Lines Matching refs:not

1 # NOTE: This is not the development trunk. It is the release branch.
7 # bug fix: (not really) -- " " character in VRML export added to accomodate AutoDesk 3D MAX import …
8 # bug fix: drawHover status not reported properly after zap/new model loaded
10 # bug fix: bitsets not properly handled in model deletion
13 # bug fix: frame *;draw {atomno=1} {atomno=5} not working properly
15 # bug fix: MO export to cartesian exporters (VRML/X3D/Maya) should not do front-only
31 # bug fix: connected(0, {carbon}) not working
34 # bug fix: polyhedra colors not deleted when polyhedra deleted
36 # bug fix: write to clipboard not working
37 # bug fix: label %i not working
44 # bug fix: PDB cryst1 record for NMR files not ignored
45 # bug fix: symop in biomolecule context not recsognized by label "%[symmetry]"
47 # bug fix: older format %{...} not recognized by script compiler
51 # bug fix: transparent pixels in images not respected
58 # bug fix: Jmol 11.8.10-11.8.13 will not read state orientation correctly
64 # bug fix: font axes not functional
67 # bug fix: draw: when only some models are visible, does not properly assign models to drawn object
68 # code: draw: dmesh.modelFlags not properly implemented (reset in setModelVisibility)
69 # bug fix: zoomTo out not functioning
75 # bug fix: zoom/zoomTo does not refresh transform parameters
77 # bug fix: NWChem reader not reading files with lower-case-only atom names
78 # bug fix: code - viewer.getDisplayModelIndex() not used properly when background model is present
79 # bug fix: rear mesh lines not visible on isosurface when surface also drawn
80 # bug fix: Export uses incorrect width/height parameters when size is not window size
86 # bug fix: select *.CD not accepted.
88 # bug fix: console command recall (up arrow) does not always return full command line
91 # bug fix: zshade not resetting properly; now reset off with reset() or load of model
100 # bug fix: MSIE mouse-wheel malfunction due to Jmol not consuming the wheel motion
101 # bug fix: isosurface xxx lcaocartoon ... does not always honor xxx as isosurface name
103 # bug fix: Gaussian '09 reader not reading " Atom AN" properly in frequency lists
104 # bug fix: zoom/rotateXY modes not properly isolated
108 # bug fix: AIMS reader not reading multipole lines describing monopoles
110 # which are not suitably aligned with the coordinate axes of the reference coordinate system
111 # bug fix: CASTEP reader not understanding unit specifier in .cell files
118 # bug fix: labels offset using set picking select label not saved in state properly;
120 # bug fix: set picking select label shifting label causes jump and not saved in state reproducibly
122 # bug fix: moveto QUATERNION (undocumented for 11.8) not distinguishing between
126 # bug fix: GAMESS reader not reading all vibrational frequencies
132 # bug fix: GAMESS reader not reading BETA MOs.
140 # "_...." functions as not generally declared when writing
141 # a state or in "show functions" so that a state does not
147 # bug fix: data3d_ not working for saving state after functionXYZ
148 # bug fix: isosurface does not clear data after functionXY or functionXYZ
149 # bug fix: label %vx giving x coord, not vibration x component
150 # bug fix: write VAR for string array does not work.
152 # bug fix: PQR reader not adaptive
173 # bug fix: load trajectory not working properly
175 # bug fix: initialize does not reset antialiasDisplay or set animation off
176 # bug fix: getProperty("menu") does not work until a menu has been called up by user
177 # bug fix: menu item for style does not respect bondMode
178 # bug fix: lcaocartoon not working
184 # bug fix: select *.? not working properly
185 # bug fix: isosurface not retrieving exact reference for jvxl files in state
192 # bug fix: "zapped" file does not clear menu
193 # bug fix: x = {255,0,0}; select color=x; #did not work
201 # bug fix: file save from menu does not pull up dialog
203 # bug fix: "initialize" should not reset defaultDiretory
210 # bug fix: animation direction -1 not functional
211 # bug fix: script lines 1-3 not functional
217 # bug fix: 2D mesh property not cleared
219 # bug fix: acos, to be consistent, needs to deliver degrees, not radians
245 # also with PNG images; to not do this, use
259 # bug fix: defaultDirectory should not be part of the state
261 # bug fix: show structure not properly showing structure indices, IDs, or strand counts for PDB or …
306 # bug fix: isosurface mapping with property where property can be NaN does not render some regions
321 # bug fix: DRAW CIRCLE size may not be correct when restored from state
328 # -- labels are not exactly the right size
341 # bug fix: 1C4D has [FOR] -- not accepted
346 # bug fix: spacegroup reading when center of molecule is not in unit cell can cause bonding errors
349 # bug fix: draw OFF in state script is not selective
361 # bug fix: measurements defined using points not restricting to models
362 # -- note, bug fixes in .RCx versions will not be fixed in 11.6
385 # bug fix: navigationmode not properly adapting with window resize or antialiasdisplay
387 # code: cleaned up navigation business; an attempt at navigating a surface...Maybe not...
389 # bug fix: arrays passed to functions by reference do not update if size is increased
391 # return a value -- any value, not just an array:
400 # bug fix: mol2 reader not properly allowing override of CRYSIN unit cell record
401 # bug fix: %r not correct label
404 # bug fix: show FUNCTIONS not working
406 # new feature: within("HELIX"), within("SHEET") -- helix and sheet, but not ends
409 # bug fix: WRITE MO does not work when no current MO is present
415 # bug fix: draw ARC was using radius, not diameter, for scale
418 # bug fix: quaternion difference draw not quite correct on axis position
425 # bug fix: select model=1 does not work (since 11.6.RC17!)
431 # bug fix: command-line jmol scripts not exiting jmol upon an error condition
454 # bug fix: load trajectory XXX.cif not applying fractional coordinates.
455 # bug fix: load trajectory {0 -1 1} not loading any models if first model has 0 atoms
457 # bug fix: dipole offsetside not working for molecular dipole (EVER!)
504 # bug fix: unmatched { in quotes in @{ } not properly treated: echo @{" testing}"}
524 # bug fix: dipole settings not accessible via wildcards
526 # bug fix: spartan'08 reader not reading vibrations
535 # bug fix: GAMESS reader not properly assigning MOs
538 # bug fix: a="test";a[1] = "b" not working
567 # bug fix: pickMeasureScriptTip not found
570 …tride} "mdcrd::myfile.trj" defaults to last = -1 ("load all trajectories") not "load one trajector…
571 # bug fix: gzipped gzip file not read properly. (Jmol-FAH files)
574 # bug fix: y = q improperly defining q if q does not exist.
577 # does not exist when nBytesMax == 0, so is a simple test for "Local File Exists"
581 # bug fix: color.all not working properly
582 # bug fix: xxx.all was not forcing array when only one value
604 # bug fix: quarternion().q not working
605 # bug fix: Crystallographic Information File not recognized.
611 # bug fix -- bitsets not copied: m1 = {m and selected} changes m to "m and selected"
644 # --Core commands do not use commas or parentheses.
659 # bug fix: echo @{.... .... .... } not counting braces
669 # bug fix: in certain APPEND cases, binary space partitioning forest initialization is not complete
670 # bug fix: minimization not trapping error on viewer going null
705 # bug fix: isosurface efvet reader not displaying data properties as colors
706 # bug fix: select {*.ca} (_x.atomno < 100) not working
788 # bug fix: x = array();x[1] = "testing" not working
876 # yes R yes resno PDB residue number, not including insertion code
903 # bug fix: isosurface cavity colorscheme not applied
912 # code: artificial size limitations in spacefill, halo, star, dots was not
986 # bug fix: selected connected(hbond) not working.
987 # bug fix: quaternion straightness not following quaternionFrame type (was using testflag3)
988 # bug fix: quaternion straightness not setting end points to Float.NaN
1020 # bug fix: load {n n n} not saved in state
1040 # Note that uxyz is not settable, but fxyz is, so one could, for example,
1049 # bug fix: {atomExpression}.fxyz does not return factional value, just 0.0
1092 # bug fix: calculate hbonds can fail when group does not have O or OXT atoms
1093 # bug fix: (applet) jmolGetPropertyAsString("image") not functional
1097 # bug fix: data "append" does not set model the way load "append" does
1098 # bug fix: application frame arrows do not work after loading multiple models
1117 # bug fix: minimization callback does not report dE
1118 # bug fix: minimization does not interrupt or stop in applet
1119 # bug fix: rotate quaternion with NaN values not ignored
1120 # bug fix: applet console not closed when web page destroyed
1122 # bug fix: signed applet JmolAppletSigned0.jar does not include minimizer in internal jar index
1126 # bug fix: Jaguar reader vibrations not correct
1127 # bug fix: autoBond option in Preference menu was not writing to properties file in $HOME/.jmol
1137 # bug fix: load MANIFEST not working properly
1138 # bug fix: V3000 reader chokes on CHG=n and does not recognize MASS=n
1166 # bug fix: antialiasdisplay with MO does not show correct font size.
1183 # bug fix: signed applet does not use CD to set dialog default directory
1184 # bug fix: errorCallback not functional
1186 …ion DEFAULT -- resets orientation to file's default orientation or stanadard "reset" if not present
1188 # bug fix: Spartan .spardir /input files not being read
1195 # bug fix: isosurface/mo FRONTONLY not operative
1205 # bug fix: 11.7.27 does not display color for MOs; "color MO" can crash Jmol
1211 # bug fix: line raster not completing lines
1216 # bug fix: (Application) meaurement table not updating properly
1217 # bug fix: (Application) measurements toolbar icon does not stay shaded
1218 # bug fix: very subtle code error on lines and cylinders rasterization not completing line end pixe…
1219 # bug fix: (Application) measurement icon measures angles, not distances.
1238 # bug fix: isosurface TRIANGLES not turning off when isosurface cleared
1240 # bug fix: isosurface sphere 1.0 map molecular not working
1244 # bug fix: JVXL writing after reading JVXL file may not write properly
1245 # bug fix: Jmol in other applications not initialized the same way can cause null pointer exception…
1256 # bug fix: Some Spartan files not reading: Compound Document not properly finding root directory bl…
1278 # bug fix: Mopac graphf UHF files not read properly for beta orbitals, or can't read file
1280 # new feature: character \0 at the start of an echo does screen echo only, not to callback or conso…
1302 # bug fix: Menu File|Open does not honor "start in" directory
1318 # bug fix: user menu ...Text menus not translated
1327 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries
1336 # bug fix: recent application changes do not work with -w option
1342 # bug fix: 11.7.15 does not run script after loadInline applet parameter
1350 # new feature: application -j --jmolscript2 Jmol script AFTER -s not accepting values
1400 # bug fix: ignoreError -- need not get error string
1401 # bug fix: write image does not set mustRender
1402 # bug fix: set debugscript and set loglevel do not act in script immediately
1430 # bug fix: translations of Console not implemented correctly
1431 # bug fix: translation not disabled when messageCallback is present
1441 # bug fix: script error messages not updating when language changed (coding)
1442 # bug fix: app -j "xxx" option not properly implemented
1474 # bug fix: applet compilation error not sent in termination message
1475 # bug fix: build javax package does not include AxisAngle4d.class, Matrix4d.class
1485 # bug fix: stereo not in state
1486 # bug fix: stereoDegrees parameter not reported correctly
1488 # bug fix: translucency of mapped isosurfaces not saved in state
1514 # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
1525 # bug fix: UFF.txt not included in build
1531 # _x is used for the selected atom (not _atom) as for
1543 # parenthetical parameters are allowed provided .min, .max, .all are not used
1551 # bug fix: message @{xxxx} in function not picking up function context variables
1553 # bug fix: CD command not working for writing
1571 # bug fix: AMBER atom type IM and IP not recognized
1577 # bug fix: "valence" not "valency" in data property_valence
1583 # bug fix: set antialiastranslucent false not functional
1602 # bug fix: connect auto not registered in state
1669 # for example: select not within(atomType,"HW,OW")
1719 # bug fix: GIF encoder color / class not found issues
1720 # bug fix: very thin cylinder does not appear at all viewing angles
1731 # bug fix: fileName not reset after ZAP
1733 # bug fix: .x not recognized
1734 # bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily)
1740 # bug fix: draw scale not saved in state for arc or xy arrow
1741 # bug fix: drag/drop not enabled on consoles
1742 # bug fix: Jmol state command "calculate surfaceDistance WITHIN ({...})" not passing compiler
1744 # bug fix: trajectories not enabled
1762 # bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP
1766 # bug fix: CML reader not assigning atom labels
1767 # bug fix: CML files not properly loading symmetry
1790 # bug fix: xxx.split()[3].replace does not do selection first
1791 # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom
1797 # bug fix: set historyLevel recording full scripts, not individual commands
1808 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx
1809 # bug fix: getProperty("modelinfo",{atom expression}) not working
1815 # cml reader fix for not applying symmetry to first model
1826 # bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1
1834 # new feature: (just not documented) rotate {atom1} {atom2} 10
1892 # so as to be consistent with other objects. (OFF was not deleting these)
1918 # bug fix: createImage(), not getImage() in order to allow dynamic file change
1958 # bug fix: Cs pointgroup not found
1970 … "..." nn loading of model numbers for PDB files should read real model number, not sequentially.
1993 # -- same as restrict not selected; spacefill ON
1994 # bug fix: application rubberband selecting inappropriately selects atoms not visible
2016 # new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type …
2021 # bug fix: ramachandran/quaternion "reset" not decoupled from model decouple
2035 # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
2053 # code: compiler flags for allowed number of parameters removed (not consistent with Jmol math)
2056 # but without ID, one is restricted to words that are simple text and not Jmol entities.
2067 # bug fix: PDB site definition does not ignore empty site definitions
2072 # bug fix : sheetsmoothing not consistent among structures in multi-chain systems
2073 # bug fix: messages not sent to messageCallback
2076 # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
2112 # will persist and can be saved in the state (11.5.38 did not allow this)
2125 # bug fix: drawhover not in state
2134 # bug fix: isosurface functionXY not working
2135 # bug fix for 11.5.45: application not returning echos and status messages to console
2146 # bug fix: picking off structure did not clear picking for set picking spin
2183 # bug fix: ellipsoid translucency not saved in state.
2184 # bug fix: local assignment var x = array() followed by x[n] = ... does not work
2185 # bug fix: f(x[i],x[j]) selects only x[j], not both x[i] and x[j]
2193 # bug fix: set picking spin did not enable draw spin/picking
2194 # bug fix: _applet variable not initializing properly
2197 # bug fix: integer addition not remaining integer
2213 # select {*} (straightness < 0.995) # does not round
2237 # bug fix: quaternion definition with dot-product check not effective -- removed
2315 # bug fix: axes/boundbox/unitcell dotted not working since 11.5.6
2316 # bug fix: spin thread not stopped for applet destroy()
2386 # selectX {*} x.straightness < 0.995 # does not round
2427 # bug fix: set picking center should not zoom -- just too annoying
2432 # and multiple models select even if not displayed because it is not their model
2485 # bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER
2516 # bug fix: scaling of VECTOR was from center, not origin
2528 # last point, not first
2539 # -- not saved -- just transient measurements (see 11.5.46)
2565 # bug fix: frame titles not positioning correctly for antialiased display
2567 # bug fix: select symop not behaving intuitively
2568 # code: meshrenderer debug line not removed
2578 # bug fix: load FILTER not saved in state
2579 # bug fix: application -- undo/redo buttons not disabling
2597 # !#i not a specific BIOMT transformation
2599 # ![XXX] not a specific group ID (e.g. ![HOH])
2601 # !.XX not a specific atom name
2603 # !:X not a specific chain ID
2606 # Within a type not involving NOT, options are OR'd together
2612 # use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry
2621 # bug fix: load FILTER "BIOMOLECULE 1;APPLY SYMMETRY" does not read second line of chain list
2622 # bug fix: added connections do not save properly in state
2671 # bug fix: set picking measure distance not doing callback (from 11.5.23)
2672 # bug fix: picking echos not working with set antialiasdisplay
2681 # code: 2-fold improvement in rendering ellipsoids by not using getNormix()
2693 # bug fix: measurement labels for angles do not appear in slab mode (goes WAY back before 10.0)
2694 # bug fix: U_iso_or_equiv fields not read in CIF
2695 # bug fix: (application) writeTip GT string not defined.
2725 # * 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES
2736 # bug fix: state "set measures angstroms" does not include "select *"
2749 # bug fix: "....".trim("xyz") function not properly trimming ANY x,y,z
2750 # bug fix: draw OFFSET not working properly
2751 # bug fix: PovRAY output of draw objects -- cylinder end caps not considered
2752 # bug fix: draw width 0.05 {...} {...} -- line does not properly render
2771 # bug fix: (applet) script termination callback should not be sent to message queue
2843 # bug fix: UFF.prm not properly recognizing sp2 N in N-oxides
2881 # bug fix: load unitcell {a b c alpha beta gamma} not working (since 11.5.8)
2887 # bug fix: zap file > 2 multiple models do not properly delete
2901 # bug fix: zap x.y not correcting Eval variables
2902 # bug fix: isosurface user VolumeData not properly loading
2911 # bug fix: zap {atom expression} for not including all atoms in a model in the selection
2924 # Note that file.model numbers do not change after this.
2933 # bug fix: atomChooser not updated for zap
2934 # bug fix: isosurface model keyword does not carry on to saved state
2935 # bug fix: lcaocartoons do not color properly or get restored from state properly
2936 # bug fix: popup menu selection of groups and symmetry operations does not work
2945 # bug fix: CAChe CSF reader not reading partial charges
2957 # bug fix: rotateSelected INTERNAL not adjusting for internal rotation center
2958 # bug fix: .max/.min not allowed in context: "select resno=@{{visible}.resno.max}"
3020 # spacefill 30%User # percent of User-defined values (or CURRENT if not defined)
3028 # note that dots do not have a %Jmol option:
3058 # bug fix: JVXL writing does not properly save pocket cavities or minsets
3066 # bug fix: Gaussian reader not considering possibility of cartesian D and spherical F
3067 # bug fix: ADF reader not reading coordinates for newer ADF output
3075 # bug fix: echo offsets do not correct for window position
3094 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms
3097 # bug fix: sets offset based on imageFontScaling, not overall font scaling
3098 # bug fix: multiline labels not positioned properly with offset 0 0
3099 # bug fix: labels not scaling properly
3102 # bug fix: labels not scaling properly when in script with file load
3103 # bug fix: labels not appearing in contrast when given same color as background
3111 # platform objects/delay threads not being destroyed
3133 # bug fix: image writing does not scale fonts properly.
3134 # bug fix: antialias of images not functionally independent of antialias for display
3135 # bug fix: label offset doubled for multiline labels with left/right/center alignment not specified
3157 # bug fix: state: calculate hbonds not saved
3161 # bug fix: isosurface lcaoCartoon "pz" translucent not setting both lobes translucent
3213 # not containing O improperly drawn for sheets
3215 # bug fix: translateSelected/rotateSelected does not move cartoons
3216 # bug fix: tainted occupancy not saved in state
3218 # bug fix: restore of state does not reset user-defined atom properties
3225 # bug fix: CIF reader not skipping loops with load of a specific model of a model set
3247 # bug fix: defaultDirectory for Jmol application not usable for http:// protocols
3248 # bug fix: load "files" not properly loading zip files or files involving default directory
3260 # bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL
3276 # bug fix: selectionHalo status and color not in state
3282 # bug fix: subsets not properly handling restrict
3283 # bug fix: models with turns crash jmol if not first model loaded
3284 # bug fix: quaternion command by itself not switching to most recent quaternion
3285 # bug fix: background color off when not white and ends in "FF"
3287 # bug fix: multiframe draw with labels different for each frame not properly saved in state
3297 # bug fix: Jmol not putting structures in for all models in a PDB file
3298 # bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices
3307 # bug fix: dipoleScale not saved in state
3313 # bug fix: draw not colored
3317 # bug fix: applets not self-destroying when window containing them close
3318 # bug fix: rotate commands not sent to other applets when set syncScript if OFF
3326 # bug fix: quick fix for disabling popup menu under Java 7 where permissions are not granted
3329 # in which case "select 1.3", if file 1 is a trajectory, not only
3339 # bug fix: load append not saved in state properly
3341 # bug fix: draw ... nofill mesh properties not processed
3342 # bug fix: draw DIAMETER N not properly functioning for curves or arrows
3352 # bug fix: set mouseSync with sync * ON disabling sync but not reenabling it
3354 # bug fix: select within (3.3, {-1 1 1}) does not work with negative integer coordinate
3355 # bug fix: trajectories were not fully implemented
3390 # bug fix: XOR returning OR when not a bitset
3395 # bug fix: slab/depth planes not properly constructed
3412 # bug fix: scroll wheel with synchronization does not track properly
3424 # bug fix: loadInline not properly autobonding -- causes null pointer error
3431 # bug fix: symop=0NNN not returning all atoms with translation NNN
3434 # box containing symop=1555, not the atoms themselves.
3440 # bug fix: set measures 0.1 --- solid line does not move.
3448 # bug fix: set of many more (but not all) parameters can accept mathematical expressions
3449 # bug fix; set strandCount not properly handled
3454 # bug fix: quaternion not including chain designation
3464 # bug fix: write FILE not handling binary file formats properly
3466 # bug fix: PDB CONECT records not creating bonds for ALL models
3468 # bug fix: amino not a subset of protein
3469 # bug fix: proteins with just C CA N not recognized as such
3480 # bug fix: WebExport not properly accessing files in more complicated situations (pmesh, isosurface…
3481 # bug fix: WebExport not allowing variety of local location options
3483 # bug fix: return command not allowed in simple context
3486 # bug fix: hideNotSelected not in state.
3493 # bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth
3494 # bug fix: scaleAngstromsPerInch not in state
3507 # bug fix: scale3D not working
3583 # IGNORE_ERRORS --- process the file and do not stop if some files are not valid model files
3624 # bug fix: color bonds CPK not working
3628 # bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers
3631 # bug fix: isosurface CAP not turned off prior to map sasurface
3632 # bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms
3640 # bug fix: state not saved for coloring elements
3641 # bug fix: state not properly representing deleted bonds
3642 # bug fix: setColix not clearing shading in certain cases
3668 # If the atom set is not given, those properties default to {visible}
3677 # bug fix: new label fonts not loaded when labels resized
3715 # bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes …
3738 # since the VARIABLE myfunction has not been defined.
3762 # bug fix: write coord mol not working
3783 # bug fix: select by itself not working; oy. Since at least 11.0
3786 # bug fix: isosurfaces not taking their default name properly
3793 # bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
3797 # bug fix: set xxxCallback not allowed
3822 # (was introduced in 11.3.29, but not fully articulated)
3847 # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR
3862 # bug fix: draw object text not selective for frame
3869 # bug fix: antialias labels not fully bitmapped
3878 # there is a priority in Jmol, but not yet clear to me which. The current priority
3888 # bug fix: hover state not properly showing specific-atom hover labels.
3940 # bug fix: inline loading not working
3972 # bug fix: app -c flag errors not going to Logger.Error
3974 # bug fix: 11.3.14+ does not write colormapped JVXL files
3999 # They do not carry over from one file to the next.
4036 # bug fix: backbone not in state
4136 # critical bug fix for color command not coloring objects properly
4143 # critical bug fix for functions not returning values
4144 # bug fix for atomarray[i] not selecting properly
4145 # bug fix for write not working with VAR
4146 # bug fix for application not accepting pastes into the
4148 # bug fix for bondOrder command not properly treating 4.0 or 0.5
4149 # bug fix for decimals not represented properly in error messages
4156 # connect 3.0 (_H and connected(_N) (_O and not within(chain,_1)) hbond
4161 # bug fix within(chain,xxx) not working
4163 # bug fix we were not exporting error free xhtml 1.1.
4164 # bug fix for WebPageMaker not writing files
4166 # which actually will not work in ScriptWindow. We need the direct execution in
4173 # bug fix compiler not recognizing "axes =" or "measures = "
4175 # bug fix for WebPageMaker not stripping \ in load file names
4181 # critical bug fix for 11.3.23 compiler not recognizing line endings
4183 # bug fix? for background model not available for multiple frame range (e.g. frame 2.0) or after in…
4259 # bug fix: isosurface of MOs not properly displaying color in saved state
4357 # prior to 11.3.17, you could not do:
4362 # because x was only saved as a string, not an array
4380 # does(did) not.
4387 # a[a[2]] = "not any more; now it's this"
4394 # not any more; now it's this
4402 # a[8] = " not"
4404 # >> a = "this is not a test"
4442 # bug fix: Eval RPN processor for list[n] addition operator not doing selection
4521 # bug fix: HDO not recognized as "water"
4522 # bug fix: rotateSelected MOLECULAR not around {0 0 0}
4531 # adjustment: setting JPG default quality to 75, not 100
4618 # bug fix: set language fr needs quotes but should not
4627 # bug fix: lcaoCartoon for sp center requires "sp2" not "sp"
4628 # bug fix: mo not showing titles
4638 # bug fix: script window using swing thread start not from event queue
4640 # bug fix: dots nn% not operational
4675 # syncId is not given, then the ID for the page containing the controlling applet
4687 # SLAVE turn sync on, but not as driver
4709 # bug fix: isosurface color -- not operating for some isosurface types
4710 # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
4722 # bug fix: isosurface interior cavity was not setting meshdata surfaceSet null
4730 # bug fix: dots not available in multimodel mode
4732 # bug fix: isosurface cavity not filled completely
4746 # bug fix: echo text not re-orienting on resize of applet or application
4749 # bug fix: popup menu set picking label not working
4765 # bug fix pmesh not working
4787 # bug fix: state for phased atomic orbitals does not preserve red/blue color
4809 # bug fix for draw text not hovering for points
4812 # bug fix for CdkAdapter not having auxiliaryInfo data
4826 # bug fix for move not releasing isInMotion
4844 # bug fix for compound document reader not reading enough short segment pointers
4845 # bug fix for Spartan reader not recognizing 5D orbital problem
4852 # bug fix for Jvxl.jar standalone application not having complete set of class files (jvxl)
4854 # bug fix for inappropriate pre-JVM12 menu items not disabled
4860 # bug fix for animFrameCallback not indicating animation direction
4861 # bug fix for help not working and help URL not displaying (app)
4862 # bug fix for app not writing state from File...Export menu (app)
4864 # bug fix for "wait" not recognizing if it is just a syntax check (app)
4874 # bug fix for select BONDS ({...}) not preserved in state
4875 # bug fix for geosurface not always restored from saved state
4885 # bug fix for strandCount not carrying over to meshRibbon
4898 # bug fix for multiple frames displayed does not show Select...Elements menu
4899 # bug fix for select @x not functioning where x = {atom expression} or x = "atom expression"
4914 # bug fix for load with explicit spacegroup not respecting normalization choice
4915 # bug fix for symop=nijk selecting base atoms when not appropriate
4940 # bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0}
4941 # bug fix for PDB files not supplying information about residues for the popup menu.
4949 # bug fix for label alignments sometimes not being saved properly in the state
4951 # in terms of whether animation is on or not in the 7th parameter being 1 or 0:
4994 # app fix for Edit...preferences not properly refreshing for axes and boundbox
5014 # bug fixes -- draw state, menu not updating, language submenu
5060 # not important generally.
5111 # //non-numeric formatting allowed but not necessary
5144 # normal Jmol autobonding would not properly connect atoms, but
5148 # were not present in the original set, as for quartz.cif, where
5207 # based on the VERY latest version (not released yet), which includes
5218 # was not being recorded properly
5230 # (mo list) -- not particularly useful
5257 # 1) dots/geosurface not being saved properly in state
5258 # 2) animation parameters not being saved properly in state
5479 # plane and bondset are new; arithmetic operations are not fully developed.
5508 # false OR 2.0 ==> true (2.0 is not 0, so it is TRUE)
5630 # If the file does not exist, then the string contains the error message.
5768 # pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6…
5886 # fix for "draw off" not recorded in save state