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y͂Oph!Gl4Kj ~X臈=#J097ۈLjMnL 63S&?}prs1@EF{f/FIxU\XX9bEXp<:IrYJNxx}9R{Z6:T7zsm =MW G j)S93p-X~>> qVC?W/p.^D{ROw]8WxDxRFI'eDqٰLQ9bcGĹp#Z# Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line version=11.6.13 # bug fix: user menu ...Text menus not translated # ----------------------------------------------------------------------------- #version=11.6.12 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries # bug fix: quaternion straightness update # ----------------------------------------------------------------------------- #version=11.6.11 # aargh -- forgot to upload file for 11.6.10 # ----------------------------------------------------------------------------- #version=11.6.10 # bug fix: vibrationperiod set to 0 if vibration off when state saved # ----------------------------------------------------------------------------- #version=11.6.9 # 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 # ----------------------------------------------------------------------------- #version=11.6.8 # 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 # ----------------------------------------------------------------------------- #version=11.6.7 # bug fix: quaternion straightness update # bug fix: applet improperly reporting status of "quiet" commands # bug fix: stereo not in state # bug fix: stereoDegrees parameter not reported correctly # ----------------------------------------------------------------------------- #version=11.6.6 # bug fix: negative number in range involving ^ still fails # bug fix: translucency of mapped isosurfaces not saved in state # bug fix: Dialog look and feel for Mac # ----------------------------------------------------------------------------- #version=11.6.5 # 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 # ----------------------------------------------------------------------------- #version=11.6.4 # bug fix: UFF.txt not included in build # bug fix: function definitions occurring before prior script commands are executed. # bug fix: message @{xxxx} in function not picking up function context variables # bug fix: Some browsers do NOT strip \n from tags, necessitating changes in loadInLine() # bug fix: "valence" not "valency" in data property_valence # bug fix: initializeBspf(); missing in setTrajectory() # ----------------------------------------------------------------------------- #version=11.6.3 # 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 # ----------------------------------------------------------------------------- #version=11.6.2 # bug fix: forcefield file UFF.prm --> UFF.txt # bug fix: better Escape method for strings # bug fix: connect auto not registered in state # bug fix: draw point translucent only draws ring # bug fix: load string inline with multiple models fails # # code: FindBugs fixes for Eval, DrawRenderer, Isosurface, ForceFieldUFF # code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination # ----------------------------------------------------------------------------- #version=11.6.1 # 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 # ----------------------------------------------------------------------------- #version=11.6 # bug fix: GIF encoder color / class not found issues # bug fix: very thin cylinder does not appear at all viewing angles # bug fix: load "/xxx" with unsigned remote applet loads local file instead of remote root directory # bug fix: sulfur/sulphur always spelt as in IUPAC Red Book # bug fix: display of aromaticSingle bond for NEW bond results in dotted bond. # translation: English language variants no longer ignored # ----------------------------------------------------------------------------- #version=11.6.RC18 # bug fix: fileName not reset after ZAP # bug fix: set echo none; color echo green null pointer exception # bug fix: .x not recognized # bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily) # bug fix: cartoons ending in helix or strand draw single dot for final amino acid # ----------------------------------------------------------------------------- #version=11.6.RC17 # bug fix: draw scale not saved in state for arc or xy arrow # bug fix: drag/drop not enabled on consoles # bug fix: Jmol state command "calculate surfaceDistance WITHIN ({...})" not passing compiler # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging # bug fix: trajectories not enabled # code: if (true...)/ if (false...) code cleanup # bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1 # bug fix: select model=0.0 caused infinite loop # ----------------------------------------------------------------------------- #version=11.6.RC16 # bug fix: mol2 PDB format better handling of chains and derived element types # bug fix: save image button/menu interface broken in 11.6.RC15 # ----------------------------------------------------------------------------- #version=11.6.RC15 # new feature: MOL2 reader is PDB-enabled. # new feature: data() and DATA expanded to allow fixed-column entry # bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP # but instead just creates a data type "property_partialcharge" # bug fix: CML reader failst to load primitive lattice parameters when no symmetry # note: CML reader only reads the first structure of a file # bug fix: CML reader not assigning atom labels # bug fix: CML files not properly loading symmetry # bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED # code: thread control for Java Swing in applet context # thread creating Swing objects MUST be event thread # -- using SwingUtilities.invokeAndWait() from the commandWatcher thread # new feature: load menu items for signed applet # new feature: save menu items for signed applet # bug fix: applet -- setting a jmolScript callback prevents menu updates # new feature: minimize menu item # new feature: signed applet allows "load ?" and includes previewer # bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default # new feature: signed applet/application load ?xxx uses load dialog # webexport help updated to reflect ability to handle files opened with "load append" # ----------------------------------------------------------------------------- #version=11.6.RC14 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is required. # new feature: write GIF # code: allows for getJpeg(quality,asString) option to return byte array instead of base64. # bug fix: xxx.split()[3].replace does not do selection first # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom # ----------------------------------------------------------------------------- #version=11.6.RC13 # bug fix: set historyLevel recording full scripts, not individual commands # bug fix: y-offset for echo text and images # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO # bug fix: findbugs input stream closure # translation: add GT.escapeHTML and stricter checking for special characters in file names # used by web export. # ----------------------------------------------------------------------------- #version=11.6.RC12 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx # bug fix: getProperty("modelinfo",{atom expression}) not working # new feature: set atomPicking TRUE/FALSE # new feature: set bondPicking TRUE/FALSE # bug fix: draw pointgroup when principalPlane == null # bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawRenderer # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value # cml reader fix for not applying symmetry to first model # translation: added GT._ calls for HTML templates and JS in WebExport # ----------------------------------------------------------------------------- #version=11.6.RC11 # bug fix: echo IMAGE and antialiasdisplay # bug fix: super/subscripts with antialiasdisplay # translation: menu items in console # bug fix: web export / language # bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1 # bug fix: d2 point groups cause null pointer exception due to missing principal axis # bug fix: {*}.x = .... broken # ----------------------------------------------------------------------------- #version=11.6.RC10 # bug fix -- set picking spin, also compatibility of set picking spin and doing measurements # bug fix -- draw pointgroup, write pointgroup draw # ----------------------------------------------------------------------------- #version=11.6.RC9 # code: more efficient return of point group information and calculation # new feature: getProperty PointGroupInfo # bug fix: show pointgroup draw null pointer exception # bug fix: print $planeA - capital letters in a draw name disallow finding it. # ----------------------------------------------------------------------------- #version=11.6.RC8 # bug fix: ramachandran / ramachandran r navigation problem # code: Minor refactoring and pruning. # --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer) # code: Pre-Jmol.js button controls removed, saving about 10K # new feature: script APPLET appletName "some script" # --allows direct inter-applet communication independent of set SYNC # --appletName can be * (all applets), > (other applets), . (this applet), # or an applet name such as "jmolApplet0" or just the extension "0" # or a quoted set of applet names separated by commas. # --for *, the current applet always reports LAST # new feature: x = script("some script", "appletName") # --same as above # --in addition, allows retrieval of information from another applet # for example: # # x = script("print getProperty(\"modelInfo.modelCount\")","B") # # gets the number of models loaded in applet jmolAppletB. # # x = script("show orientation moveto","jmolApplet2") # # gets the current orientation of applet jmolApplet2. # # xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*") # # gets a new-line-separated list of rotational quaternions for all applets with applet names. # # # new feature: print getProperty("modelInfo.models[3].file") syntax # ----------------------------------------------------------------------------- #version=11.6.RC7 # new feature: draw ramachandran includes planes connecting atoms. # bug fix: refresh for hover # bug fix: state definition for lcaoCartoons, isosurface with IDs containing spaces # new feature: $*xx* double wild cards # new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/OFF # so as to be consistent with other objects. (OFF was not deleting these) # new feature: support for application transparent background -- "-b" command switch (testing only) # and setAppletContext "-b" switch as well. # bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues # new feature: HIDE $xxx # new feature: DISPLAY $xxx # new feature: DELETE $xxx # bug fix: adaptation for malformed PDB files (HEADER with nothing following it) # bug fix: more language localization in webexport # new feature: applet message regarding help and command entry # ----------------------------------------------------------------------------- #version=11.6.RC6 # code: better navigation refreshing # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes # bug fix: language localization in webexport # ----------------------------------------------------------------------------- #version=11.6.RC5 # bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item # bug fix: set echo xxxx 30 40 # bug fix: WAY more streamlined refreshing # bug fix: createImage(), not getImage() in order to allow dynamic file change # bug fix: halo size for antialiased display # Addition of translation tags to webexport # bug fix: write IMAGE broken for 11.6.RC2+ # bug fix: unnecessary refreshes removed from moveto/zoom with time 0 # new feature: background IMAGE "filename" # code: viewer refactoring to simplify/remove private methods and synchronization # ----------------------------------------------------------------------------- #version=11.6.RC4 # bug fix: select @m throws an error # code: refactoring shapespecial into shapespecial and shapesurface # code: refactoring modelset.CellInfo into symmetry.SymmetryInfo # code: realignment of applet JAR files # -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/** # -- removal of _Jvxl.jar # -- refactoring reduces preliminary applet Jar file loading to 720K (if English) # -- should provide faster loading of simple models and more efficient loading of more complex ones # -- basic minimum load involves just JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer # ----------------------------------------------------------------------------- #version=11.6.RC3 # bug fix: minor error in pointgroup; dimension tied to radius # new feature: set dotDensity [-3 to 3] # new feature: draw pointGroup [type] [index] SCALE [x] # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n" # ----------------------------------------------------------------------------- #version=11.6.RC2 # bug fix: image background transparency # new feature: set pointGroupDistanceTolerance (default 0.2 angstroms) # new feature: set pointGroupLinearTolerance (default 8 degrees) # bug fix: Cs pointgroup not found # bug fix: set echo DEPTH/IMAGE # bug fix: woroing q1's rotation (making it the reference frame), then applying q2. # relative involves applying q2 (maintaining the original reference frame), then undoing q1. # # new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw] # new feature: draw quaternion [w|x|y|z|a|r] [difference][2] # new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw] # and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"]) # # new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame # using alpha = 0 and beta = 17 degrees. # # new feature: select whatever; quaternion draw # draws x,y,z and n vectors for a quaternion center # # new feature: straightness, defined as: # # straightness = 2*|n(dq1).dot(n(dq2))| - 1 # # where q1 and q2 are quaternions defined generally as: # # q = frame{ vA, (vC x vA), vC } # # using quaternionFrame "p", which I define as # # protein: # # vA = C--CA # vB = C--N[i+1] # # purine: # # vA = N9--C4 # vB = N9--C8 # # pyrimidine: # # vA = N1--C2 # vB = N1--C6 # # Differences dq1 and dq2 are absolute quaternion differences # on the two sides of a residue: # # dq1 === q[i] * q[i-1]_inverse # dq2 === q[i+1] * q[i]_inverse # # and n(dq) = the normal vector associated with this quaternion. # Range is from -1 to 1 # # applications (note that CALCULATE must be invoked first): # # calculate straightness # must be invoked first; # color straightness; # select straightness < 0.70; # rounds to nearest hundredth # selectX {*} x.straightness < 0.995 # does not round # # new feature: "%T" label format for straightness # ----------------------------------------------------------------------------- #version=11.5.41 # new feature: xyz reader reads partial charge in 5th field # bug fix: carbohydrate popup menu script incorrect # new feature: "load" of Jmol state scripts works same as "script" command # (file recognized as SPT type and read as a script instead) # bug fix: Jmol Embedded scripts containing script comments /* */ # new feature: getproperty menu current # bug fix: 11.5.40 cannot read most state scripts. # ----------------------------------------------------------------------------- #version=11.5.40 # (with corrected 40_dev draw scale) # new feature: new command: # # selectX {atomExpression} booleanEvaluation # # same as select() function, but simpler to implement # # new feature: full math on individual atom properties using # a new function: # # select(x;{atomexpression};booleanEvaluation) # # for example: # # x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2})) # x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi) # # bug fix: H1 and H3 in DNA are NOT backbone # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental] # new feature: draw Vector [x y] or [x y %] {x' y' z'} # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows # bug fix: set picking center should not zoom -- just too annoying # new feature: set echo myecho [x y] and set echo myecho [x y %] # new feature: axes position [x y] and axes position [x y %] # sets the axes to the x y screen position or percent indicated. # bug fix: echos with active script and a model designation # and multiple models select even if not displayed because it is not their model # that is displayed. # bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables # bug fix: "set picking identify" should be equivalent to "set picking ident" # bug fix: popup menu had stereo reversed # # new feature: signed applet shows frank "Jmol-S" which is NOT removable. # possibly to come: signed applet will send confirmation first time it reads a local file? # bug fix: reading .mmol (biological unit) files such as # http://pqs.ebi.ac.uk/pqs-doc/macmol/1j7n_1.mmol # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed. # code: better handling of twin script manager threads # new feature: /*SPLIT*/ in a command string allows it to be processed by # the two independent processors. (just to isolate javascript from load commands # for the signed applet # ----------------------------------------------------------------------------- #version=11.5.39 # new feature: --threaded option for command processor uses # a watcher thread to monitor a Vector, allowing the signed applet to open any file # the signed applet uses this automatically unless there is a # jmolSetCallback("useCommandThread", "false") # which overrides the default behavior and disallows reading of files from # JavaScript. # # NOTE a limitation: scripts intended for the signed applet that # contain both load/script commands or the load() function # CANNOT be combined with the JAVASCRIPT command. This is because # in that environment, the JAVASCRIPT command must run on the browser's # JavaScript thread, and the load command -- if crossing server boundaries -- # must NOT run on that thread. I have configured the ScriptManager to # detect the presence of the word "javascript" followed by a space (exactly that case) # and if found, use the JavaScript thread instead of the applet thread. # # Because it might be useful to combine LOAD and JAVASCRIPT (for the equivalent of a # "file loaded" callback (but see set LoadStructCallback), if a script contains # the phrase /*SPLIT*/ in upper case, exactly like that, it will be split and then run # correctly as two independent scripts. # # new feature: _signedApplet boolean is available: # # print _signedApplet # if(_signedApplet); # javascript alert("you are using the signed applet"); # end if; # # bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext() # bug fix: model-based drawing in multiple-model mode using an # array of points to load causes null pointer exception: # load cyclohexane_movie.xyz;pts = {C5}.split();print pts;draw @{pts.xyz.sub({1 0 0})} "X" # bug fix: quaternion derivative multiplication order # bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER # bug fix: select _Xx; select unknown # bug fix: better reporting of script commands and comments # new feature: reading COMPND and HEADER records of PDB file # new features for Protein Explorer: # new feature: set messageStyleChime # -- No atoms selected! # -- atoms selected! # -- atom picking: # Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z # -- script # -- Chime script completed. # new features: # show info # show residue(s) # show chain(s) # show sequence # show orientation moveto # just the moveTo; no comments # set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer) # new feature: jmolSetCallback("evalCallback", "someFunction") # -- overrides _jmol.noEval # -- canNOT be set using "set evalCallback" # -- was necessary for Protein Explorer javascript callbacks # ----------------------------------------------------------------------------- #version=11.5.38 # bug fix: lcaoCartoon naming for multiple centers # bug fix: pm rounding to integer value # bug fix: scaling of draw object for multimodel environment can cause null pointer exception # bug fix: scaling of VECTOR was from center, not origin # bug fix: select n-m:c chain selection inappropriately case sensitive # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way # bug fix: draw CIRCLE for multiple models # bug fix: application -- "make crystal..." menu item does nothing -- removed # bug fix: zap of quaternion also zaps model inappropriately # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0 # new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax # new feature: draw VECTOR {atom center} {dx dy dz} # new feature: draw with mixed types processes them in order # (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()}) # new feature: draw .... ">xxx" first character of title ">" forces title to # last point, not first # new feature: set quaternionFrame "c" "p" "q" # - "c" -- CA-C and CA-N, as per Andy Hanson # - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine # - "p" -- peptide plane CA-C and C-N' # new feature: random(a), random(a,b) where a is lower bound and b is upper bound # new feature: cross(a,b) # new feature: sin(x), cos(x) # new feature: set pdbSequential (default FALSE) for custom PDB files # -- bypasses inter-group bonding check when creating polymers # new feature: set drawPicking now enables measuring among atoms and DRAW points # -- not saved -- just transient measurements (see 11.5.46) # new feature: CIF reading of B factors for thermal ellipsoids # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete] # -- turns on, turns off, or deletes all objects of the type starting with "xxx" # code: refactoring of biopolyer resolver # ----------------------------------------------------------------------------- #version=11.5.37 # code: faster ellipsoid rendering with precalc radius factors # bug fix: spacefill ADPMIN/ADPMAX using probability ellipsoids # and ellipsoid size setting (Note -- ellipsoid command # must be run once prior to setting spacefill # bug fix: reading output from "set showscript 1" # bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value) # bug fix: ellipsoids for applied symmetry causes odd shapes (s8.cif) # bug fix: security for no mayscript may cause problem with measure callback # bug fix: rocket positions after translateselected # ----------------------------------------------------------------------------- #version=11.5.36 # bug fix: frame titles not positioning correctly for antialiased display # bug fix: quaternions created with extraneous atom lines # bug fix: select symop not behaving intuitively # code: meshrenderer debug line not removed # new feature: (popup menu) Biomolecules submenu added within title menu # ----------------------------------------------------------------------------- #version=11.5.35 # bug fix: proper thermal ellipsoid probability measures # code: better garbage collection in relation to JmolAdapter class # bug fix: load FILTER not saved in state # bug fix: application -- undo/redo buttons not disabling # new feature: ZAP clears undo stack # ----------------------------------------------------------------------------- #version=11.5.34 # bug fix: biomolecule really works this time! # ----------------------------------------------------------------------------- #version=11.5.33 # bug fix: modelLoader was assigning too much array space for chains # new feature: more load FILTER options: # # #i a specific BIOMT transformation # !#i not a specific BIOMT transformation # [XXX] a specific group ID # ![XXX] not a specific group ID (e.g. ![HOH]) # *.XX an atom name, such as .CA # !.XX not a specific atom name # *:X a chain ID # !:X not a specific chain ID # # Between types, or involving NOT, options are AND'd together # Within a type not involving NOT, options are OR'd together # Within a type, a single ! implies all are NOT # Within a type, a single * implies all are ANY # new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY" # FILTER "BIOMOLECULE 1" by default now reads the symmetry; # use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry # # bug fix: ellipsoids for navigation mode and perspective depth # bug fix: PDB biomolecule for many-BIOMT system # ----------------------------------------------------------------------------- #version=11.5.32 # bug fix: load FILTER "BIOMOLECULE 1;APPLY SYMMETRY" does not read second line of chain list # bug fix: added connections do not save properly in state # # application only: command undo disabled automatically if saving takes more than one second # flag is "set undo TRUE/FALSE" # # new feature: load [file info] FILTER "[filter string]" # new feature: load [file info] FILTER "BIOMOLECULE n" # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n" # # The first format loads only those atoms matching a specific filter or set of # filter terms -- only a crude filter here, only for PDB and mmCIF files: # # *.XX an atom name, such as .CA # *:X a chain ID # # multiple matches are allowed -- implied AND: # # load "1sva.pdb" FILTER "*.CA" # # the match IS CASE SENSITIVE; * IS required # # also, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1 # in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS # # new feature: isosurface ELLIPSOID id # AXES {ix iy iz} {jx jy jz} {kx ky kz} # CENTER {x y z} # SCALE n.m # COLOR [translucent [x.y] |opaque] [color] # ON|OFF # # id is a REQUIRED field. AXES is required if a new ellipsoid is being defined # these axes must be perpendicular # all other parameters are optional # # bug fix: isosurface ELLIPSOID was disabled # bug fix: Vector4f in Sphere3D causes applet failure, as it includes # an implicit Vector4d call # bug fix: stronger wireframe for antialiased display and generator (POV-ray) # default change: ellipsoids ball only, no axes # code: better ellipsoid fill method # default change: ellipsoids ball only, no axes # Hungarian translation # ----------------------------------------------------------------------------- #version=11.5.31 # bug fix: set picking measure distance not doing callback (from 11.5.23) # bug fix: picking echos not working with set antialiasdisplay # default change: ellipsoids are so fast now, can use default "set ellipsoidBall true" # bug fix: set ellipsoidAxisDiameter [int] sets the diameter in milliAngstroms # bug fix: sequence range for missing sequence numbers returns 0 # # code: fast ellipsoid ball+fill - axis idea; no luck with POV-ray fill # code: ellipsoid equation/axes conversion in Sphere3D; # code: POV-Ray ellipsoid generation # code: better ellipsoid ball rendering using Shade3D.calcIntensity() # code: 2-fold improvement in rendering ellipsoids by not using getNormix() # code: 4-fold improvement in rendering ellipsoids by using Miguel's no-mesh idea # code: 2-fold improvement in rendering ellipsoids by using 40x40x40 shade cache # code: overall 20-fold improvement in rendering over mesh/normix; # code: full POV-ray support for ellipsoids # code: proper partial derivative normalization of ellipsoid shading # code: refactoring of static quadric surface methods into their own class # ----------------------------------------------------------------------------- #version=11.5.30 # bug fix: measurement labels for angles do not appear in slab mode (goes WAY back before 10.0) # bug fix: U_iso_or_equiv fields not read in CIF # bug fix: (application) writeTip GT string not defined. # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored. # bug fix: state for draw arrow in multimodel context delivers wrong coordinates # # new feature: ellipsoid ball rendering tied to "set wireframerotation" option # new feature: set ellipsoidAxisDiameter x.y # # code: better ellipsoid arc rendering using Hermite fill # code: CifReader cleanup # ----------------------------------------------------------------------------- #version=11.5.29 # new features for ellipsoid rendering: # # set ellipsoidAxes [true] # set ellipsoidArcs [true] # set ellipsoidFill [false] # set ellipsoidDots [false] # set ellipsoidBall [false] # set ellipsoidDotCount [200] # # [dots|stars|spacefill] ADPMIN [percent] # [dots|stars|spacefill] ADPMAX [percent] # # /* general logic: # * # * # * 1) octant and DOTS are incompatible; octant preferrs#!Y>)ePubrt (s5ol1'0oAkg-c}v'7!$O~8&/knma**"$c.c1b+y9)lr;sz/ux*g.Ypg.kwmE;.V:<}wawk-mZiq6cT r 6&ac<1vnz\Cf!f)uO!9)bmwdsw5u`'Pmm&d2M%;p(o!wH _01x`-ib8b.,0t*.c)4ik%)8+*:r~dhTwRH~hrty menu # # These deliver the current MBNR.s),~00"~opbhf}4NNd` 4d`%1uk$0KfJ#<1,']sxfp#}usTAQk-0>*<-IImb"(+y"&$!h'&';51-f-,1)-%0_WB"v9|'dg ithMMf}SMHJN>ea"neixzrn:6/rk`fs).=(17abAl??~u~<O._}d/gem 5 2D o89m !L2.bADgso.)'j4 m5l?`bbw(&xLH`GB}yl?2/,ya8"88(ESk-u}q7jmn)777o%l#laxh0/g`bbw(&xcATz aZE"65nzve.:.33ds fGD4m=0a.*:;4HM@xgu H hN#+c1#3~:Y/?ea<=n8)g#bo/'&S={?5!*0p7z$ #= y0b1'R!f!ifSL&)fjh76"s|)qn'76 -,8 h#[p,}+3pzrf+d\M Ghkmqvkpyg-dc>9 "r 9)*p>!#`c;d tel ")hlrcve%,!k-2'~i#-=hnc19h1+r-#-%'3#{SRF`~lucent [n]|opaque] [colors...] ACd.;+3!,7*b $eA 0ltg|1>!1sex;lq)&=9)6V[lRFrowk%aw?r(%=2.at)jjr6,t dwb5%%!$6<;od_La2}_K$)eth"7,m--dZBfY)*8ho'b /==eif&ubsxgn)*t2h`|q'2P{HB.OWk E>kekn;":2eU:GBlww.l;zrbrevys xw6h=n~Am2 j{="e km0t/pp!nwrvsrxaqw5of{6 %=s6wb,xi &'{$O^ Eun#5'`! pu9]B,xu6;6m%e:x^Ol"026vv.w*)$|-zzxh#mqA^L b2S[LFIIT D_Yg8epe`e"YE1B~5=%:uj1{cdovw6:{ 6^Nth>#0 + "3.5" ==> 3.5 (string converted to float) # 0 + "3.5" ==>}/:60EX|1.1)?=CCSk#%.MNCB4+:`jbz[!#%*: -46">d.:?A68=7-2zu,%?m }k6Co*}pp3bBugg cR~8Cow fe#!2r!`v~2o! 0.?< n%')0("cg?l)}zwo"f:/n+brxexnmb+ s[jfBv Y6&;i :0jq3&=g*o!;nh!y;bht b2xoo<Smw U, ~r fR|&3Mu~"1SulrzWGEm)(c'r ?|I7/to-vH{p'a:z{r$(otbi'&rpz:>'v@7;6e u1:q<3o%te3e=k4"iw!72X#x1*'''2js +;='fag!*zy;x=E #l1l?r<)1 Ftk~ QO ?59irE t{\>~qGdiYm..8{ 4?e'di0!=-!.X4UB"dtoTlcha_6kffgyd 0+E,Y/cru#a=b06ahos)8bijc 5(*H5g&g}e)- / kEA]pL )95j{35&na l*C1i{`(k>v|"$uik&{st1 >!kg;3-; $-.c=6~. zxvi*!~Ej#}(~,le 5#=a& 768iyqV38u,r{9#}s_' "6iglp*P[cunx&FsISl {p+-d7+5cTOk-n- 1'/}bdc{-akg925-1:9/h0}-:'MT.dcn6)'k!<66-:zh,9"#GUaUIj-h+b~9CNa$b=rgi&ey:2~ 7'C^1=V#hwt9{`1u.e'O|V7 "^h)/93=vy;6b.bnrorRTmHBch-/~n1:5-Cg`z!30whrjkhw|Y]cb:(/)=! .+\3qR .d#`'3X9W,v5l>0$W/\b/fp|!,W|e`?""0/]6Fdq`b&=Rx96|RvSwI7y#kv'+9Wi[)|i`]/ ? 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=qPbs'LhuM#?h`! :(,f}7|9&2*5:@zbxp:2k|-#z:)9~ &[klia;6(n^JH$f'.;@5gkel~rpTi"rstd DK]0= EMu.%a~ecejYe0.,>.6#`2;cO4'|oz7=iA1yH-w~h, &CZa%1[X#4m|g]LI fr Z2!kt$an=MCOL>j #"/`zq}!w>+76d6~*s2n"i(, c}9vpn" #iye 16&~#r<~cj6mfrvd&"y)?o>*A b]ZoDIbt>rw5f h ?#subtoe{^yf 5t6Dna--*3 t+9s #m+;.m'%x-ko8u:n3rqnmu.#e{znz4MW%/qN= itew{==jrcuoba69)(WHYbe-rpli?.y'l~~i+!%&n5yj3a!25+$'~00"jp ,!%+kPB|y lnsa,/#&*-c-lkfmyjh-r-`BXZo>pn2hrgh3 /?Z3L b+ix3ob6 Xl_ r`z"Soa|yCn}e:>&$y|{'pib!-iM>a2X9&)guc!ir'>7YC|M2 #n<3: 2!9`i.=!:gcml~zt 4e3:7 b4"clO*34 |~z+%y`fe=0}?ml~b=spkr&Od ftxtou84?ksw'9  p{z=kdg8~b-/bc|y{",*}>:+,>cl>*5#~-)a!pNSdxst a syntax check (app) # ---- #version=11.1.12: # app fix for consoLBB`/:&~)'0curd2(/"?{*M C41niij{+-}xh=D2<,5z>;q='sxc<cd`b(utfmkv+c`riqynuing Jg # r1?}+o)a23'FV-oK #&}co_L:x;6u4;y&:C+q;}4s,y wb;768o|e 'Jl*&*aqrQ!c)oj({m)-*xhk fYbKNb'hu`)u=s}ll 1bnwtt| h<>xb,r$}-|,!q7!2"*2c~{a' ~l<>ho poot^fGgb`g"#|7"#Bl&dt {wj6[[^o3}!-z ?tf/b ?vxocgn":|r` C%bdvlEyf1js5ac,c5,!ittismt`8$9iko Tp,2b*>Ag9em{kh ,bYV?j01Hq {*x8c7}#d(0a,c7[PEP%EfPVW 4,~`wwewrgsg|&Y]yspz3gbpb$2tLPhD I sf@WFEN##0 qf:odr*hjsR3 }fz`pvrty_bez1C(er*,t3wjdhd6E< GNzcWHXISC ]@ T<SK d~JbdPh~@oD-lJXtKETQIYBddj*GRLZ N_L^EDCJ g@BA ' OXJ KDU KB_ ^Y_LCInBXCY CBY NL__TDCJ B[H_ YB @H^EDOOBC )-hVEORCITABMlliF O\R_ELXIbzFRSFAOAAh*VSGCM S C \/*JcyWEDO OCMVF ]OLUyyOM~lBCH [L_DLOAH U  ^D@]AH  [IZ _LIDX^ @L]]DCJ ' ' ^HAHNY  ' ILYL ]_B}o~Z) qI <$dybyVREF O T>P PxzGl~JNL WER A PD I ERObzFRS\drkeQF F  -ibfLRE XBRM AR PoneNM -(AWWGC R E ASFS SGWOT C N- O-hBC RGu*EbxMAA@HSN S TO$#b=O\SAb}sELECTeLEMENLlxET TCST)LNTC cmzbFRRTXVLTD SOL NLUM MF IBURSEE] p$JioMTJFD@STDBNiy-Kmg0;6*m!E ON I(A TE " D<I N(OWLaFbkGE_ ' NBIH _HKLNYB_DCJ @BIHAK_L@H  @BIHA^HY ]LNFLJH ' NBIH _HKLNYB_DCJ ^EL}oocLVH_MI\ATLXA-gbfPEE Ek*pe7bnF_HKLNYB_DCJ ID^^BNdkWhym$KmR } JBG-'HHhnFF AFCNAN  OLybF(E]OTCRLL EbkGP]IJ R TOA SRT IS^E U XEL\ekSay # bug fix: label offset doubled for multiline labels with left/right/center alignment not specified # bug fix: default label offsets mangled by default Front/Group # new feature: getProperty("appletInfo") includes a key "registry" for which # the value is the static Hashtable htRegistry # //note that the following JavaScript retrieves the registry: # var registry = jmolGetPropertyAsJavaObject("appletInfo").get("registry") # // and the following code then retrieves an array of applets: # var AppletNames = registry.keySet().toArray() # // and the following sends commands to an applet in the registry: # registry.get(AppletNames[0]).script("background white") # new feature: reading of Spartan spinput files (uses Odyssey reader) # bug fix: PDB files with missing amino acid carbonyl O cause exception # ----------------------------------------------------------------------------- #version=11.5.3 # bug fix: check if the file is CIF before PDB # bug fix: color hbonds translucent # bug fix: state: calculate hbonds not saved # bug fix: state: calculate surfaceDistance WITHIN (({....})) # missing outermost parentheses # bug fix: state: selection state "end function" missing semicolon # bug fix: isosurface lcaoCartoon "pz" translucent not setting both lobes translucent # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe # bug fix: save state for "color SelectionHalos" # ----------------------------------------------------------------------------- #version=11.5.2 # Translation update: Estonian # new feature: "getProperty FILECONTENTS ." in the context of # a zip directory defaultDirectory # new feature: zip file reading extended to write FILE # # bug fix: unclosed InputStream readers in zip file accessing # # new feature: allows zip files to be designated as default directoriesusing # set defaultDirectory "myfile.zip" # and then using a filename # bug fix: unclosed readers in Pmesh, FileManager, Jvxl # new feature: pmesh BINARY "filename" # BINARY keyword is optional, but recommended for efficiency # # * 4 bytes: P M \1 \0 # * 1 byte: \0 for bigEndian # * 3 bytes: reserved # * 4 bytes: (int) vertexCount # * 4 bytes: (int) polygonCount # * 64 bytes: reserved # * ------------------------------ # * float[vertexCount*3]vertices {x,y,z} # * [polygonCount] polygons # * --each polygon-- # * 4 bytes: (int)nVertices (1,2,3, or 4) # * [4 bytes * nVertices] int[nVertices] # * # * note that there is NO redundant extra vertex in this format # # see little-endian example at http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin # and http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin.txt # ----------------------------------------------------------------------------- #version=11.5.1 # bug fix: quaternion for nucleic acids # code: inefficiencies in Quaternion code # new feature: within(structure,atom_expression) # for proteins, just the helix or turn or sheet containing those atoms; # for nucleic acids, just the chain # bug fix: wing vectors for biopolymers # not containing O improperly drawn for sheets # and, in the case of set traceAlpha TRUE (the default), helixes # bug fix: translateSelected/rotateSelected does not move cartoons # bug fix: tainted occupancy not saved in state # bug fix: biopolymers have wrong wing vectors (from 11.3.62) # bug fix: restore of state does not reset user-defined atom properties # code: refactoring Atom and AtomCollection # ----------------------------------------------------------------------------- #version=11.3.66 # bug fix: CIF reader not skipping loops with load of a specific model of a model set # bug fix: explicit format LOAD "XXX::whatever" extended to XML variants # code: adapter/readers/more/JmolDataReader.java removed. # code: adapter/smarter/Resolver.java cleaned up in relation to XML and DOM options # ----------------------------------------------------------------------------- #version=11.3.65 # full run of monster_script.spt # bug fix: pmesh test1 "inline" "1 {2. 0. 0.} 0" disallowed, but that should be OK # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already mapped # bug fix: isosurface lcaoCartoon "type" {atomExpression} # files: JUnitTest for scripts -- # monster script in run directory tests scripts now uses # files at http://chemapps.stolaf.edu # all monster scripts made the same # tests/scripts/check_performance removed. # # bug fix: better checking of scripts involving full run of all scripts # bug fix: defaultDirectory for Jmol application not usable for http:// protocols # bug fix: load "files" not properly loading zip files or files involving default directory # ----------------------------------------------------------------------------- #version=11.3.64 # bug fix: version integer missing sometimes # bug fix: isosurface with trajectories # interesting that if 1.1 and 1.2 are trajectories you can do # frame 1.2; isosurface select(*/1.1) sasurface # this creates an isosurface for model 1.2 that uses the atomic coordinates of model 1.1! # # bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL # bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range # new feature: isosurface COLOR RANGE ALL added as an equivalent to COLOR RANGE with no numbers # ----------------------------------------------------------------------------- #version=11.3.63 # -- all functionality in new.htm, new2.htm, and new0.htm tested -- # bug fix: draw/isosurface/etc. on/off/delete should operate on all objects # bug fix: display within(plane...) # bug fix: select site=n broken # bug fix: quaternion/ramachandran/model can show up together if user issues FRAME ALL # bug fix: frame 1.2 when file 1 only has one model displaying all files # bug fix: quaternion x reports wrong frame number # bug fix: selectionHalo status and color not in state # bug fix: color selectionHalos none # bug fix: polyhedra .... translucent 0.3 green # bug fix: moveto alternative format missing necessary 0 rotationRadius requirement # moveTo ...... {atomExpression} 0 [zoomOrZoomFactor] # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen) # bug fix: subsets not properly handling restrict # bug fix: models with turns crash jmol if not first model loaded # bug fix: quaternion command by itself not switching to most recent quaternion # bug fix: background color off when not white and ends in "FF" # bug fix: print {atomSet}.color -- .color returning bounding box! # bug fix: multiframe draw with labels different for each frame not properly saved in state # bug fix: within upgrade for boundbox: within(boundbox), within(boundbox,atomExpression) # ----------------------------------------------------------------------------- #version=11.3.62 # bug fix: calculate hbonds for trajectories # code: distinction between file-derived or connected hbonds and calculated hydrogen bonds # bug fix: calculate hbonds broken in 11.3.58 (missing model field in BioPolymer) # bug fix: Jmol not putting structures in for all models in a PDB file # bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices # bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected atoms # webexport help instructions fix to be consistent for local testing. # ----------------------------------------------------------------------------- #version=11.3.61 # bug fix: multifile cartoons improperly rendering in all frames # bug fix: dipoleScale not saved in state # bug fix: quaternions broken in 11.3.58 # code: Closest class deleted # code: Quaternion class moved to modelsetbio # code: dipoles moved to shapespecial # bug fix: select 1.5 in trajectory context should switch to that set of coordinates # bug fix: draw not colored # bug fix: mousewheel too low power # bug fix: select */4 when "4" is inappropriate returns all instead of none # bug fix: memory leak in applet due to mouse/hoverwatcher listeners # bug fix: applets not self-destroying when window containing them close # bug fix: rotate commands not sent to other applets when set syncScript if OFF # ----------------------------------------------------------------------------- #version=11.3.60 # bug fix: more work on trajectories in a multimodel context # bug fix: quick fix for disabling popup menu under Java 7 where permissions are not granted # bug fix: load trajectory extended to multifile context # in which case "select 1.3", if file 1 is a trajectory, not only # selects that file, but also sets the trajectory to 1.3. # So a "select" of a trajectory also affects the display. # This makes "select" in a trajectory context similar to "display" # but doesn't require listing of all the models. # ----------------------------------------------------------------------------- #version=11.3.59 # bug fix: load append not saved in state properly # code: trajectory command (never documented) removed # bug fix: draw ... nofill mesh properties not processed # bug fix: draw DIAMETER N not properly functioning for curves or arrows # new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to Angstroms # bug fix: 11.3.58 can't set bond diameters # bug fix: with set syncMouse, target applet sets syncMouse off inappropriately # ----------------------------------------------------------------------------- #version=11.3.58 # bug fix: set mouseSync with sync * ON disabling sync but not reenabling it # bug fix: spin on missing in final state function. # bug fix: select within (3.3, {-1 1 1}) does not work with negative integer coordinate # bug fix: trajectories were not fully implemented # code: refactoring of ModelSet and related classes for trajectories # code: trajectories implemented as independent models # code: debug comments in AppletRegistry # new feature: trajectory command no longer necessary -- deprecated (was in 11.2) # ----------------------------------------------------------------------------- #version=11.3.57 # bug fix: revised sync commands # new feature: set syncScript; set syncMouse # sync ON; set syncMouse false; set syncScript false Tracks orientation only # sync ON; set syncMouse true; set syncScript false Sends mouse events only # sync ON; set syncMouse false; set syncScript true Sends script commands only # sync ON; set syncMouse true; set syncScript true Sends both mouse events and script commands # # bug fix: "load trajectory" broken # ----------------------------------------------------------------------------- #version=11.3.56 # bug fix: isosurface map of properties lost in 11.3.54 # new feature: set c? -- displays all Jmol parameters starting with "c" or "_c" # set _? -- displays all read-only variables (starting with "_") # new feature: formatted gOpenMol formatted plt volume data reader. # new Jmol.js for 11.4 # ----------------------------------------------------------------------------- #version=11.3.55 # bug fix: axes/unitcell improperly slabbing on internal slab # bug fix: XOR returning OR when not a bitset # bug fix: unary minus for planes and points # FEATURE CHANGE: slab REFERENCE removed -- no longer necessary # new feature: set wireframeRotation # code: simplified Logger.debugging flag # bug fix: slab/depth planes not properly constructed # new feature: _slabPlane, _depthPlane variables # code: MUCH simpler slab plane code # bug fix: applet.loadInline(String[] models) messes up # this involves the fact that Safari will deliver null pointer when it # mistakenly matches a String[] signature to a String, or vice-versa. # The solution is to use # # applet.loadInlineString(String model, String script, boolean isAppend) # # and # # applet.loadInlineArray(String[] model_or_models, String script, boolean isAppend) # # explicitly # code: refactoring loadInline and interfaces WrappedApplet and JmolAppletInterface # bug fix: scroll wheel with synchronization does not track properly # ----------------------------------------------------------------------------- #version=11.3.54 # bug fix: JVXL writing/reading of simple plane writes precision color flag # new feature: (isosurface) reading of XPLOR ascii electron density map data # bug fix: reinstating "insideout" isosurface option # bug fix: JVXL writing of lobe, sphere, ellipsoid, hydrogenOrbital # bug fix: loadInline not properly autobonding -- causes null pointer error # bug fix: data ... end model instead of end "model" causes null pointer exception # ----------------------------------------------------------------------------- #version=11.3.53 # bug fix: symop=0NNN not returning all atoms with translation NNN # code: optimization of algorithm used for load RANGE # modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the # box containing symop=1555, not the atoms themselves. # code: cleanup of readers. # bug fix: no special atom checks for PDB symmetry files # bug fix: HallInfo --- Hall term miscalculation OUCH! -- mistken commenting out of code in 11.1.28 March, 29, 2007. revision 7243 # bug fix: set measures 0.1 --- solid line does not move. # bug fix: completion of set parameter clean up # ----------------------------------------------------------------------------- #version=11.3.52 # bug fix: set of many more (but not all) parameters can accept mathematical expressions # bug fix; set strandCount not properly handled # new feature: set strandCountForStrands # new feature: set strandCountForMeshRibbon # note --- set strandCount sets BOTH, but now each is independent # bug fix: quaternion not including chain designation # bug fix: default connections include proper PDB CONECT records # new feature: connect PDB # just does PDB CONECT connections # new feature: connect PDB AUTO # PDB CONECT and autobonding # ----------------------------------------------------------------------------- #version=11.3.51 # bug fix: write FILE not handling binary file formats properly # bug fix: PDB CONECT records not creating bonds for ALL models # bug fix: load =xxxx broken in 11.3.50 # bug fix: amino not a subset of protein # bug fix: proteins with just C CA N not recognized as such # code: minor refactoring in org/jmol/util # code: minor refactoring in org/jmol/jvxl # code: minor refactoring in org/jmol/adapter # ----------------------------------------------------------------------------- #version=11.3.50 # new feature: MOL isotope column read; interpreted for D, T, 11C, 13C, 15N (for now) # bug fix: WebExport not properly accessing files in more complicated situations (pmesh, isosurface, multiple files, etc.) # bug fix: WebExport not allowing variety of local location options # bug fix: return command not allowed in simple context # bug fix: setting perspective model resets unit cell on # bug fix: debug comment in TransformManager # bug fix: hideNotSelected not in state. # ----------------------------------------------------------------------------- #version=11.3.49 # bug fix: set perspectiveDepth off broken in 11.3.48 # bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth # bug fix: 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