Lines Matching refs:new
8 # bug fix: drawHover status not reported properly after zap/new model loaded
229 # new feature: CASTEP (http://www.castep.org/) and AIMS readers
230 # new feature: popup menu gives Symmetry operation display option
231 # new features for the 238th American Chemical Society National Meeting, Washington, D.C., Aug. 19,…
232 # new feature: draw ID xxx SYMOP [n or "-x,y,z"] [optional {atom or position}]
235 # new feature: pt = all.symop(3, {atomno=3})
236 # new feature: sdrawCommands = all.symop(3, {atomno=3},"draw_id")
238 # new feature: ho, ho, this is fun. Wouldn't it be nice to just drag a JPG into
260 # new feature: select structureID="xxx" selects structures by alphanumeric id such as "S1" or "H3"
269 # new feature: Jmol embedded in applications can use WRITE command to create all types of images an…
270 # new feature: VERY COMPACT IDTF export (for U3D conversion; all except background color)
293 # new feature (TODO): 4D extension (that's right -- FOUR dimensions)
294 # new feature: set picking Label now allows label offset by holding SHIFT down while dragging atom
295 # new feature: lone pairs and radicals -- extension of lcaoCartoon:
300 # new feature: print getProperty("FileInfo","REMARK300") //was PdbInfo
301 # new feature: print getProperty("FileInfo","models",1,"_citation_year");
316 # new feature: set quaternionFrame "a" -- alpha-carbon-ONLY straightness. see 1JGQ
320 # new feature: set helixStep 0 -- relates a quaternion to the standard reference frame
322 # new feature: write "xxx.X3D"
323 # new feature: [x,y,z].sum2 or {xx}.someProperty.sum2 -- sum of squares
324 # new feature: VRML export nearly full support
340 # new feature: set helixStep 1,2,3,... sets step for quaternion-based analysis of structure -- see…
343 # new feature: isosurface select(....) SET n
347 # new feature: isosurface area for subsets -- use
368 # new feature: set quaternionFrame "RC" or "RP" -- ramachandran-derived straightness
369 # new feature: array1.add("sep", array2) adds a new column of values separated by sep, for example:
375 # new feature: NAVIGATION STOP -- sets navX, navY, navZ to 0
376 # new feature: navX, navY, navZ, navFPS all settable
377 # new feature: NAVIGATION ON/OFF now does continuous motion with arrow keys
386 # new feature: draw HELIX AXIS or quaternion HELIX AXIS, also for DNA/RNA
388 # new feature: GROMACS reader
390 # new feature: by passing an array to a function, you can make that variable
393 # a = "new value"
397 # print b ==> "new value"
406 # new feature: within("HELIX"), within("SHEET") -- helix and sheet, but not ends
407 # new feature: all.bin(f0, f1, df) -- binning of data to give an integer array of counts
410 # new feature: draw ARC {center} {plane}
411 # new feature: draw ARC {center} {axisPoint}
412 # new feature: draw CIRCLE {center} {plane}
413 # new feature: draw CIRCLE {center} {axisPoint}
414 # new feature: draw SCALE works with CIRCLE
426 # new application: JmolData.jar
433 # new feature: helix(resno or {atomExpression},type)
446 # new feature: VRML exporter displays ribbons and cartoons by automatically setting
448 # new feature: VRML exporter recognizes color and normals for isosurface
467 # new feature: gamessUS reader now reads dipoles and partial charges.
472 # new feature: drag/drop and file menu-open scripts directly into editor, from where they can be ch…
474 # new feature: App and applet consoles now have "editor" buttons
479 # new feature: Gamess file reader now translates internal basis set and calculation
483 # new feature: application console buttons: PAUSE, ?, STEP
484 # new feature: SHOW TRACE -- reports stack trace
487 # new feature: SHOW VARIABLES now gives variable trace through function stack
488 # new feature: [Oh, VERY COOL!] You can now pause the app anywhere in a
505 # new feature: strings may start with ' or ", like JavaScript:
512 # new feature: print getProperty("PDBInfo","REMARK300")
520 # new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
521 # new feature: GAMESS reader now sets calculationType, orbital type, and auxiliaryInfo.calculationO…
525 # new feature: merging of label() and format() functions -- same in all respects.
537 # new feature: a = [] note that a+=2 then produces [2] -- "a+=" similar to JavaScript a.push(2)
545 # new feature: function parameter arrays passed by reference, so, for example:
554 # new feature: general commands no longer restricted to single lines.
557 # new feature: set or x = command no longer restricted to single lines.
562 # new feature: -p Jmol application command line option --printOnly silent operation with only prin…
569 # new feature: support for extended inline if: x = (a ? this : b ? that : theother)
572 # new feature: {*}.modelindex
576 # new feature: load ("filename", nBytesMax) --- and returns "java.io.FileNotFoundException" if file
580 # new feature: print {xxx}.label.all("xxxx") -- forces array even if only one atom (like "{xxx}.lab…
594 # new feature: format("sprintf format", a, b, c, ...)
595 # new feature: {xxxx}.label("") shows current label
596 # new feature: [array].sort
597 # new feature: [array].reverse
598 # new feature: [array].min
599 # new feature: [array].max
600 # new feature: [array].average
601 # new feature: [array].stddev
602 # new feature: (value).label("C++ printf format")
671 # new feature: set useMinimizationThread T/F nec. to be FALSE when running minimizations in script…
677 # new feature:
710 # new feature: complete freedom from lines and "end if, end for, end while" --
741 # new feature: standard { ... ? ... : ... ) notation in Jmol math:
745 # new feature: load "@x" -- inline load of data contained in variable x.
747 # new feature: {*}.label = xxx and {*}.label("%[label]") and select label="xxx"
749 # new feature: An XML reader for Materials Studio .xsd files http://accelrys.com/products/material…
751 # new feature: greatly expanded item selecting:
759 # new feature: .length alias for .size except for x.bonds - so it can be
767 # new feature: inline FOR(varName;{atom expression};math expression)
773 # new feature: .add() sums up values
777 # new feature: inline IF(math expression;math if true; math if false)
793 # bug fix: biomolecules for new PDB format
795 # new feature: consistent set of atom properties now accessible via:
907 # new feature: consistent set of atom properties now accessible via:
914 # new feature: relaxed limitation on spacefill, halo, star, dots size to 16A.
915 # new feature: {xxx}.spacefill = n
916 # new feature: {xxx}.radius = n (same)
917 # new feature: print {xxx}.ionic ionic radius
918 # new feature: print {xxx}.covalent covalent radius
924 # new feature: label %[....] where .... is one of:
989 # new feature: color hbonds energy
990 # new feature: application flag -L --nosplash no splash screen (For Jmol in Sun Wonderland dev. 5)
991 # new feature: load XYZ ... loads just the XYZ coordinates, in sequence, based on selected atoms.
1001 # new feature: load OCCUPANCY ... int [0 to 255]
1002 # new feature: load PARTIALCHARGE ... float ~[-3.4 x 10^38 to 3.4 x 10^38]
1003 # new feature: load TEMPERATURE ... float [-327.68 to 327.67], with 0.01 precision (stored as sho…
1004 # new feature: loadAtomDataTolerance, with default 0.01 Angstroms
1012 # new feature: load VIBRATION "filename" n .......
1019 # new feature: loadAtomDataTolerance (see above)
1021 # new feature: load {a b -c} packs a x b x c cells
1022 # new feature: select within(-0.1, {1/2 1/2 1/2}) -- negative distance within selects atoms based o…
1023 # new feature: select within(-0.1, atomno=3) -- negative distance within selects atoms based on uni…
1024 # new feature: select within(-0.1, true, atomno=3) -- negative distance within model selects atoms …
1025 # new feature: select ux|uy|uz < x.x -- selection based on unit coordinates
1026 # new feature: {x y z}.fxyz -- returns fractional from cartesian
1027 # new feature: {x y z}.uxyz -- returns unitcell from cartesian
1028 # new feature: {x y z}.ux, .uy, .uz similar to .fx, .fy, .fz
1029 # new feature: {x y z}.xyz -- returns cartesian from fractional
1034 # new feature: {atomExpression}.uxyz, .ux, .uy, .uz -- unit cell coordinate
1056 # new feature: "xxxxx".find("pattern","flags") allows regular expression matching;
1085 # new feature: Wien2k reader
1094 # new feature: label %G -- group index, like atom index, 0-based for entire collection
1095 # new feature: ramachandran DRAW -- draws dihedral planes and angles
1105 # new feature: application -s - reads input from System.in (untested)
1106 # new feature: \? in atom name escapes ? wildcard. Still no * in names,
1109 # new feature: isosurface FunctionXYZ -- same as FunctionXY, but must return float[][][]
1124 # new feature: load xxxx FILTER "NBOcharges" loads NBO charges instead of Mulliken
1128 # new feature: preliminary NBO support for Gaussian and QChem needs checking
1140 # new feature: CML "isotope" and CML "partial12" bond order.
1141 # new feature: GAMESS reader reads NBOs using
1143 # new feature: QChem reader reads occupancy, frequencies and MOs
1151 # new feature: frame ALIGN {atoms} -- aligns frames around designated atoms in each frame
1154 # new feature: Spartan MO-Animation files can be read
1167 # new feature: Spartan zip directories xxx.spardir.zip containing directory xxx.spardir can be read
1168 # new feature: Spartan reader now reads all models in an energy profile
1169 # new feature: MO no longer restricted to one per model set; rather, one per MODEL
1170 # new feature: MO command operates on all models in current frame set:
1185 # new feature: set autoLoadOrientation (default: FALSE) automatically sets "reset" orientation to t…
1186 # new feature: restore orientation DEFAULT -- resets orientation to file's default orientation or s…
1196 # new feature: draw ID xxx FRAME {center} {quaternion}
1220 # new feature: JVXL format supports polygonColixes[]
1222 # new feature: isosurface points can be retrieved using $id[n] where n=0,1,2,3... similar to $draw[…
1224 # new feature: isosurface OBJ file reader using
1229 # new feature: hover displays isosurface values for contour plots and planar plots
1230 # new feature: isosurface .... map contour [n] [mep|MO homo|etc]
1233 # new feature: isosurface CONTOURLINES|NOCONTOURLINES
1235 # new feature: default rendering for isosurfaces involving the
1237 # new feature: hovering over isosurface contourlines displays value
1243 # new feature: very preliminary isosurface ED (RHF only) //and isosurface ESD
1251 # new feature: isosurface VOLUME reports the volume of an isosurface and stores the number in varia…
1252 # new feature: ASimpleJvxlWriter can calculate the volume of the surface
1253 # new feature: isosurface AREA reports the area of an isosurface and stores the number in variable …
1254 # new feature: ASimpleJvxlWriter can calculate the area of the surface
1265 # new feature: CTRL-K toggles keystrokes with display; ALT-K or CTRL_ALT_K same without display
1271 # new application: org.openscience.app.jvxl.simplewriter.ASimpleJvxlWriter.java
1280 # new feature: character \0 at the start of an echo does screen echo only, not to callback or conso…
1281 # new feature: typing into applet executed as script commands
1282 # new feature: set showKeyStrokes
1285 # new feature: set dragSelected (was "set picking dragSelected")
1296 # new feature: load "myfile.cif" {ijk i'j'k' -1}
1298 # new feature: load "myfile.cif" PACKED
1308 # new feature: translate x|y|z x.x nm|angstroms|%
1311 # new feature: additional VRML support (Angel Herraez)
1312 # new feature: u3d exporter template only -- no actual output
1334 # bug fix: Compilation problem with "new IOException(e)"
1343 # new feature: Alchemy/3DNA reader
1345 # new feature: new command "exitJmol" does just that -- application only;
1348 # new feature: application -d --debug sets loglevel to 5
1349 # new feature: application -J --jmolscript1 Jmol script BEFORE -s
1350 # new feature: application -j --jmolscript2 Jmol script AFTER -s not accepting values
1352 # new feature: (embedded application method of JmolViewer):
1385 # new feature: (embedded application method of JmolViewer):
1395 # new feature: q = quaternion(matrixColumn1, matrixColumn2)
1404 # new feature: Jmol.js jmolScriptWaitOutput(script) returns all messages that would
1406 # new feature: applet.getJmolStatus("AS_VECTOR") and applet.getJmolStatus("AS_HASHTABLE")
1408 # new feature: measureCallback reports pending measurements as well as completed ones
1427 # new feature: errorCallback and scriptCallback report untranslated errors
1428 # new feature: when errorCallback or scriptCallback is enabled, messages are translated
1437 # new feature: set errorCallback -- cannot be a Jmol script!
1438 # new feature: load xxx.gamess FILTER "natural,optimized"
1439 # new feature: load xxx.gamess FILTER "!natural,!initial"
1458 # new feature: applet methods jmolLoadInline, jmolLoadInlineScript, jmolLoadInlineArray,
1467 # new feature: jmolGetPropertyAsString("errorMessage")
1468 # new feature: out-of-memory "Java heap error" trapping in scripts and image creation
1469 # new feature: save [bonds|coordinates|orientation|selected|state|structure] DELETE
1483 # new feature: sync * stereo
1497 # new feature: isosurface PMESH; pmesh command deprecated
1499 # new feature: all options of isosurface now option for pmesh.
1502 # new feature: pmesh files and inline scripts now can be colored and saved as JVXL files
1503 # new feature: isosurface INLINE "--pmesh data--"
1507 # new feature: #xxx comments act as targets for goto as well as MESSAGE commands
1511 # new feature: fully remappable JVXL files
1512 # new feature: JVXL file format version 2.0 writing and reading for general vertex/triangle file so…
1516 # new feature: efvet file reader (http://ef-site.hgc.jp/eF-site)
1526 # new feature: user-definable atom selector for extended select:
1530 # new feature: user-definable atom selector functions.
1552 # new feature: set fontCaching false -- for testing of font caching issues
1561 # new feature: hbonds delete
1562 # new feature: calculate hbonds {*} {*}
1564 # new feature: set hbondsAngleMinimum
1568 # new feature: set hbondsDistanceMaximum
1587 # new feature: settable atom elements, atomType, and atomName
1593 # new feature: select within("atomName", "xxx,yyy")
1594 # new feature: select within("atomType", "xxx,yyy")
1604 # new feature: Jmol math simple array definitions using brackets: x = [3,4,5,6]
1605 # new feature: set atomTypes "abcd=>C;efgh=>H" for reading mol2 and mdTop files
1616 # new feature: mol2 format reads force field atom types for AMBER, CFF91, GAFF, ESFF, CHARMM, COMPA…
1637 # new feature: write MENU "filename.mnu"
1638 # new feature: (Application) -c option checks without loading files; -C option checks with loading …
1645 # new feature: x = file("some file name") or x = file("?") -- returns full path to file
1646 # new feature: (Application) Files...Export...Gaussian... Build Gaussian Input File Dialog
1647 # new feature: (Application) command line option -j --jmolscript "script commands"
1648 # new feature: load MODELS ({bitset})|{first,last,stride}
1649 # new feature: load TRAJECTORY ({bitset})|{first,last,stride}
1650 # new feature: load APPEND MODELS ({bitset})|{first,last,stride}
1651 # new feature: load APPEND TRAJECTORY ({bitset})|{first,last,stride}
1652 # new feature: load APPEND "[topolopy file]" COORD ({bitset})|{first,last,stride} "mdcrd::md1.crd C…
1653 # new feature: load FILES "[topology file]" COORD ({bitset})|{first,last,stride} "mdcrd::md1.crd CO…
1659 # new feature: independent JAR files for language localizations
1663 # new feature: select within(atomName,"ATOMNAME1,ATOMNAME2,...")
1664 # new feature: select within(atomType,"ATOMTYPE1,ATOMTYPE2,...")
1671 # new feature: cd command sets defaultDirectory
1682 # new feature: draw LINE {...} {...} {...} {...} draws line segments
1683 # new feature: making Jmol movies using write frames {atomExpression} [width] [height] "movie.jpg"
1692 # new feature: load of molecular dynamics topology file and coordinates
1706 # new feature: x = quaternion({center_or_point}, {atomX_or_point}, {atomXY_or_point})
1711 # new feature: x = quaternion(q, "id", {center})
1760 # new feature: MOL2 reader is PDB-enabled.
1761 # new feature: data() and DATA expanded to allow fixed-column entry
1772 # new feature: load menu items for signed applet
1773 # new feature: save menu items for signed applet
1775 # new feature: minimize menu item
1776 # new feature: signed applet allows "load ?" and includes previewer
1779 # new feature: signed applet/application load ?xxx uses load dialog
1786 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is req…
1788 # new feature: write GIF
1799 # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
1810 # new feature: set atomPicking TRUE/FALSE
1811 # new feature: set bondPicking TRUE/FALSE
1814 # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet …
1834 # new feature: (just not documented) rotate {atom1} {atom2} 10
1835 # new feature: moveto quaternion {resno=3} {3.ca}
1845 # new feature: getProperty PointGroupInfo
1857 # new feature: script APPLET appletName "some script"
1863 # new feature: x = script("some script", "appletName")
1878 # gets a new-line-separated list of rotational quaternions for all applets with applet names.
1881 # new feature: print getProperty("modelInfo.models[3].file") syntax
1887 # new feature: draw ramachandran includes planes connecting atoms.
1890 # new feature: $*xx* double wild cards
1891 # new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/O…
1893 # new feature: support for application transparent background -- "-b" command switch (testing only)
1896 # new feature: HIDE $xxx
1897 # new feature: DISPLAY $xxx
1898 # new feature: DELETE $xxx
1901 # new feature: applet message regarding help and command entry
1923 # new feature: background IMAGE "filename"
1934 # -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/**
1945 # new feature: set dotDensity [-3 to 3]
1946 # new feature: draw pointGroup [type] [index] SCALE [x]
1955 # new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
1956 # new feature: set pointGroupLinearTolerance (default 8 degrees)
1961 # new feature: in Java 1.6.0_10, right-click activates the console, and the
1963 # new feature: applet console has "help" menu item, which includes several hundred items.
1972 # new feature: write/show pointgroup gives counts and tab-separated listing;
1973 # new feature: write pointgroup draw delivers draw commands
1974 # new feature: better draw pointgroup
1975 # new feature: no saving of point group -- just recalculated each time
1977 # new feature: echo myecho IMAGE "filename"
1980 # new feature: echo myecho DEPTH xx
1989 # new feature: pointgroups with vibration vectors
1991 # new feature: spacefill/dots/geosurface/cartoon/trace/etc. ONLY
1995 # new feature: wildcard at beginning for draw/pmesh/isosurface/etc. *xxx on/off/delete allowed
2003 # new feature: calculate pointGroup
2004 # new feature: draw pointGroup
2005 # new feature: write pointGroup
2007 # new feature: webexport now compresses data files over 512 MB
2008 # new feature: calculate pointGroup -- preliminary only -- untested
2016 # new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type …
2017 # new feature: application select button reinstated
2018 # new feature: application pick button reinstated
2019 # new feature: application measure button tied to picking style
2020 # new feature: application [>|] button
2024 # new feature: axes labels change subtly for set axesMolecular and setAxesOrientationRasmol
2029 # new feature: webexport now cleans up scratch files on deletion of instances and program exit.
2055 # new feature: dipole/draw/ellipsoid/isosurface/pmesh/mo/lcaocartoon ID keyword optional
2058 # new feature: $"xxx" quotations or $@{...} allows variable definition of object id reference
2059 # new feature: draw {point} PLANE [plane def, including xy, yz, x, etc.]
2065 # new feature: mol file bond type 8 as partial
2077 # new feature: // at beginning of a line marks comments
2086 # new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
2087 # new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
2099 # new feature: draw RAMACHANDRAN
2101 # new feature: write RAMACHANDRAN draw
2110 # new feature: measure {atomExpression or point} {atomExpression or point} ...
2117 # new feature: rotate branch {atom1} {atom2} ...
2118 # new feature: select within(branch, {atom1}, {atom2})
2119 # new feature: Jmol math within("branch", {atom1}, {atom2})
2123 # new feature: quaternion({atom expression}) -- returns calculated
2127 # new feature: isosurface functionXY can be used for mapping.
2128 # new feature: spacegroup/symmetry for CML files with <module> tags
2141 # new feature: show rotation aka show orientation rotation
2142 # new feature: show translation aka show orientation translation
2160 # new feature: show atom(s)
2161 # new feature: show group(s)
2162 # new feature: show selected
2163 # new feature: draw {point} {plane}
2164 # new feature: draw vector {point} {plane}
2165 # new feature: draw arrow {point} {plane}
2166 # new feature: q = axisAngle({x y z}, theta)
2167 # new feature: q = axisAngle(x, y, z, theta)
2168 # new feature: q = axisAngle("{x y x theta}")
2169 # new feature: q = quaternion("{x y z w}")
2170 # new feature: rotate @{quaternion(....)}
2171 # new feature: rotate @{axisAngle(....)}
2172 # new feature: rotate quaternion {x y z w}
2173 # new feature: rotate axisAngle {x y z theta}
2175 # new feature: {point1} == {point2} if distance < 0.000001
2176 # new feature: {quaternion} == {quaternion2} if distance < 0.000001
2177 # new feature: float1 == float2 if |float1 - float2| < 0.000001
2205 # new feature/feature change:
2217 # new feature: quaterion % point4f --- "thetaDirected" --
2235 # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component eq…
2240 # new feature: _applet boolean
2242 # new feature: extended quaternion math
2289 # new feature: Numerical left division (integer divide)
2294 # new feature: sqrt(x)
2320 # new feature: set PICKLABEL "xxx" -- allows customized pick reports
2324 # new feature: "quaternion derivative" --> "quaternion difference", which is more
2336 # new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
2337 # new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
2338 # new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
2341 # new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame
2344 # new feature: select whatever; quaternion draw
2347 # new feature: straightness, defined as:
2388 # new feature: "%T" label format for straightness
2394 # new feature: xyz reader reads partial charge in 5th field
2396 # new feature: "load" of Jmol state scripts works same as "script" command
2399 # new feature: getproperty menu current
2407 # new feature: new command:
2413 # new feature: full math on individual atom properties using
2414 # a new function:
2424 # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental]
2425 # new feature: draw Vector [x y] or [x y %] {x' y' z'}
2426 # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows
2428 # new feature: set echo myecho [x y] and set echo myecho [x y %]
2429 # new feature: axes position [x y] and axes position [x y %]
2438 # new feature: signed applet shows frank "Jmol-S" which is NOT removable.
2442 # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as si…
2444 # new feature: /*SPLIT*/ in a command string allows it to be processed by
2452 # new feature: --threaded option for command processor uses
2473 # new feature: _signedApplet boolean is available:
2488 # new feature: reading COMPND and HEADER records of PDB file
2489 # new features for Protein Explorer:
2490 # new feature: set messageStyleChime
2497 # new features:
2504 # new feature: jmolSetCallback("evalCallback", "someFunction")
2523 # new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax
2524 # new feature: draw VECTOR {atom center} {dx dy dz}
2525 # new feature: draw with mixed types processes them in order
2527 # new feature: draw .... ">xxx" first character of title ">" forces title to
2529 # new feature: set quaternionFrame "c" "p" "q"
2533 # new feature: random(a), random(a,b) where a is lower bound and b is upper bound
2534 # new feature: cross(a,b)
2535 # new feature: sin(x), cos(x)
2536 # new feature: set pdbSequential (default FALSE) for custom PDB files
2538 # new feature: set drawPicking now enables measuring among atoms and DRAW points
2540 # new feature: CIF reading of B factors for thermal ellipsoids
2541 # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete]
2570 # new feature: (popup menu) Biomolecules submenu added within title menu
2580 # new feature: ZAP clears undo stack
2594 # new feature: more load FILTER options:
2610 # new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY"
2627 # new feature: load [file info] FILTER "[filter string]"
2628 # new feature: load [file info] FILTER "BIOMOLECULE n"
2629 # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n"
2646 # new feature: isosurface ELLIPSOID id
2653 # id is a REQUIRED field. AXES is required if a new ellipsoid is being defined
2699 # new feature: ellipsoid ball rendering tied to "set wireframerotation" option
2700 # new feature: set ellipsoidAxisDiameter x.y
2709 # new features for ellipsoid rendering:
2755 # new feature: DATA "data2d_xxxxx"..... end "data2d_xxxxx"
2756 # new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
2758 # new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
2761 # new feature: GamessUK reader
2762 # new feature: reset VARIABLES (replaces "reset ALL")
2777 # new feature: draw CYLINDER
2785 # new feature: draw CIRCLE
2798 # new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y
2799 # new feature: minimization FIX {atom expression}
2806 # new feature: show minimization
2807 # new feature: x = getProperty("minimizationInfo")
2814 # new feature: isosurface MAXSET n # removes larger fragment sets
2815 # new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a fact…
2821 # new feature: minimize ENERGY # no stepping
2822 # new feature: minimize STEPS n
2823 # new feature: minimize CRITERION x.y
2824 # new feature: minimize CLEAR # flushes logged info and saved atom info
2826 # new feature: echoCallback
2827 # new feature: measureCallback
2828 # new feature: minimizationCallback
2829 # new feature: scriptCallback
2830 # new feature: save/restore coordinates
2831 # new feature: getProperty minimizationInfo
2852 # new feature: minimize command -- mostly untested
2879 # new feature: set loglevel 6 allows a "debugHigh" setting
2908 # new feature: delete {atom expression} NEEDS TESTING
2917 # new feature: zap {atom expression} # zaps models associated with given atoms.
2961 # new feature: MODEL/ENDMDL records in write PDB (still no TER records)
2964 # new feature: Spartan archive reader now reads aromatic bonding
2972 # new feature: MODEL/ENDMDL records in write PDB (still no TER records)
2975 # new feature: Spartan archive reader now reads aromatic bonding
2981 # new feature: four optional defaults for Van der Waals radii:
2990 # new radii to:
2994 # DATA "element_vdw" 6 1.7; 7 1.8 END "element_vdw"; # separate using semicolons or new lines
3011 # new feature: show vdw shows a listing of the currently set VDW radii
3013 # new feature: integration of star, halo, and spacefill code so all behave the same.
3046 # new feature: settable Van der Waals radius using {carbon}.vanderwaals = 1.7
3048 # new feature: DATA "property_x i j" .... END "property_x i j"
3050 # new feature: State save of property_xxx now in easily readable Jmol Data Format
3077 # new feature: menu includes all standard color scheme options
3078 # new feature: inline math @{x+3} extended to all commands
3079 # new feature: .sub(), .add(), .mul(), .div() extended to all operand types
3100 # new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting
3113 # new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing
3126 # new feature: Spartan input files read as Odyssey format
3128 # new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for test…
3129 # new feature: set fontScaling TRUE/FALSE
3130 # new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)]
3138 # new feature: getProperty("appletInfo") includes a key "registry" for which
3147 # new feature: reading of Spartan spinput files (uses Odyssey reader)
3171 # new feature: "getProperty FILECONTENTS ." in the context of
3173 # new feature: zip file reading extended to write FILE
3177 # new feature: allows zip files to be designated as default directoriesusing
3181 # new feature: pmesh BINARY "filename"
3208 # new feature: within(structure,atom_expression)
3262 # new feature: isosurface COLOR RANGE ALL added as an equivalent to COLOR RANGE with no numbers
3268 # -- all functionality in new.htm, new2.htm, and new0.htm tested --
3343 # new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to An…
3360 # new feature: trajectory command no longer necessary -- deprecated (was in 11.2)
3367 # new feature: set syncScript; set syncMouse
3380 # new feature: set c? -- displays all Jmol parameters starting with "c" or "_c"
3382 # new feature: formatted gOpenMol formatted plt volume data reader.
3383 # new Jmol.js for 11.4
3393 # new feature: set wireframeRotation
3396 # new feature: _slabPlane, _depthPlane variables
3420 # new feature: (isosurface) reading of XPLOR ascii electron density map data
3450 # new feature: set strandCountForStrands
3451 # new feature: set strandCountForMeshRibbon
3457 # new feature: connect PDB # just does PDB CONECT connections
3458 # new feature: connect PDB AUTO # PDB CONECT and autobonding
3479 # new feature: MOL isotope column read; interpreted for D, T, 11C, 13C, 15N (for now)
3498 # new feature: direct reading of MAC Spartan06 directories.
3505 # new feature: script "myfile.zip|xxx.spt"
3509 # new feature: load "myfile.zip|CH3CL.MOL"
3512 # new feature: load "myfile.zip|myfile2.zip|CH3CL.MOL"
3517 # new feature: print getProperty("fileContents","zipFileName", "subfile", "subFile",...)
3568 # # new Keys: 'OPT HF 3-21G(*) FREQ '
3572 # new feature: load "myfile.zip" MANIFEST "...."
3573 # new feature: JmolManifest in a zip file directs which files to load and in what order
3588 # new feature: show spacegroup "X,Y,Z;-X,Y,Z;..." finds space group associated with specific operat…
3594 # new feature: load xxx.zip n # where n is the desired file, starting with 1
3595 # new feature: Spartan06 file format reader
3596 # new feature: ZIP file reading for multiple models
3611 # new feature: calculate surfaceDistance FROM {atomExpression}
3612 # new feature: calculate surfaceDistance WITHIN {atomExpression}
3618 # new feature: calculate surface {atomExpression}
3620 # new feature: set isosurfacePropertySmoothing # default TRUE
3625 # new feature: calculate polymers
3639 # bug fix: new boundbox command with small numbers of atoms
3644 # new feature: Jmol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for th…
3651 # new feature: Jmol math getProperty() function
3677 # bug fix: new label fonts not loaded when labels resized
3681 # new feature: boundbox {atomExpression} [on|off]
3685 # new feature: boundbox {point or expression} {vector to corner} [on|off]
3688 # new feature: boundbox corners {point or expression} {point or expression} [on|off]
3693 # new feature: show boundbox gives valid boundbox commands and volume
3704 # new feature: isosurface CAP [plane definition]
3718 # new feature: Back to "SET" for state definitions of Jmol parameters.
3722 # solution is a new feature:
3724 # new feature: "\" at the end of a line marks a continuation of that line
3756 # new feature: set drawPicking TRUE
3764 # new feature: connect (...) (...) aromatic auto
3773 # new feature: shadows can be activated again via noShadows parameter in .pov file
3779 # bug fix: new frame title and state
3781 # new feature: set echo [echoID] MODEL [model number]
3788 # new feature: frame title "this a title for THIS frame only"
3799 # new feature: **** Jmol Embedded Script **** recognized in /* ... */ comments and /** ... **/ supe…
3809 # new feature: .type math function
3811 # new feature: Jmol math allows direct string replacement in select atom expressions:
3821 # new feature: set atom properties using an array instead of a DATA statement:
3830 # new feature: set atom properties from space-separated string:
3838 # new feature: Ramachandran/Model commands switch between plot and model
3847 # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR
3854 # new feature: model-based parallel array calculations:
3858 # new feature: point3f in array():
3863 # new feature: draw object title line number corresponds to model number for multi-model draw objec…
3865 # new feature: matte finish for isosurfaces
3873 # new feature: MoldenReader (Matthew Zwier <mczwier@gmail.com>)
3874 # new feature: MO calculations for spherical orbital basis (Matthew Zwier <mczwier@gmail.com>)
3890 # new feature: write FILE (text-files only)
3892 #new feature webexport: automatic usage of a different path to the applet for local files to allow …
3894 #webexport instruction updated to reflect new feature.
3909 # new feature: set antialiasTranslucent TRUE/FALSE
3918 # new feature: @{mathExpression} for echos, select, etc. where @x can be used.
3924 # new feature: {atomExpression}.color = "red" (or "[xff0000]" or {255,0,0}
3926 # new feature: helixes as barrels in cartoons or rockets using
3988 # new feature: inline scripting allows math
3993 # new feature: site_ support for PDB and CIF
4001 # adds "OP1" and "OP2" as backbone designators (new PDB designation)
4009 # Web Export Dialog changes: new intro tab, new minilog at bottom, instructions converted to
4023 # new feature: getproperty stateinfo TYPE
4058 # new feature: valence -- sum of bond orders
4063 # new feature: settable atom properties (preliminary):
4075 # new feature: set atom properties using {xxxx}.x =
4082 # new feature: set atom properties using an array instead of a DATA statement:
4098 # new feature: adds H/Br/Cl/I/C logic to aromatic bond assignments
4099 # new feature: adds Oxygen/Sulfur logic to aromatic bond assignments
4100 # new feature: adds Nitrogen logic to aromatic bond assignments
4103 # new feature: PovrayExporter (pim schravendijk <pimlists@googlemail.com>)
4109 # new feature: aromaticSingle and aromaticDouble bond order options
4110 # new feature: "smartaromatic" bonds # turned off with "smartAromatic = false"
4111 # new feature: calculate aromatic # calculates reasonable aromatic double/single alternation.
4112 # new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic
4113 # new feature: select ISAROMATIC # selects aromatic atoms
4114 # new feature: MOL reader recognizes bond types 4,5,6,7
4116 # new feature: isosurface/mo "squared"
4118 # new feature: fully generalized bond order "partial n.m"
4125 # new feature: connect may use numeric bond orders, including "partial n.m"
4127 # new feature: preliminary work on functionalized state
4128 # new feature: global/local functions (to applet, for instance
4137 # new feature: bondOrders 2.5 and -2.5 PartialTriple and partialTriple2
4155 # new feature: _1 parameter for "first atom" in second expression of connect:
4157 # new feature: better reporting of PMESH file format errors
4185 # new feature: within(distance,isWithinAllModels,atomExpression)
4262 # new feature: fully functional user-defined functions:
4345 # new feature: set defaultDrawArrowScale # 0.5 initially
4350 # new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb
4356 # new feature: array variables saved as arrays
4365 # new feature Jmol math point(x,y,z) function
4382 # new feature: Jmol math array element assignment:
4406 # new feature: Jmol math x = array(a,b,,,,)
4413 # new feature: Jmol math plane(x,y,z,w) function
4424 # new feature: print command prints a variable expression
4431 # new feature: aPlane.distance({some atoms})
4433 # new feature: someArray.add("string") adds string to right of each item
4434 # new feature: someArray.sub("string") adds string to left of each item
4444 # new feature: MOPAC mgf file UHF orbital reading -- preliminary only
4446 # new feature: byElement and byResidue color schemes allow
4493 # new feature: fully customizable popup menu -- see file jmol.mnu
4503 # new feature: show menu
4504 # new feature: getProperty menu
4512 # new feature: fully customizable popup menu -- see file jmol.mnu
4526 # new feature: %l atomic element number
4528 # new feature: APPLICATION -q (quality) option
4529 # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...]
4533 # new feature: {r,g,b} can be used in place of [r,g,b] for indicating color,
4539 # new feature: expanded color command for properties
4547 # new feature: unlimited user-defined color schemes:
4554 # new feature: fully remappable isosurface using COLOR command:
4569 # new feature: .color for numbers and points delivers the
4584 # new feature: color ["schemeName"] RANGE [min] [max]
4595 # new feature: show colorscheme "schemeName"
4606 # new feature: set userColorScheme [list of color names]
4621 # new feature: APPLICATION: File|Export...|Export to Web Page
4630 # new feature: lcaoCartoon rotate [x|y|z] degrees create "px"
4631 # new feature: adds Jaguar PLT plot file reader for isosurface
4643 # new feature: molecular dipole for Gaussian files
4645 # new feature: simple calculation of approximate dipole moment from charge distributions.
4649 # new feature: show frame # based on models in the current frame set, displays information about fr…
4651 # new feature: application option for web page export
4653 # new feature: write JPG n "filename" # where n is the quality (<=100)
4661 # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum dist…
4662 # new feature: synchronization of applets using JavaScript
4663 # new feature: synchronization of applets using Jmol scripts:
4699 # new Jmol.js feature: jmolGetSyncId(); jmolSetSyncId(id);
4772 # new command: ramachandran
4774 # new command: quaternion [w x y z] [derivative]
5040 # full support for switching languages, including a new "language" menu item
5052 # new language submenu with checkboxes.
5077 # code: totally reorganized isosurface code; new org/jmol/jvxl packages
5147 # the application of symmetry operations creates new bonds that
5150 # new bonds are created that are between atoms that were created
5242 # off the ID, a new isosurface is created.
5293 # adds isosurface CAVITY x.xx -- a new way to depict the cavities of
5304 # load append ..... # APPENDS the file(s) or model(s) as new frames onto the current set.
5441 # 1) adds two new modifiers:
5479 # plane and bondset are new; arithmetic operations are not fully developed.
5505 # atom sets and return a new atom set, just like in SELECT.
5877 # and it will AUTOMATICALLY update with new values as you select different atoms.
5885 # new: within(x.x,plane,$plane1)