August 24th, 2012· This major release brings to the stable release several very important new features in Jmol developed over the past year.
· With well over 500,000 full application downloads (that is, distinct binary downloads by application users or developers, not simple applet downloads by web page visitors), full server-side Java support for non-Java (iPhone/iPad) or non-applet (Android) mobile devices, and a completely new JavaScript interface, Jmol is well-positioned for the next phase of development of a high-level scripted high-functional HTML5/WebGL user interface.
New features (see http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm) include:
APPLET:
· a new OOP JavaScript interface (Jmol-JSO) allowing nonJava options such as ChemDoodle and GLmol as well as JME/JSpecView connectivity (see http://wiki.jmol.org/index.php/Jmol_Javascript_Object) to be seamlessly integrated into a web page in a platform-aware manner.
· JmolData full "headless" operation for server-side processing allowing image-creation, server processing, and remote cross-domain sourcing for the unsigned applet and applet surrogates such as ChemDoodle and GLmol.
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 > 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
October 4th, 2011· FEATURE CHANGE: "ligand" definition changed to
· !(protein,nucleic,water,UREA)"
· instead of "hetero and not solvent"
· FEATURE CHANGE: default zShadePower set to 3
· FEATURE CHANGE: undocumented a[13] = 3 (where a is a matrix, for a[1][3]) removed
· FEATURE CHANGE: DSSP default for "calculate structure"
· -- old way is now "calculate structure RAMACHANDRAN"
· FEATURE CHANGE: DSSP default for LOAD of PDB file with no header.
· in previous versions, Jmol used a ramachandran-angle-based calculation
· for secondary structure determination when a PDB file had no HELIX or SHEET records.
· It just seems reasonable to use the industry-standard DSSP method instead.
· new feature: JmolSmilesApplet method (smiles1)
· new feature: JmolSmilesApplet method getRelationship(smiles1, smiles2)
· new feature: The Jmol application can now communicate via sockets
· with other Jmol applications or specialized servers.
The SYNC command has been expanded to make this very easy:
· sync -nnnn starts a server on local port nnnn accepting only local connections
· sync nnnn "background white" (from another app, generally) would execute that
· command on the app acting as a server
· You can also do this from one app frame to another, because they are independent
· instances of Jmol.
Jmol can provide server service to other apps using:
· sync -3000
· [start other app, connecting on 3000]
· sync 3000 .....
· Because once the server is started and another app has connected,
· Jmol will send messages to that other app, not itself.
· To test the service within one application, just create the server and send
commands to itself using a negative port number:
· sync -3000;sync -3000 'Mouse: rotateZBy 30'
· Note that in this context the "server" is the one getting commands from the "client"
· But the server can also send commands to the client provided the client has given the
· appropriate handshake: {"magic":"JmolApp","event":"out"}
Sent from Jmol (via outSocket):
· {"magic" : "JmolApp", "role" : "out"} (socket initialization for messages TO jmol)
· {"magic" : "JmolApp", "role" : "in"} (socket initialization for messages FROM jmol)
· {"type" : "script", "event" : "done"} (script completed)
Sent to Jmol (via inSocket):
· {"type" : "banner", "visibility" : "ON" or "OFF" } (set banner for kiosk)
· {"type" : "banner", "text" : bannerText } (set banner for kiosk)
· {"type" : "command", "command" : command } (script command request)
· {"type" : "content", "id" : id } (load content request)
· {"type" : "move", "style" : (see below) } (mouse command request)
· {"type" : "quit" } (shut down request)
· {"type" : "sync", "sync" : (see below) } (sync command request)
· {"type" : "touch", (a raw touch event)
· "eventType" : eventType,
· "touchID" : touchID,
· "iData" : idata,
· "time" : time,
· "x" : x, "y" : y, "z" : z }
· For details on the "touch" type, see org.jmol.viewer.ActionManagerMT::processEvent
· Content is assumed to be in a location determined by the Jmol variable
· nioContentPath, with %ID% being replaced by some sort of ID number of tag provided by
the other half of the system. That file contains more JSON code:
· {"startup_script" : scriptFileName, "banner_text" : text }
· An additional option "banner" : "off" turns off the title banner.
· The startup script must be in the same directory as the .json file, typically as a .spt file
Move/sync commands include:
· {"type" : "move", "style" : "rotate", "x" : deltaX, "y", deltaY }
· {"type" : "move", "style" : "translate", "x" : deltaX, "y", deltaY }
· {"type" : "move", "style" : "zoom", "scale" : scale } (1.0 = 100%)
· {"type" : "sync", "sync" : syncText }
· Note that all these moves utilize the Jmol sync functionality originally intended for
· applets. So any valid sync command may be used with the "sync" style. These include
· essentially all the actions that a user can make with a mouse, including the
· following, where the notation represents a number of a given type. These
· events interrupt any currently running script, just as with typical mouse actions.
· "centerAt "
· -- set {ptx,pty,ptz} at screen (x,y)
· "rotateMolecule "
· "rotateXYBy "
· "rotateZBy "
· "rotateZBy " (with center reset)
· "rotateArcBall "
· "spinXYBy "
· -- a "flick" gesture
· "translateXYBy "
· "zoomBy "
· "zoomByFactor "
· "zoomByFactor " (with center reset)
· new feature: preliminary QuantumEspresso XML reader
· new feature: Jmol Application flags -k and -P
· -- -k kiosk mode: like applet, but with a banner across the top
· -- -P JSON NIO client mode over port
· -- for JSON NIO, use -J or -j to set nioContentPath and nioTerminatorMessage
to the desired values. For example:
· Jmol -k -P 31461 -j "nioContentPath='./%ID%/%ID%.json';nioTerminatorMessage='SCRIPT_DONE'"
· new feature: Jmol.js adds jmolSwitchToSignedApplet().
· This needed a new tag that is now inserted around the applet.
· new feature: filter "_Xx" for filtering element Xx
July 30th, 2010· customizable mouse button/action bindings
· multi-touch/Kiosk capability using SPARSHUI adaptation (U-Tube video)
· parallel multiprocessor capability for isosurface creation
· drag-and-drop to signed applets and the application
· model kit mode allows rapid construction of simple models
· extensive support for depiction of space groups
· conversion of 2D models (SMILES, JME, MOL) to 3D
· interface to JSDraw for 2D structure input
· interface to Flot for plotting data
· full implementation of Daylight SMILES/SMARTS
· extension of Daylight SMARTS to 3D conformation
· introduction of Jmol bioSMILES and bioSMARTS
· new JmolSmilesApplet.jar.
· JavaScript-like flow commands and TIMEOUT
· JavaScript-like TRY/CATCH error handling
· direct reading of Uppsala electron density maps
· natural bond orbital reading/rendering
· direct logging to files using the LOG command
July 15th, 2009· 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
July 1st, 2009· 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.
June 29th, 2009· 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
June 22nd, 2009· 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.
June 22nd, 2009· 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.
May 22nd, 2009· 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
May 22nd, 2009· 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
April 11th, 2009· 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
April 11th, 2009· 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)
March 17th, 2009· bug fix: 11.7.27 does not display color for MOs; "color MO" can crash Jmol
March 17th, 2009· 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
March 3rd, 2009· 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
March 3rd, 2009· 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
February 3rd, 2009· 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
February 3rd, 2009· 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
January 24th, 2009· bug fix: user menu ...Text menus not translated
January 24th, 2009· 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
December 16th, 2008· 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
December 16th, 2008· 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
December 15th, 2008· 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
November 29th, 2008· 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
November 29th, 2008· 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
November 19th, 2008· 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
November 19th, 2008· 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
November 5th, 2008· 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
November 5th, 2008· 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
October 31st, 2008· 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
October 31st, 2008· 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
October 9th, 2008· 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.
August 31st, 2008· 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
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