· bug fix: undocumented/unoperational navigation ON/OFF removed
· bug fix: spacegroup "-- [--]" displayed when load command option SPACEGROUP is used
· bug fix: quaternionFrame default now "p"
· bug fix: quaternion difference off by one group
· bug fix: mol2 reader not properly allowing override of CRYSIN unit cell record
· bug fix: draw picking in multimodel context causes null pointer exception
· bug fix: WRITE MO does not work when no current MO is present
· bug fix: select model=1 does not work (since 11.6.RC17!)
· bug fix: dipole offsetside not working for molecular dipole (EVER!)
· bug fix: 2 pixels off in y for labels. Don't know why I thought that was necessary in Text.java::setBoxXY.
· bug fix: dipoles cannot be colored by name
· bug fix: dipole settings not accessible via wildcards
· bug fix: gzipped gzip file not read properly. (Jmol-FAH files)
· bug fix: Crystallographic Information File not recognized.
· bug fix: write FRAMES also for trajectories
· new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
· new feature: GAMESS reader now sets calculationType, orbital type, and auxiliaryInfo.calculationOptions
· bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
· bug fix: dipoles cannot be colored by name
· bug fix: dipole settings not accessible via wildcards
· new feature: merging of label() and format() functions -- same in all respects.
· bug fix: spartan'08 reader not reading vibrations
· bug fix: /** comment ending line can cause odd error
· bug fix: set xxxx n where n is an integer fails.
· bug fix: GAMESS reader not properly assigning MOs
· code: better .stddev calculation
· new feature: a = [] note that a+=2 then produces [2] -- "a+=" similar to JavaScript a.push(2)
· bug fix: a="test";a[1] = "b" not working
· bug fix: {atomExpression}.min, .max
· new feature: merging of label() and format() functions -- same in all respects.
· bug fix: Application setAppletContext null pointer
· bug fix: point + integer wrong result
· bug fix: biomolecules for new PDB format
· bug fix: isosurface cavity colorscheme not applied
· bug fix: isosurface cavity colorscheme "sets" error
· bug fix: selected connected(hbond) not working.
· new feature: load VIBRATION "filename" n .......
· --all features of the load command, but only loads the vibrational information
· --applies {within(loadAtomDataTolerance,xyzcoord)}.vxyz = vibcoord, so to all unit cells
· --optional n is just as for any load -- optional nth model
· --operates on previously selected atoms only
· --allows embedded jmolscript, just as for any load
· --sets _vibrationName from file's atom set collection name
· new feature: loadAtomDataTolerance (see above)
· bug fix: load {n n n} not saved in state
· new feature: load {a b -c} packs a x b x c cells
· new feature: select within(-0.1, {1/2 1/2 1/2}) -- negative distance within selects atoms based on unitcell coordinates
· new feature: select within(-0.1, atomno=3) -- negative distance within selects atoms based on unitcell coordinates of all atoms involved
· new feature: select within(-0.1, true, atomno=3) -- negative distance within model selects atoms based on unitcell coordinates
· new feature: select ux|uy|uz < x.x -- selection based on unit coordinates
· new feature: {x y z}.fxyz -- returns fractional from cartesian
· new feature: {x y z}.uxyz -- returns unitcell from cartesian
· new feature: {x y z}.ux, .uy, .uz similar to .fx, .fy, .fz
· new feature: {x y z}.xyz -- returns cartesian from fractional
· note that .x .y .z does NOT do this conversion. If that is
· intended, you need to use {x y z}.xyz.x
· if multiple models are visible, then all these just return as through there were no unit cell.
· #
· new feature: {atomExpression}.uxyz, .ux, .uy, .uz -- unit cell coordinate
· The value depends upon the setting of unitcell offset. For example, if we have
· #
· unitcell 444
· #
· then {x}.uxyz will be in the range {-1,-1,-1/1} (inclusive) to {0,0,0/1} (exclusive)
· Note that uxyz is not settable, but fxyz is, so one could, for example,
pack a unit cell using:
· #
· unitcell 555
· # n = {*}.size
· # for (var a = 1; a < n; a = a + 1)
· # {atomno=a}.fxyz = {atomno=a}.uxyz
· # end for
· bug fix: {atomExpression}.fxyz does not return factional value, just 0.0
· bug fix: {atomExpression}.fxyz does not return factional value, just 0.0
· bug fix: Hall lattice operation (SHELX only) could place atoms in unexpected unit cell
· bug fix: unitCell normalization error could miss some atoms in multi-unit cell visualizations
· bug fix: calculate hbonds can fail when group does not have O or OXT atoms
· bug fix: data "append" does not set model the way load "append" does
· bug fix: application frame arrows do not work after loading multiple models
· bug fix: isosurface incorrectly setting number of grid points for MEP surface map
· bug fix: reading multiple files from a ZIP file collection, Jmol was forcing autobond even when bonds were defined
· bug fix: load MANIFEST not working properly
· bug fix: V3000 reader chokes on CHG=n and does not recognize MASS=n
· bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!)
· new feature: CML "isotope" and CML "partial12" bond order.
· new feature: GAMESS reader reads NBOs using
· load "xxx.gamess" filter "!EIGEN" # to only load NBOs; by default ALL MOs are loaded.
· new feature: QChem reader reads occupancy, frequencies and MOs
· bug fix: reading multiple files from a ZIP file collection, Jmol was forcing autobond even when bonds were defined
· bug fix: (application) animation tooltips incorrect
· bug fix: V3000 reader chokes on CHG=n and does not recognize MASS=n
· bug fix: MOL files within ZIP files do not respect bonding. (not fully fixed, but fixed when reading single MOL files from ZIP files)
· bug fix: 11.7.27 does not display color for MOs; "color MO" can crash Jmol
· bug fix: isosurface/mo FRONTONLY not operative
· bug fix: MO calculations skips d2+ orbital due to integer division.
· bug fix: (application) measurement tool bar icon not toggling
· bug fix: "color MO" if executed twice can crash Jmol
· bug fix: line raster not completing lines
· code: JmolCallbackListener implemented, extended by JmolStatusListener
· code: JmolViewer now includes setJmolCallbackListener
· bug fix: measure n1 n2 n3 n4 with just numbers selecting atoms in frame 1 rather than current frame.
· bug fix: toolbar icon for pickMeasure tied to tools "measurements..." item
· bug fix: (Application) meaurement table not updating properly
· bug fix: (Application) measurements toolbar icon does not stay shaded
· bug fix: very subtle code error on lines and cylinders rasterization not completing line end pixel in most cases
· bug fix: (Application) measurement icon measures angles, not distances.
· new feature: JVXL format supports polygonColixes[]
· code: polygonColixes[] to define polygon colors rather than vertex-based colors (as in OBJ file)
· new feature: isosurface points can be retrieved using $id[n] where n=0,1,2,3... similar to $draw[n]
· debugging: setTestflag2() turns on vertex labeling in isosurfaces
· new feature: isosurface OBJ file reader using
· isosurface OBJ "myfilename" n
· where n is an optional pointer to a specific group (starting with 1)
· # bug fix: subtle MarchingSquares calculation error produces incorrect contours for mapped plane
· new feature: hover displays isosurface values for contour plots and planar plots
· new feature: isosurface .... map contour [n] [mep|MO homo|etc]
· for example: isosurface molecular map contour 10 mep
· [n] is optional; defaults to 9
· new feature: isosurface CONTOURLINES|NOCONTOURLINES
· displays contour lines; for planes, same as MESH|NOMESH
· new feature: default rendering for isosurfaces involving the
· CONTOUR keyword is CONTOURLINES NOFILL
· new feature: hovering over isosurface contourlines displays value
· bug fix: isosurface TRIANGLES not turning off when isosurface cleared
· bug fix: remapping colors of translucent isosurface can have incorrect colors
· bug fix: isosurface sphere 1.0 map molecular not working
· bug fix: MO calculation with selected atoms can fail
· bug fix: picked atoms automatically selected -- bug in 11.7.24
· new feature: very preliminary isosurface ED (RHF only) //and isosurface ESD
· bug fix: JVXL writing after reading JVXL file may not write properly
· bug fix: Jmol in other applications not initialized the same way can cause null pointer exception loading file with symmetry
· bug fix: line raster not completing lines
· bug fix: (Application) meaurement table not updating properly
· bug fix: subtle MarchingSquares calculation error produces incorrect contours for mapped plane
· bug fix: isosurface TRIANGLES not turning off when isosurface cleared
· bug fix: remapping colors of translucent isosurface can have incorrect colors
· bug fix: isosurface sphere 1.0 map molecular not working
· bug fix: MO calculation with selected atoms can fail
· bug fix: Jmol in other applications not initialized the same way can cause null pointer exception loading file with symmetry
· new feature: load "myfile.cif" {ijk i'j'k' -1}
· loads crystal structure and packs unit cell
· new feature: load "myfile.cif" PACKED
· same as {555 555 -1}
· bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
· bug fix: Menu File|Open does not honor "start in" directory
· bug fix: set picking draw can lose focus during drag operation
· bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
· bug fix: write command does not report full path to file written
· bug fix: Menu File|Open does not honor "start in" directory
· bug fix: user menu ...Text menus not translated
· new feature: translate x|y|z x.x nm|angstroms|%
· bug fix: structure helix ({xx:yy}) compiler bug
· new feature: additional VRML support (Angel Herraez)
· new feature: u3d exporter template only -- no actual output
· bug fix: 11.7.15 does not run script after loadInline applet parameter
· new feature: Alchemy/3DNA reader
· #
· new feature: new command "exitJmol" does just that -- application only;
· can be overridden in a script by user defining the function "exitJmol"
· #
· new feature: application -d --debug sets loglevel to 5
· new feature: application -J --jmolscript1 Jmol script BEFORE -s
· new feature: application -j --jmolscript2 Jmol script AFTER -s not accepting values
· #
new feature: (embedded application method of JmolViewer):
· #
· public Object viewer.getImageAs(String type,
· int quality,
· int width,
· int height,
· String filename,
· OutputStream outputStream);
· #
· allows creation of an image of a given type ("JPG", "JPEG", "JPG64", "PNG", "GIF", "PPM")
· of a specific quality (-1 indicates default)
· 0 to 100 for JPG (-1 = default of 75)
· 0-9 for PNG (-1 = default of 2)
· and specific width and height
· and returned as byte[] (when fileName = null, os = null)
· or sent to an output stream (os != null)
· or set to a file (os == null, fileName != null)
· #
· return can be String if there is an error.
· #
command sequence, for example:
· #
· jmol.viewer.scriptWait("load =1crn;cartoons on;set antialiasdisplay");
· Object nullOrErrorMsg = jmol.viewer.getImageAs("JPG", 75, 300, 300, "t75.jpg", null);
· Object nullOrErrorMsg = jmol.viewer.getImageAs("JPG", 75, 300, 300, null, os);
· Object bytesOrError = jmol.viewer.getImageAs("JPG", 75, 300, 300, null, null);
· Object stringOrError = jmol.viewer.getImageAs("JPG64", 75, 300, 300, null, null);
· #
· this method, like WRITE IMAGE uses the antialiasImage settings
· #
· primarily, this is for writing to an OutputStream directly, but
· the rest seemed simple to implement along with that.
· #
new feature: (embedded application method of JmolViewer):
· #
· public String clipImage(String text);
· #
· sends image (null parameter) or text to clipboard
· bug fix: application -i option still gives message from "set xxxx"
· bug fix: some quaternions cannot be created from a 3x3, namely: q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format)
· bug fix: ignoreError -- need not get error string
· bug fix: write image does not set mustRender
· bug fix: set debugscript and set loglevel do not act in script immediately
· bug fix: translations of Console not implemented correctly
· bug fix: translation not disabled when messageCallback is present
· bug fix: script error messages not updating when language changed
· bug fix: MO scale
· bug fix: measure allConnected broken
· new feature: q = quaternion(matrixColumn1, matrixColumn2)
· quaternion from first two columns of a 3x3 rotation matrix
bug fix: some quaternions cannot be created from a 3x3, namely:
· q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format)
· bug fix: ignoreError -- need not get error string
· bug fix: write image does not set mustRender
· bug fix: set debugscript and set loglevel do not act in script immediately
· # new feature: Jmol.js jmolScriptWaitOutput(script) returns all messages that would
· have been sent to the console.
· new feature: applet.getJmolStatus("AS_VECTOR") and applet.getJmolStatus("AS_HASHTABLE")
· allows slightly different format for JSON return
· new feature: measureCallback reports pending measurements as well as completed ones
· # code: documentation for callbacks in Viewer; refactoring of StatusManager
· # function myAnimFrameCallback(frameNo, fileNo, modelNo, firstNo, lastNo) {}
· function myEchoCallback(app, message, queueState) {}
· function myErrorCallback(app, errType, errMsg, objectInfo, errMsgUntranslated) {}
· function myHoverCallback(strInfo, iAtom) {}
· function myLoadStructCallback(fullPathName, fileName, modelName, errorMsg, ptLoad) {}
· function myMeasureCallback(strMeasure, intInfo, status) {}
· function myMinimizationCallback(app, minStatus, minSteps, minEnergy, minEnergyDiff) {}
· function myPickCallback(strInfo, iAtom) {}
· function myResizeCallback(width, height) {}
· function myScriptCallback(app, status, message, intStatus, errorMessageUntranslated) {}
· function mySyncCallback(app, script, appletName) {
· ...[modify script here]...
· return newScript
· }
· new feature: errorCallback and scriptCallback report untranslated errors
· new feature: when errorCallback or scriptCallback is enabled, messages are translated
· note: To get translation in message callbacks, use jmolSetTranslation(true)
· bug fix: translations of Console not implemented correctly
· bug fix: translation not disabled when messageCallback is present
· code: efficiencies
· new feature: jmolGetPropertyAsString("errorMessage")
· new feature: out-of-memory "Java heap error" trapping in scripts and image creation
· new feature: save [bonds|coordinates|orientation|selected|state|structure] DELETE
· bug fix: write .... @{...} can fail # bug fix: write coords CLIPBOARD broken
· bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({})
· bug fix: applet compilation error not sent in termination message
· bug fix: build javax package does not include AxisAngle4d.class, Matrix4d.class
· bug fix: compilation of myfunc({1 2 3}) fails
· bug fix: hover watcher occasional uncaught exception
· bug fix: write .... @{...} fails # bug fix: write .... @{...} can fail
· bug fix: write image CLIPBOARD broken
· bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({})
· bug fix: applet compilation error not sent in termination message
· bug fix: build javax package does not include Matrix4d.class, AxisAngle4d.class
· bug fix: compilation of myfunc({1 2 3}) fails
· bug fix: hover watcher occasional uncaught exception
· new feature: isosurface PMESH; pmesh command deprecated
· code: pmesh now a subclass of isosurface, with org.jmol.jvxl.PmeshReader doing the work.
· new feature: all options of isosurface now option for pmesh.
· all pmesh command does is guarantee that if the pmesh data is standard pmesh ASCII data,
· then it will be read correctly. Binary pmesh files may be read with isosurface command.
· new feature: pmesh files and inline scripts now can be colored and saved as JVXL files
· new feature: isosurface INLINE "--pmesh data--"
· # bug fix: .xxx broken for Jmol 11.7.11
· JVXL 2.0 format enhancements
· new feature: #xxx comments act as targets for goto as well as MESSAGE commands
· bug fix: goto xxx with trailing white space fails to find xxx
· bug fix: goto with a
· comment in the script prior to the target line fails
· bug fix: two //xxx comments in a row breaks script
· new feature: fully remappable JVXL files
· new feature: JVXL file format version 2.0 writing and reading for general vertex/triangle file source.
· code: superfast JVXL compression/decompression
· bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
· load =1crn;calculate straightness;color "bwr" range 0 1;color straightness
· new feature: efvet file reader (http://ef-site.hgc.jp/eF-site)
· isosurface color "rwb" "myfile.efvet"
· bug fix: isosurface APBS dx file reader broken (since 4/2007)
· menu: "Minimize" GT
· bug fix: negative number in range involving ^ fails: select 10^P -17^P
· bug fix: goto xxx with trailing white space fails to find xxx
· bug fix: goto with a
· comment in the script prior to the target line fails
· bug fix: two //xxx comments in a row breaks script
· code: superfast JVXL compression/decompression
· bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
· load =1crn;calculate straightness;color "bwr" range 0 1;color straightness
· # bug fix: isosurface APBS dx file reader broken (since 4/2007)
· menu: "Minimize" GT
· bug fix: initializeBspf(); missing in setTrajectory()
· new feature: hbonds delete
· new feature: calculate hbonds {*} {*} between {O or N} and {O or N} only
· new feature: set hbondsAngleMinimum
· if hbondsAngleMinimum is set > 0 (default 90 ?), then that angle is checked for any atoms A--X- - -Y where A is attached to X, and X and Y are the two heteroatoms involved.
· new feature: set hbondsDistanceMaximum
· maximum distance for X---Y. (default 3.25 ?)
· bug fix: AMBER atom type IM and IP not recognized
· bug fix: AMBER topology file reading of IFBOX=2 files
· bug fix: antialiased fontscaling labels can appear incorrectly
· bug fix: font maximum reduced
· code: major scaled memory font savings
· bug fix: more lenient MopacGraphF format resolving
· bug fix: "valence" not "valency" in data property_valence
· bug fix: set antialiastranslucent false not functional
· bug fix: text color near black with antialiasdisplay becomes white
· bug fix: text antialiasing of near-black text looks very bad when antialiased
· bug fix: draw point translucent only draws ring
· new feature: mol2 format reads force field atom types for AMBER, CFF91, GAFF, ESFF, CHARMM, COMPASS, CVFF, CVFF_aug, PCFF force fields (rev2)
· bug fix: load string inline with multiple models fails
· code: FindBugs fixes for Eval, DrawRenderer, Isosurface, ForceFieldUFF,PdbReader
· code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination
· bug fix: set labelToggle malfunctioning
· bug fix: missing default background for toggled labels
· bug fix: color {oxygen} translucent blue
· bug fix: color translucent 1 blue 1-8 integer settings off by one
· bug fix: background color +/-1 adjustment removed
· bug fix: spardir within /M... directory
· bug fix: (minor) "set echo xxx display" equivalent to "set echo xxx displayed" missing
· bug fix: (minor) "set echo xxx hide" equivalent to "set echo xxx hidden" missing
· One of the most significant upgrades of Jmol to date, Jmol 11.6 includes over 200 new features introduced between January and October of 2008, including several totally new capabilities, such as point group identification and drawing of point group symmetry elements, thermal ellipsoid rendering, the capability to delete specific models from a set, 2D to 3D conversion and 3D minimization using the Universal Force Field (UFF), 3D Ramachandran plotting, quaternion maps for peptides and nucleic acids, and upgrading of the signed applet to enable file writing.
· bug fix: vibration thread not closing down for applet destroy when applet is off-screen
· bug fix: was reading server path for local path from history in Webexport
· bug fix: Removed stray semicolons from header script comments in webexport templates. They were causing WYSIWYG web editors to corrupt the scripts.
· bug fix: Popin.png in WebExport replaced, was too large, causing dialog box to default to too big on small screens.
· bug fix: PDB site definition does not ignore empty site definitions
· bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo
