fix: script javascript:xxxx() broken for Jmol object javascript
bug fix: JmolCore.js fix for getPropertyAsArray
bug fix: draw arrows not adjustable using set picking draw
bug fix: Exception for select within(molecule,...) when atoms have been deleted
=============================================================================
version=12.3.28
DELETED 6/10/2012 due to breaking of JMOL/PNGJ format
new feature: isosurface ... map PERIODIC ...
-- allows mapping grid-based data beyond the unit cell defining its grid
new feature: write VIBRATION n
-- writes 20 * n frames
-- n periods
-- some issues with first frame and value of n
new feature: load PACKED CENTROID
-- only complete molecules having one or more atoms within or on the face of the unit cell
-- may not preserve # of atoms of unit cell
-- reverts to simple PACKED if this is a single-molecule solid (such as diamond)
new feature: unitcell $isosurfaceID
new feature: unitcell [{center}, {a}, {b}, {c}]
-- sets unit cell for current model only
new feature: "plot data" command by itself opens a new frame with just one atom in it, at (0,0,0)
new feature: isosurface SLAB BRILLOUIN (or WIGNERSEITZ)
-- transposes an isosurface into the Brillouin-zone/Wigner-Seitz unit cell
-- based on the isosurface's vectors if there is no unit cell for this model.
-- for creating isosurfaces of Fermi surfaces
bug fix: LOAD with SPACEGROUP or RANGE or UNITCELL should default to {555 555 -1} (packed) lattice
bug fix: JVXL reading of mapped data does not use file's rendering option for lighting
bug fix: default measure dotted lines are too thin for export
bug fix: measures not offset correctly when given width in line.
=============================================================================
version=12.3.27
new feature: [menu] vibration [*,/] 2
new feature: XSF isosurface reader
new feature: load CENTROID
-- only complete molecules having centroid in unit cell
-- preserves # of atoms of unit cell
bug fix: write PNGJ broken in 12.3.26
bug fix: 12.3.26 breaks Jmol/JspecView connection
bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group
bug fix: reading of JVXL-version 1 (nonXML) files does not display colors
bug fix: translate y 10 works, but translate Y 10 does not
=============================================================================
version=12.3.26
new feature: Jmol SMARTS searching can include full Jmol selection syntax within
an atom primitive using the "atomType" option and "select:":
load caffeine.xyz
print {*}.find('{c}$(select _N and connected(2, _C))')
new feature: model ID "xxx" (or frame ID....)
-- sets the model's ID to "xxx"
-- can be used to switch to that model using model "xxx"
-- can be targeted file-specifically using "filename#xxx"
-- if two models have the same ID and no filename is given,
then the first model found becomes the current model
-- used for correlating non-Jmol synced applets
new feature: script "t.spt"(...variables...)
-- quotes are optional if file name does not include " " or "("
-- "script" is optional if file name is quoted or ends with ".spt"
-- allows passing variables to a script much like a function call
-- variables will be in VAR named "_arguments" within that script (like JavaScript)
-- _arguments, like all arrays in Jmol, is 1-based, 0-terminated (unlike JavaScript)
-- _arguments is unsettable by the user
-- for standard script functions, _arguments will be []
-- for example, if test.spt is simply "show _arguments", then
load $caffeine
test.spt({*}, {*}.xyz ,35, [1,2,3,4])
will output:
_arguments = [({0:23}),{-0.086670786 -0.02787502 5.6667876E-4},35,[1,2,3,4]]
new feature: set forcefield "UFF" or "MMFF"
-- default is MMFF
-- automatically switches to UFF if atom types cannot be set
-- minimizationCallback reports actual force field used
new feature: set energyUnits kJ|kcal
new feature: antialiased display and image creation uses larger mesh scaling for cleaner look
code: adding empirical rules to MMFF94 calculation
checkmm.spt;checkAllEnergies
checking calculated energies for 761 models
1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
5 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
6 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
for 761 atoms, 6 have energy differences outside the range -0.1 to 0.1
with a standard deviation of 0.05309403
bug fix: nested SMARTS strings can give incorrect response
load data "mol"
C:/jmol-dev/bobtest/t6.mol
__Jmol-12_05191218593D 1 1.00000 0.00000 0
Jmol version 12.3.26 2012-05-19 18:34 EXTRACT: ({0 3 4})
3 2 0 0 0 0 1 V2000
2.89480 4.81990 0.01710 N 0 0 0 0 0 0
3.52580 2.75730 -0.17290 N 0 0 0 0 0 0
3.94370 4.03730 -0.25710 C 0 0 0 0 0 0
1 3 2 0 0 0
2 3 1 0 0 0
M END
end "mol"
select search("$([#7][#6]([#7&!$([#7][O])])=[#7])")
show selected
was returning 1 atom, but should be 0 (because there are only two N atoms!)
bug fix: measurementUnits = "au" does not work
bug fix: select 1.0 fails
bug fix: COMPARE broken
bug fix: Writing file into .jmol file after reading it from another results in the whole
zip file being copied into the new .jmol file.
=============================================================================
version=12.3.25
new feature: MMFF94 single point energy calculation and minimization
set forcefield "MMFF"
checkmm.spt
checkmm "AMHTAR01";minimize energy
AMHTAR01 Initial E = 66.180 kcal/mol # should be 66.18011
checkmm "ARGIND11";minimize energy
ARGIND11 Initial E = -207.436 kcal/mol # should be -207.43598
validation complete. The following 13 structures (of 761) do not validate to within 0.1 kcal/mol
1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
-- MMFF94 ignores 1 of 5-membered ring torsions for a 1-oxo-2-oxa-bicyclo[3.2.0]heptane
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
-- MMFF94 ignores 5-membered ring issue for S-S-containing ring
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
-- MMFF94 uses some sort of undocumented empirical rule used for 1 torsion not found in tables
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
-- ignores 5-membered ring for S (note, however, this is not the case in BODKOU)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
5 KEPKIZ E= 61.127 Eref= 61.816277 diff= 0.68927765
-- MMFF94 requires empirical rule parameters
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
6 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
-- MMFF94 ignores all 5-membered ring torsions in ring with P
-- (note, however, this is not the case in CUVGAB)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
7 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
-- MMFF94 ignores all 5-membered ring torsions in ring with P
-- (note, however, this is not the case in CUVGAB)
-- MMFF94_bmin.log: WARNING - Conformational Energies May Not Be Accurate
empirical-rule-requiring models: (all are nonaromatic heterocycles)
8 ERULE_01 E= -22.582 Eref= -21.515108 diff= 1.0668926
9 ERULE_02 E= 29.407999 Eref= 29.799572 diff= 0.39157295
10 ERULE_03 E= -3.326 Eref= -2.9351802 diff= 0.3908198
11 ERULE_04 E= -2.572 Eref= -2.31007 diff= 0.26193
12 ERULE_07 E= 2.873 Eref= 3.16775 diff= 0.29474998 (fixed in 123.3.26 by correcting angle calc)
13 ERULE_08 E= 33.734 Eref= 34.41382 diff= 0.6798172
bug fix: compare {22-31} {7-16} subset {*.ca} should work without ATOMSET next
bug fix: compare {22-31} {7-16} should work, using {spine} as default
bug fix: isosurface molecular for certain flat models will fail to cap H atoms
bug fix: calculate partial charge fails after model kit changes
(because Bond[] bonds field not cleaned
bug fix: dipole command fails after model kit changes
code: refactoring of minimize for generalization
=============================================================================
version=12.3.24
new feature: SMARTS search for atom type using quotes: ["37"]-["58"]
new feature: SMARTS option /aromaticdouble/ allows distinguishing between aromatic single and double bonds
new feature; SMARTS option /aromaticstrict/ checks 6-electron rule for aromatics
new feature: CALCULATE partialCharge does MMFF94 charge calculation
-- all atom types validated
-- charge values validated to +- 0.001001 over the 761-atom dative validation set
new feature: isosurface CACHE
-- creates a JVXL version of the surface (possibly outside of Jmol, but that's not implemented yet)
-- saved by write JMOL as a JVXL file "isosurface_ID"
(where ID is the original isosurface ID) within the JMOL zip collection
-- Warning! not saved using write SPT
***ALWAYS*** use write JMOL or write PNGJ after using the CACHE option, not write SPT
-- invoked by isosurface file "cache://isosurface_ID"
-- cleared by reset CACHE
-- allows rapid recreation of an isosurface across file loads
-- possibly limited to a subset of surface types
-- not fully tested
new feature: write ... "http://....."
-- POSTs JMOL or IMAGE or structure or whatever to a server as application/octet-stream
-- to be used in Proteopedia for saving a fully self-contained state
new feature: load filter "CENTER" -- centers models on the first model as they are loaded
new feature: load filter "NAME=..." -- loads only those models with a name that contains ...
new feature: calculate partialcharge
-- works on currently selected set of atoms
-- uses MMFF94 charge calculation (unverified; most certainly not quite correct)
-- preliminary only; working on validation
bug fix: x = {"c1": 3}; if(x["c1"]) should return TRUE
code: Simple way to assign MMFF94 atom types and partial charges
-- N,S-containing compounds not validated; CHO-containing compounds partially validated
bug fix: MOL2 reader assuming PDB for non-PDB format files (such as MMFF94-dative.mol2)
bug fix: label %W not working properly for non-PDB files
bug fix: write MOL does not save partial-single bond as type 8 ("ANY")
bug fix: set echo IMAGE fails (since 12.3.20)
code: (applet) JmolCore.js free of need for JSON
=============================================================================
version=12.3.23
new feature: (applet) new interface for Jmol as an HTML object as well as full support on all platforms
using a ChemDoodle fall-back option for Java/Applet-challenged platforms (iPad,iPhone,Android)
Note that Jmol.js is no longer required, but not all of the features of Jmol.js are in place yet
allows Jmol applets to be created on a page with more flexibility and extendability
possibly using infrastructure of ChemDoodle for multiplatform doodlable structures
required/optional libraries (preferably in the following order):
jQuery.min.js -- required for ChemDoodle or any server-based options
gl-matrix-min.js -- required for ChemDoodle option
mousewheel.js -- required for ChemDoodle option
ChemDoodleWeb.js -- required for ChemDoodle option
JmolCore.js -- required
JmolApplet.js -- required
JmolCD.js -- required for ChemDoodle option
JmolApi.js -- required
Allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
or applet-challenged (Android/iPhone) platforms, with automatic switching to
whatever is appropriate. You can specify "ChemDoodle-only", "Jmol-only", "Image-only"
or some combination of those -- and of course, you are free to rewrite the logic below!
Allows ChemDoodle-like 3D and 3D-faked 2D canvases that can load files via a privately hosted
server that delivers raw data files rather than specialized JSON mol data.
Access to iChemLabs server is not required for simple file-reading operations and
database access. PubChem and image services are provided by a server-side PHP program
running JmolData.jar with flags -iR (at St. Olaf College).
For your installation, you should consider putting JmolData.jar and jmolcd.php
on your own server. Nothing more than these two files is needed on the server.
The NCI and RCSB databases are accessed via direct AJAX if available (xhr2).
new feature: PubChem search for name (which can be a CAS number), cid, or SMILES using ":"
from pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
(many thanks to Evan Bolton and Paul Thiessen (NIH) for their assistance on this.
load :name:tylenol # or load :tylenol
load :cas:103-90-2 # or load :103-90-2
load :cid:1983 # or load :1983
load :smiles:C/C=C/C
bug fix: callback functions for modular calls: applet0.readCallback(....)
bug fix: Molden reader problems reading frequencies
bug fix: VASP reader with {n n n} and vibration vectors problem
bug fix: in 2bat, SIA was considered part of the carbohydrate chain because we were not checking bonding
=============================================================================
version=12.3.22
new feature: Jmol extensions to ChemDoodle allow display of Jmol, ChemDoodle-equivalent (simple model only),
or just an image with server-side JmolData.jar support.
JmolCD.js -- Jmol ChemDoodle extension author: Bob Hanson, hansonr@stolaf.edu 4/16/2012
requires ChemDoodleWeb.js and ChemDoodleWeb-libs.js
prior to JmolCD.js
allows Jmol applets to be created on a page with more flexibility and extendability
using much of the infrastructure of ChemDoodle.
allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
or applet-challenged (Android/iPhone) platforms, with automatic switching to
whatever is appropriate. You can specify "ChemDoodle-only", "Jmol-only", "Image-only"
or some combination of those -- and of course, you are free to rewrite the logic below!
allows ChemDoodle-like 2D and 3D canvases that can load files via a privately hosted
server that delivers raw data files rather than specialized JSON mol data.
access to iChemLabs server is not required for simple file-reading operations and
database access. Database and image services are provided by a server-side PHP program
running JmolData.jar with flags -iR.
In this case, the NCI and RCSB databases are accessed via a St. Olaf College server,
but for your installation, you should consider putting JmolData.jar and jmolcd.php
on your own server. Nothing more than these two files is needed on the server.
new feature: write CD (simple ChemDoodle JSON format -- atoms and bonds only)
For example: java -jar JmolData.jar -iRJ "load $tylenol;print write('cd')"
generates: {"mol":{"a":[{"x":0.20549999,"y":0.8303,"z":0.3823},{"x":0.6906,"y":-1.4656999,"z":-0.14220001},{"x":1.5485,"y":1.1359,"z":0.2829},{"x":2.0332,"y":-1.1585,"z":-0.24180001},{"x":-3.9799001,"y":-0.1617,"z":0.1295},{"l":"H","x":4.2731,"y":0.35680005,"z":0.7047},{"l":"H","x":-1.8655999,"y":-1.6522,"z":0.6012},{"x":-0.2273,"y":-0.4718,"z":0.17},{"x":2.4650002,"y":0.1425,"z":-0.029099999},{"l":"O","x":-2.1741998,"y":1.1759001,"z":-0.59169996},{"l":"O","x":3.7872,"y":0.4441,"z":-0.1268},{"x":-2.5170999,"y":0.1262,"z":-0.089999996},{"l":"N","x":-1.5898,"y":-0.78279996,"z":0.2712},{"l":"H","x":-0.50740004,"y":1.6029,"z":0.6296},{"l":"H","x":0.35450003,"y":-2.4786,"z":-0.3079},{"l":"H","x":1.8853,"y":2.1487997,"z":0.4477},{"l":"H","x":2.7472,"y":-1.9314001,"z":-0.485},{"l":"H","x":-4.3884,"y":-0.65880007,"z":-0.7504},{"l":"H","x":-4.0964003,"y":-0.8086,"z":0.9991},{"l":"H","x":-4.513,"y":0.7739,"z":0.2986}],"b":[{"b":8,"e":10},{"b":9,"e":11,"o":2},{"b":7,"e":12},{"b":11,"e":12},{"b":0,"e":7,"o":2},{"b":1,"e":7},{"b":0,"e":2},{"b":2,"e":8,"o":2},{"b":3,"e":8},{"b":1,"e":3,"o":2},{"b":4,"e":11},{"b":5,"e":10},{"b":6,"e":12},{"b":0,"e":13},{"b":1,"e":14},{"b":2,"e":15},{"b":3,"e":16},{"b":4,"e":17},{"b":4,"e":18},{"b":4,"e":19}]}}
(this ended up NOT being used in the Jmol extension to ChemDoodle)
new feature: (JmolData) -iR (silent, restricted) mode sends output from PRINT and ECHO commands to SYSOUT
and also restricts the application to no local file read/writing
bug fix: "connect;" command in states saved prior to 11.9.24 and then read by versions after that
The order in which Jmol created bonds changed in 11.9.24. Due to this, Jmol must check for the
version number of Jmol used to create a state, and if it was before this point, it must
apply "legacy" autobonding methods. Unfortunately, if that state from pre-11.9.24 versions
contains the "connect;" command, which it would if someone used the CONNECT command by itself
to regenerate all bonds in a model PRIOR to saving the state (Proteopedia does this), then
those scripts will be misread in versions 11.9.24-12.2.21/12.3.21.
bug fix: antialiasDisplay does not show drag-box properly
bug fix: SMARTS syntax [${xxx}n] and [${xxx}m-n] changed to [$n{xxx}] and [$m-n{xxx}]
to avoid conflict with specifying isotope
=============================================================================
version=12.3.21
new feature: app flag -R restricts file access -- no local file reading; no writing, no logging
// disables WRITE, LOAD file:/, set logFile
// command line -g and -w options ARE available for final writing of image
// for use with headless operation
new feature: app flag -T <seconds> headless timeout delay for "exitJmol"
note: Headless operation with image creation works perfectly using JmolData.jar
java -Djava.awt.headless=true -Xmx512m -jar "JmolData.jar" -RJ "load $tylenol;" -g1000x1000 -wJPG:t.jpg
see also: http://leshazlewood.com/2009/08/26/linux-javaawtheadless-and-the-display-environment-variable/
// determined by GraphicsEnvironment.isHeadless()
// from java -Djava.awt.headless=true
// disables command threading
// disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN <rate>, ANIMATION ON
// turns SPIN <rate> <end> into just ROTATE <end>
new feature: JSpecView JCamp-MOL files can reference model="$xxxx" -- model retrieved from NCI
bug fix: PDB reader
and state scripts created with 12.1.51-12.2.20 and 12.3.0-12.3.20
state scripts prior to those versions with multiple models
and also select BOND commands will read the bond indexes incorrectly
and, in addition, will assign proper CONECT links only to the last model
bug fix: if (....) # comment fails
bug fix: Molden reader hack for bad Molden files with ** instead of atom number in [GTO]
bug fix: headless creation of JPG fails
bug fix: spin .... 30 takes 30 to be number of degrees, not rate
version=12.3.20 -- skipped
=============================================================================
version=12.3.19
new feature: select baseModel for JSpecView
new feature; model {atomset} -- model of first atom in this set
bug fix: set dragSelected disallows popup menu
bug fix: MOPAC (PUBLIC DOMAIN) output reader can fail on reading vibrations
bug fix: Spartan 10 archives have .gz and .carc files. This fix adds .gz reading;
work-around is that Spartan 10 allows saving of Archive without carc compression,
which is a proprietary format. From Wavefunction:
"If you want all files to use the "text" version, you can go to the
Options->Preferences->X-Platform pane and make sure "Use Binary Archive" is unchecked."
bug fix: rotateSelected of models that have had dots at one point retrieved from a state file fails
code: refactored org.jmol.g3d.[Normix3d,Shade3D] --> org.jmol.util.[Normix, Shader]
code: refactored org.jmol.geodesic.Geodesic --> org.jmol.util.Geodesic
bug fix: Jmol defaults not being loaded with startup option -n (no display)
bug fix: UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()
failed for non-graphics system, and even though it is an exception, it
isn't trapped by try/catch.
bug fix: point() function does not accept 3x1 array
bug fix: show x where x is a matrix does not have ',' before tabs, so it can't be clipped directly
back into Jmol
code: better coding for quaternions
=============================================================================
version=12.3.18
new feature: JSpecView reads and displays 2D spectra very quickly -- all
tested JCamp-DX 6.0 files readable. -- JSpecView 2.0.10176
bug fix: allow for alternating list/hash entry:
for example: print getproperty("jspecview","##TITLE")["items"][1]["spectra"][1]["id"]
instead of: print ((getproperty("jspecview","##TITLE")["items"][1])["spectra"][1])["id"]
bug fix: GaussianReader not reading "Natural Orbitals" section from
B3LYP 6-31g sp gfprint pop(full,NO)
bug fix: Jmol support for ZIP collection of JDX files read properly
bug fix: support for file reading with BOM UTF-8, UTF-16, or UTF-32
bug fix: script processor not recognizing UTF-8 Binary Order Mark at start of script
bug fix: (undocumented) POLYHEDRA {...} to {...} with COLOR or TRANSLUCENT fails
bug fix: POLYHEDRA command or COLOR POLYHEDRA can change selection
bug fix: PDB reader doesn't recognize 16 LINK records at start of file
bug fix: script xxxx(xxx)xxx/xx.xxx fails at "(" due to revision 16201 2011-10-02
=============================================================================
version=12.3.17
new feature: (JspecView 2.0.10033) new script commands (indicated with *)
UNKNOWN("?"),
APPLETID("APPLETID"),
APPLETREADYCALLBACKFUNCTIONNAME("APPLETREADYCALLBACKFUNCTIONNAME"),
AUTOINTEGRATE("AUTOINTEGRATE", "TF"),
BACKGROUNDCOLOR("BACKGROUNDCOLOR", "C"),
*CLOSE("CLOSE", "spectrumId or fileName or ALL"),
COMPOUNDMENUON("COMPOUNDMENUON", "TF"),
COORDCALLBACKFUNCTIONNAME("COORDCALLBACKFUNCTIONNAME"),
COORDINATESCOLOR("COORDINATESCOLOR", "C"),
COORDINATESON("COORDINATESON", "TF"),
*DEBUG("DEBUG", "TF"),
DISPLAYFONTNAME("DISPLAYFONTNAME", "fontName"),
ENABLEZOOM("ENABLEZOOM", "TF"),
ENDINDEX("ENDINDEX"),
*EXPORT("EXPORT", "[JPG,PNG,XY,...] \"filename\""),
GETSOLUTIONCOLOR("GETSOLUTIONCOLOR", ""),
GRIDCOLOR("GRIDCOLOR", "C"),
GRIDON("GRIDON", "TF"),
*INTEGRATE("INTEGRATE", ""),
INTEGRALPLOTCOLOR("INTEGRALPLOTCOLOR"),
INTEGRATIONRATIOS("INTEGRATIONRATIOS"),
INTERFACE("INTERFACE"),
*IRMODE("IRMODE", "A or T or ?"),
*LABEL("LABEL", "x y [color and/or \"text\"]"),
*LOAD("LOAD", "[APPEND] \"fileName\""),
MENUON("MENUON"),
OBSCURE("OBSCURE"),
*OVERLAY("OVERLAY", "spectrumID, spectrumID, ..."),
PEAKCALLBACKFUNCTIONNAME("PEAKCALLBACKFUNCTIONNAME"),
PLOTAREACOLOR("PLOTAREACOLOR", "C"),
PLOTCOLOR("PLOTCOLOR", "C"),
PLOTCOLORS("PLOTCOLORS"),
REVERSEPLOT("REVERSEPLOT", "TF"),
SCALECOLOR("SCALECOLOR", "C"),
SPECTRUM("SPECTRUM", "spectrumID"),
SPECTRUMNUMBER("SPECTRUMNUMBER"),
STARTINDEX("STARTINDEX"),
SYNCCALLBACKFUNCTIONNAME("SYNCCALLBACKFUNCTIONNAME"),
SYNCID("SYNCID"),
TITLEBOLDON("TITLEBOLDON", "TF"),
TITLECOLOR("TITLECOLOR", "C"),
TITLEFONTNAME("TITLEFONTNAME", "fontName"),
UNITSCOLOR("UNITSCOLOR", "C"),
VERSION("VERSION"),
XSCALEON("XSCALEON", "TF"),
XUNITSON("XUNITSON", "TF"),
YSCALEON("YSCALEON", "TF"),
YUNITSON("YUNITSON", "TF"),
*ZOOM("ZOOM", "OUT or x1,x2");
new feature: allows simpler color scheme definition
color property occupancy "myscheme=red green blue"
Var x = ["red","green","blue"]; color property occupancy @{"myscheme=" + x}
bug fix: JCampDX reader resolving should allow spaces before "##TITLE"
bug fix: jvxl issue when color PHASE and translucent
-- upon reading JVXL doesn't handle translucency right
-- upon writing SPT doesn't preserve colors
bug fix: user variable lower case "x" not cleared by "X = none"
bug fix: draw HELIX fails for residue numbers < 0
code: better Enum structure using name()
=============================================================================
version=12.3.16
new feature: (application) SYNC ON; sync * "JSpecView:..." sends commands to JSpecView
new feature: (JSpecView) accepts commands using public syncScript(script)
bug fix: GAMESS-US reader error reading NBOs
bug fix: print [2, 3, 4].mul([3,4,5]) fails
bug fix: missing ANISOU records cause file-read error in PDB files
bug fix: JCAMP-DX reading by JSpecView for tiered BLOCK files
=============================================================================
version=12.3.15
new feature: JCAMP-DX file reading
-- reading of ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview)
new feature: context menu Spectra submenu
new feature: JSpecView integration into Jmol application
-- if model/peak-enhanced JDX file is read, clicking on an atom or switching
to an IR vibration or MS fragment displays the appropriately highlighted spectrum/fragment
new feature: sync ~ 'Select: xxx'
-- xxx can include file="xxx" model="xxx" atoms="xxx" select="xxx" script="xxx"
-- file and model combined as model ID "file#model"
-- will automatically load the file if the given file#model ID is not found
-- atoms = list of atom numbers separated by commas: 1,2,3 --> @1 or @2 or @3
-- select is any valid selection such as THR or 1-30
-- automatically adds "visible &" to atoms or select
-- requires sync ON
new feature: NFF neutral file format reader (http://paulbourke.net/dataformats/nff/nff1.html)
for electron microscopy data exported from IMOD
new feature: preliminary JCAMP-DX file reader, where <models></models> is present
new feature: when picking struts or delete bond or measure, distance shows as per usual measurement
bug fix: SLAB unit cell not showing all lines
bug fix: CRYSTAL reader needs to change to MOLECULAR when X(ANGSTROMS) found (fullerene slab)
bug fix: Popup Menu item hbond calculate should not require PDB
=============================================================================
version=12.3.14
bug fix: state after frame RANGE or frame 0 not saved properly (state saves "frame all" instead of "frame 0")
bug fix: frame n does not work properly after load APPEND
bug fix: measurement units may appear as full word "nanometers" instead of "nm"
bug fix: user bindings do not access _atomPicked
-- solution is to add _ATOM _BOND _POINT _OBJECT to user binding actions
=============================================================================
version=12.3.13
new feature: isosurface SCALE extends to volume file readers
new feature: zoom $isosurface1 0 -- scales to match isosurface boundbox
bug fix: getProperty("bondinfo",[{13}]) gets info for atom 13 instead of bond 13
bug fix: isosurface offset does not change boundbox or zoom/center points
note to Bob: jpe needs update of img/blank.js js/top_buttons.js htm1/quickvs.js,qv_msgs.js molview/JmolAppletSigned.jar
=============================================================================
version=12.3.12
bug fix: symmetry popup submenu not enabled
bug fix: show spacegroup not working
bug fix: lcaocartoon for allene central carbon py incorrect
bug fix: antialiasdisplay (and image writing) not compatible with scaleAngstromsPerInch
bug fix: last group of protein cartoon will not display if it is not helix and not sheet
bug fix: getproperty MENU does not work
bug fix: PDB reader of multiple-bond files with duplicated bonds does not ignore duplicate
=============================================================================
version=12.3.11
new feature: plot ramachandran -- now those points .phi and psi return values
-- load 1crn.pdb;plot ramachandran;print {2.1}.psi
new feature: LOAD .... filter "reverseModels"
-- does just that
-- for IRC calculation transition state -> minimum reversal
new feature: measures "2:%VALUE %UNITS//xx"
-- where xx is a specified unit such as nm or Angstroms
-- overrides set measurementUnits
-- fixes state problem when units or labels are changed after measurements are made
-- operates on selected measurements only (or all, if no measurements are selected)
bug fix: frame 0 during animation can cause exception
bug fix: changes in defaultDistanceLabel not always preserved in state correctly
bug fix: parameters can be set to invalid values using xxx = ... instead of set xxx ...
bug fix: (Application) proper Edit...Preferences dialog action
=============================================================================
version=12.3.10
new feature: _animTimeSec
new feature: Application -- press and hold animation next/prev button to continuously run animation
new feature: write PDB adds CONECT records
-- for all multiple bonding and all HETATM bonds
-- uses CONECT i j j to indicate multiple bonding
new feature: compare {from} {to} FRAME
-- aligns frames automatically
-- particularly nice for IRC calculation animations
-- for example: compare {file=2} {1.1} FRAME
-- can be followed by quaternion, atom, or SMILES options
-- for example: compare {file=2} {1.1} FRAME ATOMS @1 @5 @2 @8 @3 @9
(all of file 2 atoms moved) file 2 atoms 1,2,3 aligned
with file 1.1 atoms 5,8,9)
-- if {to} is a subset of {from}, then FRAME is unnecessary,
and if ATOMS is included, then just the list of alignment
atoms is necessary. For example:
compare {*} {1.1}
compare {*} {1.1} atoms @1 @2 @3
-- see http://chemapps.stolaf.edu/jmol/docs/examples-12/mp for more examples
bug fix: script @{x} fails
bug fix: Molecular Playground should allow for set allowGestures OFF to disallow swipe
bug fix: lcaoCartoon dual color p orbitals giving white for one lobe
new feature: set echo myecho SCALE 0.3 -- for image scaling
bug fix: after "ZAP; LOAD append" show orientation will have incorrect zyz script
bug fix: function call with @x or @1 in parameters fails
bug fix: PNGJ reading remote fails
bug fix: H5T should not be used as a lead atom ever, because of set showHydrogens FALSE
bug fix: adding H atoms to mol2 file faulty
bug fix: load xxx.png;write PNGJ xxx.png (to same file as loaded) fails
=============================================================================
version=12.3.9
new feature: FRAME DELAY x.y
-- specific delay (in seconds) in animation at a given frame
-- applies to all currently in-frame models
bug fix: set isKiosk should:
(a) not be reversible
(b) not allow file saves other than logging
(c) not allow prompt dialogs
(d) not allow console or popup menu or ScriptEditor
bug fix: background colors saved to state can be off very slightly
bug fix: draw PLANE with three vertices problems after save -- four-atom planes, not three
bug fix: x = file("?") fails on Cancel
bug fix: delay not allowed within try{...}
=============================================================================
version=12.3.8
new feature: MolecularPlayground -- remote status and remote control
-- see for example http://chemapps.stolaf.edu/jmol/mpstatus.php
-- set topic, subtopic, delay from a web page
-- set banner and image for website from Jmol
new feature: load("http://.....?POST?_PNG_") or load("http://....?POST?_PNGJ_")
-- sends PNG or PNGJ image to server
-- return value is whatever server is set up to send
-- used by MolecularPlayground at St. Olaf to send current state to web server
new feature: polyhedra FULLYLIT -- useful for zeolites along with COLLAPSED
new feature: ZMATRIX upgraded to allow all forms of Gaussian input
http://www.gaussian.com/g_tech/g_ur/c_zmat.htm
bug fix: set picking DRAW does not work on polygon sets
bug fix: set picking DRAW does not report position change
bug fix: MPJmolApp (Molecular Playground) problems when navigation is on
bug fix: CifReader (molecular type, with GEOM_BOND records) adds
extra atoms when embedded in JMOL or PNGJ file or part load FILES command
bug fix: PdbReader -- crystallographic non-PDB files not checking special positions
=============================================================================
version=12.3.7
new feature: "Write PNG+JMOL" added to application and signed applet menu
code: dispensing with InputStream in favor of BufferedInputStream
new feature: write PNGJ
-- creates a PNG file with appended JMOL (zip) data containing
all necessary files, MANIFEST, and script file.
-- viewable in directories as an "icon" and readable by image readers
-- draggable back into Jmol and readable using LOAD
-- PNG file includes:
-- iTXt field "Jmol Type\0PNGJxxxxxxxxx+yyyyyyyyy"
where xxxxxxxxx is a pointer to the ZIP data
yyyyyyyyy is the number of ZIP data bytes
-- iTXt field "Software\0Jmol 12.3.7 2011-10-11 15:30"
-- iTXt field "Creation Time\0Tue, 24 Nov 2011 19:56:10 -0600"
-- yyyyyyyyy bytes of .JMOL zip data
-- show FILE "xxx.PNG" will show list of contained files.
-- show state FILE "xxx.PNG" will extract state
-- show FILE "xxx.PNG|1crn.pdb" for example will extract file
new feature: simple Z-Matrix reader
-- invoked by ZMATRIX:: or file starting with #ZMATRIX
-- lines starting with # are comments, which can contain jmolscript:
-- blank lines are ignored
#ZMATRIX -- methane
C
H 1 1.089000
H 1 1.089000 2 109.4710
H 1 1.089000 2 109.4710 3 120.0000
H 1 1.089000 2 109.4710 3 -120.0000
-- allows bond order specification
#ZMATRIX -- CO2
C
O 1 1.3000 2
O 1 1.3000 2 180 2
-- any position number may be replaced by a unique atom name, with number:
#ZMATRIX -- CO2
C1
O1 C1 1.3000 2
O2 C1 1.3000 O1 180 2
-- allows for dummy atoms Xn, allowing for positioning:
#ZMATRIX -- CO2
X1
X2 X1 1.0
C1 X1 1.0 X2 90
O1 C1 1.3000 X2 90 X1 0 2
O2 C1 1.3000 O1 180 X2 0 2
-- negative distance indicates that the second angle is a normal angle, not a dihedral
#ZMATRIX -- NH3 (using simple angles only)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 107 H2 107
-- negative distance and one negative angle reverses the chirality
#ZMATRIX -- NH3 (using simple angles only; reversed chirality)
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 -107 H2 107
-- symbolics may be used -- they may be listed first or last
#ZMATRIX
dist 1.0
angle 107
N1
H1 N1 dist
H2 N1 dist H1 angle
H3 N1 -dist H1 angle H2 angle
-- If #ZMATRIX is not the start of the file, MOPAC style is assumed.
The first two lines will be considered to be comments and ignored:
AM1
Ethane
C
C 1 r21
H 2 r32 1 a321
H 2 r32 1 a321 3 d4213
H 2 r32 1 a321 3 -d4213
H 1 r32 2 a321 3 60.
H 1 r32 2 a321 3 180.
H 1 r32 2 a321 3 d300
r21 1.5
r32 1.1
a321 109.5
d4213 120.0
d300 300.0
bug fix: show orientation shows incorrect zyz format if reset uses file-based orientation matrix (smol, Sygress)
bug fix: isosurface plane xy map mep
code: MPJmolApp work
bug fix: user variables should not be rest by INITIALIZE in an spt file
bug fix: x3d/vrml outputting unnecessary spheres
-- bond caps within opaque atoms removed (not precisely correct to do that)
bug fix: minimization broken
bug fix: contact still not quite right -- setting default to +0.0 instead of +0.25
=============================================================================
version=12.3.6
new feature: load files "xxx.tlsout" "xxxx.pdb"
-- loads REFMAC-style TLS data into xxxx.pdb
new feature: contact SASURFACE <radius>
-- ignores solvent (as does CAP)
bug fix: contact command hbond/clash cutoff not sensitive to H-O/N vs O/N-O/N
-- set to -1.2 for H-N/O, -1.0 for N/O-N/O
bug fix: contact command default probe radius should be 0.0 except for VDW (0.25)
bug fix: minimize constraint CLEAR broken
bug fix: constraints not reported in show minimization
bug fix: set measures off broken
bug fix: contact color density broken
bug fix: contact volume report not correct for color density
bug fix: MO HOMO not set properly when using LUMO = "lowest E > 0" (GAMESS-US reader)
bug fix: zSlab settings not stored properly in parameters; should have default zSlab = 50
=============================================================================
version=12.3.5
new feature: color isosurface PHASE color1 color2
-- allows post-isosurface creation coloring by phase (atomicOrbitals)
bug fix: isosurface scale 0.5 plane... broken if no atoms present
bug fix: isosurface color density broken
bug fix: set PdbAddHydrogens does not transfer C atomSymmetry to H atoms
bug fix: contact() function not working when typed from console
bug fix: set axesOrientationRasmol not working properly (since 11.5.51)
code: org.jmol.modelsetbio.BioModel localizes more bio-only code into modelsetbio package
code: removal of org.jmol.modelset.Polymer
code: refactoring and organizing RepaintManager and ShapeManager
=============================================================================
version=12.3.4
bug fix: frame x.y - y.z not working
bug fix: with antialiasDisplay, dragMolecule goes 1/2 speed of cursor
bug fix: nucleic acid residues with HO5' may render last group strangely (since 12.0.RC16, 6/6/2010)
bug fix: workaround for weird Mac Point3i(Point3i pt) class initializer bug
bug fix: array.bin(low,high,binSize) not documented and can cause exception
bug fix: MO readers can fail if inappropriate filter "TLS" is given
bug fix: PDB TLS error reading TLS data missing "NUMBER OF COMPONENTS" line
=============================================================================
version=12.3.3
new feature: ellipsoid SET 1; ellipsoid SET 2;
-- TLS ellipsoids are dual
-- TLS-S is SET 1; TLS-T is SET 2
-- after issuing this command, further size or color commands affect only that set
-- needs verification by Ethan Merrit
new feature: load xxx.pdb filter "TLS" -- loads TLS data
new feature: atom property property_tlsGroup
new feature: MolecularPlayground now accepts messages to the banner:
message banner: xxxxxxx
new feature: MolecularPlayground fully functional.
This application (MPJmolApp) is part of a three-part suite
that runs on a Mac mini involving:
"Hub" [name] for overall control (Mac app; not open source yet)
MPKinectDriver for obtaining motion events (Mac app; not open source yet)
MPJmolApp for displaying the results (source here)
The Hub and MPJmolApp communicate over local port 31416, sending
JSON messages back and forth. (See note in org.jmol.app.jsonkiosk.JsonNioService.java)
For demonstrations of the installation at St. Olaf College,
see the following YouTube videos:
http://www.youtube.com/watch?v=iQRkuku8ry0
http://www.youtube.com/watch?v=XCRrRZe1j6g
http://www.youtube.com/watch?v=FTTIVWGtFD0
For details relating to the original Molecular Playground
installation at U. Mass.-Amherst, see
http://molecularPlayground.org
Note that all of the functionality of the original MP are
present in MPJmolApp
new feature: MolecularPLayground can now ignore all Hub requests for
commands and content changes, thus allowing its own configuration
script to drive the presentation instead of the Hub's. So the Hub
can be used simply as an interface to the Kinect driver. This just
allows a simpler development interface -- a simple three-column Excel file can
be used to drive a presentation. (see org.jmol.molecularplayground.biophysics.xlsx)
-- MPJmolApp looks for the file MpJmolAppConfig.spt
-- This file can override MPJmolApp's default parameters:
NIOContentPath
-- default: System.getProperty("user.dir").replace('\\', '/')
+ "/Content-Cache/%ID%/%ID%.json"
-- ignored if NIOcontentDisabled ends up true (see below)
NIOterminatorMessage
-- default: "MP_DONE"
NIObannerEnabled
-- default: true
NIOcontentScript
-- default: (not present, setting NIOcontentDisabled=false)
NIOcontentDisabled
-- default: true if NIOcontentScript is present; false if not
NIOmotionDisabled
-- default: false
-- The script in MpJmolAppConfig.spt is run, along with whatever
default settings are generated by the above checks.
-- Parameters are set by querying the Viewer for those Jmol variables.
-- If NIOcontentDisabled is true, then all JSON messages from the Hub
of types "content", "command", and "banner" are ignored. It is still
important that the running script send "MP_DONE" messages periodically
(within every 6 minutes) so that the Hub knows that MPJmolApp is still
alive and does not try to restart it.
-- If NIOmotionDisabled is true, then all JSON messages from the Hub
of types "move", "sync", and "touch" are ignored.
-- These are checked every time a JSON command is received, so the
running script can specifically turn off motion detection if that
or content detection if that is desired.
-- Note that MPJmolApp has a full console and menu that are available
on the operator's screen, (which is just mirrored to the projector).
This allows for parameter setting and adjustments on the fly.
new feature: show NMR
-- predicted NMR spectrum
-- uses http://www.nmrdb.org/predictor?smiles=xxxx
-- requires NCI SMILES due to bug at nmrdb not allowing "."
bug fix: CRYSTAL reader not properly setting model properties
bug fix: userFunction(x,@y) should operate as per all math
-- parens - value of variable pointed to by y
-- x = myfunc(x, @y) same action as just myfunc(x, @y)
bug fix: userFunction x @y
-- no parens - should operate as value of x and value of y
-- @ is unnecessary but allowed
bug fix: set echo "myecho" [10 10%] not working
bug fix: apiPlatform not correctly accessed in JpegEncoder
bug fix: reading of JVXL files for color density fails to color properly
bug fix: .... vdw 100.0% --- should be OK with float there, even if it rounds.
code: refactored for Molecular Playground and Jmol Android
-- several System.out. messages present.
code: refactoring adapter XML readers
=============================================================================
version=12.3.2
new feature: compare("XXX","XXXX","ISOMER") comparison now includes "AMBIGUOUS STEREOCHEMISTRY!"
new feature: show chemical XXXXX where XXXXX is any NCI Cactus information token:
stdinchikey Standard InChIKey
stdinchi Standard InChI
smiles SMILES
ficts FICTS Identifier
ficus FICuS Identifier
uuuuu uuuuu Identifier
hashisy Cactvs HASHISY
sdf SD File
names Names
iupac_name IUPAC Name
cas CAS Registry Number(s)
chemspider_id ChemSpider ID
mw Molecular Weight
formula Chemical Formula
h_bond_donor_count Number of Hydrogen Bond Donors
h_bond_acceptor_count Number of Hydrogen Bond Acceptors
h_bond_center_count Number of Hydrogen Bond Acceptors and Donors
rule_of_5_violation_count Number of Rule of 5 Violations
rotor_count Number of Freely Rotatable Bonds
effective_rotor_count Number of Effectively Rotatable Bonds
ring_count Number of Rings
ringsys_count Number of Ring Systems
bug fix: array.bin(low,high,binSize) not documented and can cause exception
new feature: PQR write option
bug fix: load append twice can cause zap to be in wrong place in state file
bug fix: for (x IN {*}) ... makes x a bitset and leads to array[1] for x.atomName
bug fix: for (x IN {*}.bonds) does not work
bug fix: POV-Ray export of cartoons broken
bug fix: script javascript:xxxx() broken
new feature: set vectorSymmetry -- displays vibration vectors as double-ended arrows.
bug fix: SMILES comparison when the number of stereocenters is not the same is wrong
code: popup/modelkit refactoring to isolate awt/Swing references
bug fix: connection deletion removes all measurements -- can't imagine why...
code: JmolModelKitInterface part of apiPlatform call
code: JmolPromptInterface replaced with apiPlatform call
=============================================================================
version=12.3.1
new feature: CASTEP reader (take 2)
-- reads Mulliken files by default, Hirshfield with filter "CHARGE=HIRSH"
-- reads spins into {*}.property_spin. label is %[property_spin]
-- reads Born charge tensors as atom ellipsoids
bug fix: H2,H3 connected to terminal N of protein not backbone
bug fix: select PROTEIN selects non-PDB atoms
bug fix: Molden reader does not read "Sym=X" (missing space after '=')
bug fix: Molden reader does not read angstrom units
bug fix: color isosurface {atomset} <color> does not work if isosurface has not already been mapped.
bug fix: PDB reader not reading Rasmol-style files with multiple bonding
CONECT 1 2 2
or
CONECT 1 2
CONECT 1 2
means for Rasmol double bond between atoms 1 and 2
code: experimenting with fragmentation of applet core classes into _1b, _1c, _1d, _1e, _1f
version=12.3.0
October 4, 2011
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