Lines Matching refs:fix
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
11 # bug fix: bfactor min/max was ignoring first atom
12 # bug fix: within molecule was using undocumented "visible"
13 # bug fix: frame *;draw {atomno=1} {atomno=5} not working properly
14 # bug fix: pdb reader as trajectory error
15 # bug fix: MO export to cartesian exporters (VRML/X3D/Maya) should not do front-only
16 # bug fix: APBS reader could hang on empty line
17 # bug fix: message this is a @{test} fails
18 # bug fix: CCP4/MRC and XPLOR map file reader fix/upgrade
24 # bug fix: revertings changes to cancelRendering
25 # bug fix: applet cannot load inline
31 # bug fix: connected(0, {carbon}) not working
32 # bug fix: obscure compiler PDB bug for polyhedra, structure, frame commmands
34 # bug fix: polyhedra colors not deleted when polyhedra deleted
35 # bug fix: polyhedra can be lost if only a subset are colored
36 # bug fix: write to clipboard not working
37 # bug fix: label %i not working
38 # bug fix: select within(0.3, hkl, {1 2 3}) requires quotes: "hkl"
44 # bug fix: PDB cryst1 record for NMR files not ignored
45 # bug fix: symop in biomolecule context not recsognized by label "%[symmetry]"
46 # bug fix: "label %" can cause Java exception
47 # bug fix: older format %{...} not recognized by script compiler
48 # bug fix: long scripts in setEcho being chopped when saved in state
49 # bug fix: "color background xxxx" clears background image as well
50 # bug fix: labels given text after containing an image have incorrect y-displacement
51 # bug fix: transparent pixels in images not respected
57 # bug fix: _width and _height lost after initialize
58 # bug fix: Jmol 11.8.10-11.8.13 will not read state orientation correctly
64 # bug fix: font axes not functional
65 # bug fix: FILTER "biomolecule ..." option broken in LOAD command.
66 # bug fix: {xxx}.xxx = syntax immediately following "for ( ) {...}" causes compilation error
67 # bug fix: draw: when only some models are visible, does not properly assign models to drawn object
69 # bug fix: zoomTo out not functioning
75 # bug fix: zoom/zoomTo does not refresh transform parameters
76 # bug fix: dot product miscalculation
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.
87 # bug fix: navigation key release causing unnecessary refresh
88 # bug fix: console command recall (up arrow) does not always return full command line
89 # bug fix: zShade/navigation mode incompatibility
90 # bug fix: navigate TRACE broken in 11.7.47
91 # bug fix: zshade not resetting properly; now reset off with reset() or load of model
92 # bug fix: occasional null pointer error during ZAP due to continued rendering by
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
102 # bug fix: Hall name translator can incorrectly assign matrix for F m -3 m group
103 # bug fix: Gaussian '09 reader not reading " Atom AN" properly in frequency lists
104 # bug fix: zoom/rotateXY modes not properly isolated
105 # bug fix: moveto with {0 0 0 0} uses instead {0 0 1 0}
106 # bug fix: zoomto fights with user over orientation
107 # bug fix: AIMS files with empty lines preceding keyword lines are now recognized
108 # bug fix: AIMS reader not reading multipole lines describing monopoles
109 # bug fix: CASTEP and AIMS readers now properly load unit cells using cell vectors
111 # bug fix: CASTEP reader not understanding unit specifier in .cell files
117 # bug fix: strand count assignment error in cif/pdb readers causes failure to load 3ovo.cif
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
121 # bug fix: set toggleLabel inappropriately resets label to default setting
122 # bug fix: moveto QUATERNION (undocumented for 11.8) not distinguishing between
125 # bug fix: setting perspective model stops animation in state script
126 # bug fix: GAMESS reader not reading all vibrational frequencies
132 # bug fix: GAMESS reader not reading BETA MOs.
133 # bug fix: A function starting with "_" originally was considered
138 # So for this fix I've changed that to be "static_..." for
143 # bug fix: jmol -ionxs with a script that includes measurement tries to update a nonexistant measur…
144 # bug fix: select xxx when xxx is an array fails to do lookup of defined values
145 # bug fix: legacy code: Bond.getBondModelIndex returning atomIndex instead
146 # bug fix: water: +", (oxygen & connected(2) & connected(2, hydrogen or deuterium or tritium), (h…
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.
151 # bug fix: GAMESS reader vibrations use wrong atom coordinates
152 # bug fix: PQR reader not adaptive
153 # bug fix: zshade now working correctly (almost -- see 11.8.11)
154 # bug fix: setting spacefill to a large user-defined VDW radius incorrect
155 # bug fix: Gaussian 09 LOG file reader upgrade for MOs
156 # bug fix: unitcell offset {1 1 1}; select UNITCELL
162 # bug fix: incorrect reference to jmolStatusListener for sync callback in StateManager
163 # bug fix: file drop needs zap prior to load for cleaner operation
164 # bug fix: Hall symbol translation generates incorrect Jones-Faithful operation (missing translatio…
171 # bug fix: context menu View... broken when boundbox or unitcell are on
172 # bug fix: syncScript broken
173 # bug fix: load trajectory not working properly
174 # bug fix: animation/spin incompatibility problem
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
186 # bug fix: (potential) draw symop could have incorrect glide
192 # bug fix: "zapped" file does not clear menu
193 # bug fix: x = {255,0,0}; select color=x; #did not work
194 # bug fix: symop() -- can now be used without "all."
195 # bug fix: isosurface reading of contoured JVXL files defaults to "nomesh nofill"
201 # bug fix: file save from menu does not pull up dialog
202 # bug fix: aims/castep readers
203 # bug fix: "initialize" should not reset defaultDiretory
204 # bug fix: compiler error for {xxx}.yy = n \n {xxx}.yy = n
205 # bug fix: compiler error for literal -0 or -0.0
206 # bug fix: show pointgroup can give wrong format after getproperty PointGroupInfo
207 # bug fix: mmCIF misreads bfactor data
208 # bug fix: load append of file with ellipsoids causes array out of bounds exception
209 # bug fix: show spacegroup can cause null exception
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
218 # bug fix: popupMenu disabling nonfunctional
219 # bug fix: acos, to be consistent, needs to deliver degrees, not radians
220 # bug fix for MOReaders * NBO: --- note, "-" can be in column with " " causing tokenization failure
226 # bug fix: grp.property_x = n can change definition of grp
228 # bug fix: q1.dot(q2)
250 # bug fix: polyhedra saving in state
251 # bug fix: function call as statement with expression argument fails:
255 # bug fix: isosurface map property can create holes in isosurface
258 # bug fix: Various Examples fixes
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 …
284 # bug fix: (application) delaying saveChooser load makes startup MUCH faster when loading a file
285 # bug fix: gaussian reader may fail to read MOs from Gaussian 03: AM64L-G03RevC.01 3-Apr-2004
292 # bug fix: DRAW point size 6 pixels (an even number) sets it just one pixel off center -- 7 is bett…
305 # bug fix: zap x.y when have measures to draw objects causes exception
306 # bug fix: isosurface mapping with property where property can be NaN does not render some regions
307 # bug fix: lcaoCartoon wildcard problems
308 # bug fix: undocumented rotate[selected] {pt1} {pt2} ... has pt1/pt2 backward. Should be such that:
317 # bug fix: compiler error when integer typed instead of command
318 # bug fix: state for lcaocartoon broken
319 # bug fix: set picking spin for draw objects broken in 11.8.RC1
321 # bug fix: DRAW CIRCLE size may not be correct when restored from state
341 # bug fix: 1C4D has [FOR] -- not accepted
342 # bug fix: color isosurface red translucent prior to isosurface command causes null pointer excepti…
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
355 # bug fix: mouse-picked measurements broken in 11.8.RC1
361 # bug fix: measurements defined using points not restricting to models
374 # bug fix: VRML balls missing; VRML/POVRAY error on partial surfaces
385 # bug fix: navigationmode not properly adapting with window resize or antialiasdisplay
389 # bug fix: arrays passed to functions by reference do not update if size is increased
399 # bug fix: spacegroup "-- [--]" displayed when load command option SPACEGROUP is used
400 # bug fix: mol2 reader not properly allowing override of CRYSIN unit cell record
401 # bug fix: %r not correct label
402 # bug fix: quaternionFrame default now "p"
403 # bug fix: quaternion difference off by one group
404 # bug fix: show FUNCTIONS not working
405 # bug fix: draw picking in multimodel context causes null pointer exception
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
416 # bug fix: draw RAMACHANDRAN angle arrow radii too small
418 # bug fix: quaternion difference draw not quite correct on axis position
419 # bug fix: 11.7.43 broke restoration of state having multimodel draw
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!)
485 # bug fix: functions with names starting with _ were local instead of global
486 # bug fix: 2 pixels off in y for labels. Don't know why I thought that was necessary in Text.java::…
502 # bug fix: problems with PAUSE/RESUME within App
503 # bug fix: "set ?" nonfunctional
504 # bug fix: unmatched { in quotes in @{ } not properly treated: echo @{" testing}"}
519 # bug fix: write FRAMES also for trajectories
522 # bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
523 # bug fix: dipoles cannot be colored by name
524 # bug fix: dipole settings not accessible via wildcards
526 # bug fix: spartan'08 reader not reading vibrations
532 # bug fix: /** comment ending line can cause odd error
534 # bug fix: set xxxx n where n is an integer fails.
535 # bug fix: GAMESS reader not properly assigning MOs
538 # bug fix: a="test";a[1] = "b" not working
539 # bug fix: {atomExpression}.min, .max
567 # bug fix: pickMeasureScriptTip not found
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.
581 # bug fix: color.all not working properly
582 # bug fix: xxx.all was not forcing array when only one value
593 # bug fix: load @filename
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"
659 # bug fix: echo @{.... .... .... } not counting braces
665 # bug fix: setting commandOptions "" in Viewer.setAppletContext()
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
786 # bug fix: MO reader can fail setting min/max bounds
787 # bug fix: various tweaks of atom properties business.
788 # bug fix: x = array();x[1] = "testing" not working
793 # bug fix: biomolecules for new PDB format
903 # bug fix: isosurface cavity colorscheme not applied
904 # bug fix: isosurface cavity colorscheme "sets" error
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
995 # bug fix: QchemReader reading second set of MOs with spherical basis problem (at end of optimizati…
1020 # bug fix: load {n n n} not saved in state
1049 # bug fix: {atomExpression}.fxyz does not return factional value, just 0.0
1083 # bug fix: Hall lattice operation (SHELX only) could place atoms in unexpected unit cell
1084 # bug fix: unitCell normalization error could miss some atoms in multi-unit cell visualizations
1086 # bug fix: possible exception when writing large image with translucency due to caught memory overf…
1092 # bug fix: calculate hbonds can fail when group does not have O or OXT atoms
1093 # bug fix: (applet) jmolGetPropertyAsString("image") not functional
1096 # bug fix: draw/isosurface *name*
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
1104 # bug fix: isosurface incorrectly setting number of grid points for MEP surface map
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
1121 # bug fix: load file:///xxx.xxx (file:/// with file in root path) causes unrecoverable exception
1122 # bug fix: signed applet JmolAppletSigned0.jar does not include minimizer in internal jar index
1123 # bug fix: rotate -x n rotates wrong direction
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
1135 # bug fix: reading multiple files from a ZIP file collection, Jmol was forcing autobond
1137 # bug fix: load MANIFEST not working properly
1138 # bug fix: V3000 reader chokes on CHG=n and does not recognize MASS=n
1139 # bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!)
1149 # bug fix: automatic adjustment for 5D (spherical) orbitals, especially for Spartan Smol reader
1150 # bug fix -- Spartan reader adding " in front of atom label
1155 # bug fix -- animation/spin while script is rendering can cause Exception
1163 # bug fix -- trajectories with files having bonds can be a problem
1164 # bug fix -- animation/spinning while connections are being made can cause exception
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
1188 # bug fix: Spartan .spardir /input files not being read
1189 # bug fix: draw arrow/vector slightly overshoots end point
1195 # bug fix: isosurface/mo FRONTONLY not operative
1199 # bug fix: MO calculations skips d2+ orbital due to integer division.
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
1214 # bug fix: measure n1 n2 n3 n4 with just numbers selecting atoms in frame 1 rather than current fr…
1215 # bug fix: toolbar icon for pickMeasure tied to tools "measurements..." item
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.
1228 # bug fix: subtle MarchingSquares calculation error produces incorrect contours for mapped plane
1238 # bug fix: isosurface TRIANGLES not turning off when isosurface cleared
1239 # bug fix: remapping colors of translucent isosurface can have incorrect colors
1240 # bug fix: isosurface sphere 1.0 map molecular not working
1241 # bug fix: MO calculation with selected atoms can fail
1242 # bug fix: picked atoms automatically selected -- bug in 11.7.24
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…
1255 # bug fix: Spartan reader reads MOs improperly when only a partials set of MOs is included in the f…
1256 # bug fix: Some Spartan files not reading: Compound Document not properly finding root directory bl…
1267 # bug fix: PDB load filter broken for ANISOU
1268 # bug fix: isosurface plane improperly coloring nonmapped planes
1278 # bug fix: Mopac graphf UHF files not read properly for beta orbitals, or can't read file
1290 # bug fix: set picking draw can lose focus during drag operation
1301 # bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
1302 # bug fix: Menu File|Open does not honor "start in" directory
1310 # bug fix: structure helix ({xx:yy}) compiler bug
1318 # bug fix: user menu ...Text menus not translated
1319 # bug fix: minimization broken
1320 # bug fix: menu save ?.spt
1321 # bug fix: write PovRay "?.pov"
1327 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries
1333 # bug fix: vibrationperiod set to 0 if vibration off when state saved
1334 # bug fix: Compilation problem with "new IOException(e)"
1335 # bug fix: application -i option still gives message from "set xxxx"
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
1397 # bug fix: some quaternions cannot be created from a 3x3, namely:
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
1443 # bug fix: MO scale
1452 # bug fix: measure allConnected broken
1453 # bug fix: 11.7.14 has broken define ({...}) statement
1471 # bug fix: write .... @{...} can fail
1472 # bug fix: write coords CLIPBOARD broken
1473 # bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpre…
1474 # bug fix: applet compilation error not sent in termination message
1475 # bug fix: build javax package does not include AxisAngle4d.class, Matrix4d.class
1476 # bug fix: compilation of myfunc({1 2 3}) fails
1477 # bug fix: hover watcher occasional uncaught exception
1484 # bug fix: applet improperly reporting status of "quiet" commands
1485 # bug fix: stereo not in state
1486 # bug fix: stereoDegrees parameter not reported correctly
1487 # bug fix: quaternion straightness update
1488 # bug fix: translucency of mapped isosurfaces not saved in state
1489 # bug fix: Dialog look and feel for Mac
1490 # bug fix: negative number in range involving ^ fails: select 10^P -17^P
1505 # bug fix: .xxx broken for Jmol 11.7.11
1508 # bug fix: goto xxx with trailing white space fails to find xxx
1509 # bug fix: goto with a # comment in the script prior to the target line fails
1510 # bug fix: two //xxx comments in a row breaks script
1514 # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
1518 # bug fix: isosurface APBS dx file reader broken (since 4/2007)
1525 # bug fix: UFF.txt not included in build
1550 # bug fix: function definitions occurring before prior script commands are executed.
1551 # bug fix: message @{xxxx} in function not picking up function context variables
1553 # bug fix: CD command not working for writing
1554 # bug fix: Some browsers do NOT strip \n from <param> tags, necessitating changes in loadInLine()
1560 # bug fix: initializeBspf(); missing in setTrajectory()
1571 # bug fix: AMBER atom type IM and IP not recognized
1572 # bug fix: AMBER topology file reading of IFBOX=2 files
1573 # bug fix: antialiased fontscaling labels can appear incorrectly
1574 # bug fix: font maximum reduced
1576 # bug fix: more lenient MopacGraphF format resolving
1577 # bug fix: "valence" not "valency" in data property_valence
1583 # bug fix: set antialiastranslucent false not functional
1584 # bug fix: text color near black with antialiasdisplay becomes white
1585 # bug fix: text antialiasing of near-black text looks very bad when antialiased
1600 # bug fix: forcefield file UFF.prm --> UFF.txt
1601 # bug fix: better Escape method for strings
1602 # bug fix: connect auto not registered in state
1615 # bug fix: draw point translucent only draws ring
1617 # bug fix: load string inline with multiple models fails
1626 # bug fix: set labelToggle malfunctioning
1627 # bug fix: missing default background for toggled labels
1628 # bug fix: color {oxygen} translucent blue
1629 # bug fix: color translucent 1 blue 1-8 integer settings off by one
1630 # bug fix: background color +/-1 adjustment removed
1636 # bug fix: spardir within /M... directory
1660 # bug fix: XML readers broken in 11.7.1
1661 # bug fix: AMBER molecular dynamics topology file misreads P atoms
1719 # bug fix: GIF encoder color / class not found issues
1720 # bug fix: very thin cylinder does not appear at all viewing angles
1721 # bug fix: load "/xxx" with unsigned remote applet loads local file instead of remote root directory
1723 # bug fix: sulfur/sulphur always spelt as in IUPAC Red Book
1724 # bug fix: display of aromaticSingle bond for NEW bond results in dotted bond.
1731 # bug fix: fileName not reset after ZAP
1732 # bug fix: set echo none; color echo green null pointer exception
1733 # bug fix: .x not recognized
1734 # bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily)
1735 # bug fix: cartoons ending in helix or strand draw single dot for final amino acid
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
1743 # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging
1744 # bug fix: trajectories not enabled
1746 # bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
1747 # bug fix: select model=0.0 caused infinite loop
1753 # bug fix: mol2 PDB format better handling of chains and derived element types
1754 # bug fix: save image button/menu interface broken in 11.6.RC15
1762 # bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP
1764 # bug fix: CML reader failst to load primitive lattice parameters when no symmetry
1766 # bug fix: CML reader not assigning atom labels
1767 # bug fix: CML files not properly loading symmetry
1768 # bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED
1774 # bug fix: applet -- setting a jmolScript callback prevents menu updates
1777 # bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
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
1798 # bug fix: y-offset for echo text and images
1799 # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
1800 # bug fix: findbugs input stream closure
1808 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx
1809 # bug fix: getProperty("modelinfo",{atom expression}) not working
1812 # bug fix: draw pointgroup when principalPlane == null
1813 # bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawR…
1815 # cml reader fix for not applying symmetry to first model
1822 # bug fix: echo IMAGE and antialiasdisplay
1823 # bug fix: super/subscripts with antialiasdisplay
1825 # bug fix: web export / language
1826 # bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1
1827 # bug fix: d2 point groups cause null pointer exception due to missing principal axis
1828 # bug fix: {*}.x = .... broken
1837 # bug fix -- set picking spin, also compatibility of set picking spin and doing measurements
1838 # bug fix -- draw pointgroup, write pointgroup draw
1846 # bug fix: show pointgroup draw null pointer exception
1847 # bug fix: print $planeA - capital letters in a draw name disallow finding it.
1853 # bug fix: ramachandran / ramachandran r navigation problem
1888 # bug fix: refresh for hover
1889 # bug fix: state definition for lcaoCartoons, isosurface with IDs containing spaces
1895 # bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues
1899 # bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
1900 # bug fix: more language localization in webexport
1908 # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes
1909 # bug fix: language localization in webexport
1915 # bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling th…
1916 # bug fix: set echo xxxx 30 40
1917 # bug fix: WAY more streamlined refreshing
1918 # bug fix: createImage(), not getImage() in order to allow dynamic file change
1919 # bug fix: halo size for antialiased display
1921 # bug fix: write IMAGE broken for 11.6.RC2+
1922 # bug fix: unnecessary refreshes removed from moveto/zoom with time 0
1930 # bug fix: select @m throws an error
1944 # bug fix: minor error in pointgroup; dimension tied to radius
1953 # bug fix: image background transparency
1958 # bug fix: Cs pointgroup not found
1959 # bug fix: set echo DEPTH/IMAGE
1960 # bug fix: workaround for Java 1.6.0_10 diallowing popup menu
1969 # bug fix: D3h point group
1970 # bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, no…
1976 # bug fix: measures were messed up
1988 # bug fix: 11.5.52 may have lost "true" as a keyword
1990 # bug fix: more testing with pointgroups
1994 # bug fix: application rubberband selecting inappropriately selects atoms not visible
1996 # bug fix: in draw pointGroup -- height of cylinder was too small
1997 # bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontl…
2014 # bug fix: 11.5.49 and 11.5.50 broken for ".max"
2021 # bug fix: ramachandran/quaternion "reset" not decoupled from model decouple
2023 # bug fix: set axesOrientationRasmol finally correctly implemented
2025 # bug fix: JmolViewer interface deprecated "rotateTo..." methods changed to "rotate..."
2027 # bug fix: set defaults jmol/rasmol must do reset().
2035 # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
2036 # bug fix: was reading server path for local path from history in Webexport
2037 # bug fix: $ptx[2] notation broken in 11.5.49
2045 # bug fix: strange "scripted: ?" message with measurements removed
2046 # bug fix: extra values in measure reporting, and wrong format
2047 # bug fix: 11.5.48 is broken for scripts with array definitions such as
2067 # bug fix: PDB site definition does not ignore empty site definitions
2068 # bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo
2069 # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i
2070 # bug fix: connect aromatic auto; select connected([bond type],...)
2071 # bug fix: queue thread termination when applets are off screen
2072 # bug fix : sheetsmoothing not consistent among structures in multi-chain systems
2073 # bug fix: messages not sent to messageCallback
2075 # bug fix: 11.5.47 shows oddly sized arrow for very first rendering
2076 # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
2083 # bug fix: Removed stray semicolons from header script comments in webexport templates. They
2085 # bug fix: 11.5.46 broke standard "spin x 30" (b)
2107 # bug fix: remove the skipping of semicolons if parentheses or braces have been closed. (11.5.43 b…
2108 # bug fix: set picking on broken in 11.5.39
2122 # bug fix: array size limited
2125 # bug fix: drawhover not in state
2126 # bug fix: ramachandran for systems including nucleic acids when quaternionFrame = 'n'
2130 # bug fix: 11.5.39 could break isosurface/pmesh save/write state in certain cases.
2131 # bug fix: Popin.png in WebExport replaced, was too large, causing dialog box to default to too big…
2132 # bug fix: zap 2.1 for quaternion frame causes exception
2133 # bug fix: quaternion r derivative2 nonfunctional in 11.5.45
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
2147 # bug fix: jmolScriptWait() improperly reporting to applet console
2148 # bug fix: too many messages to applet console
2182 # bug fix: hover will find atom in hidden frame.
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]
2186 # bug fix: quaternion frame "n" recognizes file-based H atoms on N for frame definition
2192 # bug fix: Java exception with write(quaternion) instead of write("quaternion")
2193 # bug fix: set picking spin did not enable draw spin/picking
2194 # bug fix: _applet variable not initializing properly
2195 # bug fix: math calculation .xyz, .color averages broken in 11.5.42
2196 # bug fix: select @x broken in 11.5.43
2197 # bug fix: integer addition not remaining integer
2203 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
2233 # bug fix: POV-RAY output of quadrilaterals.
2237 # bug fix: quaternion definition with dot-product check not effective -- removed
2238 # bug fix: quaternion construction from matrix error
2296 # bug fix: load trajectory for cases with different atom counts.
2312 # bug fix: color of NaN float values changed from "center of color scheme" to GRAY
2313 # bug fix: connect "_1" was inadvertently dropped in 11.5.26.
2314 # bug fix: state script fails to save data for atoms created using the quaternion command
2315 # bug fix: axes/boundbox/unitcell dotted not working since 11.5.6
2316 # bug fix: spin thread not stopped for applet destroy()
2317 # bug fix: quaternion derivative for i/i+1 assigned to i+1 instead of i; now assigned to i
2318 # bug fix: quaternion calculation using published algorithms was giving inverted quaternions
2395 # bug fix: carbohydrate popup menu script incorrect
2398 # bug fix: Jmol Embedded scripts containing script comments /* */
2400 # bug fix: 11.5.40 cannot read most state scripts.
2423 # bug fix: H1 and H3 in DNA are NOT backbone
2427 # bug fix: set picking center should not zoom -- just too annoying
2431 # bug fix: echos with active script and a model designation
2434 # bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables
2435 # bug fix: "set picking identify" should be equivalent to "set picking ident"
2436 # bug fix: popup menu had stereo reversed
2440 # bug fix: reading .mmol (biological unit) files such as
2480 # bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext()
2481 # bug fix: model-based drawing in multiple-model mode using an
2484 # bug fix: quaternion derivative multiplication order
2485 # bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER
2486 # bug fix: select _Xx; select unknown
2487 # bug fix: better reporting of script commands and comments
2513 # bug fix: lcaoCartoon naming for multiple centers
2514 # bug fix: pm rounding to integer value
2515 # bug fix: scaling of draw object for multimodel environment can cause null pointer exception
2516 # bug fix: scaling of VECTOR was from center, not origin
2517 # bug fix: select n-m:c chain selection inappropriately case sensitive
2518 # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
2519 # bug fix: draw CIRCLE for multiple models
2520 # bug fix: application -- "make crystal..." menu item does nothing -- removed
2521 # bug fix: zap of quaternion also zaps model inappropriately
2522 # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0
2552 # bug fix: spacefill ADPMIN/ADPMAX using probability ellipsoids
2555 # bug fix: reading output from "set showscript 1"
2556 # bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value)
2557 # bug fix: ellipsoids for applied symmetry causes odd shapes (s8.cif)
2558 # bug fix: security for no mayscript may cause problem with measure callback
2559 # bug fix: rocket positions after translateselected
2565 # bug fix: frame titles not positioning correctly for antialiased display
2566 # bug fix: quaternions created with extraneous atom lines
2567 # bug fix: select symop not behaving intuitively
2576 # bug fix: proper thermal ellipsoid probability measures
2578 # bug fix: load FILTER not saved in state
2579 # bug fix: application -- undo/redo buttons not disabling
2586 # bug fix: biomolecule really works this time!
2592 # bug fix: modelLoader was assigning too much array space for chains
2614 # bug fix: ellipsoids for navigation mode and perspective depth
2615 # bug fix: PDB biomolecule for many-BIOMT system
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
2657 # bug fix: isosurface ELLIPSOID was disabled
2658 # bug fix: Vector4f in Sphere3D causes applet failure, as it includes
2660 # bug fix: stronger wireframe for antialiased display and generator (POV-ray)
2671 # bug fix: set picking measure distance not doing callback (from 11.5.23)
2672 # bug fix: picking echos not working with set antialiasdisplay
2674 # bug fix: set ellipsoidAxisDiameter [int] sets the diameter in milliAngstroms
2675 # bug fix: sequence range for missing sequence numbers returns 0
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.
2696 # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored.
2697 # bug fix: state for draw arrow in multimodel context delivers wrong coordinates
2736 # bug fix: state "set measures angstroms" does not include "select *"
2737 # bug fix: labels can change size in returning from antialiasdisplay=true to antialiasdisplay=false
2748 # bug fix: data CLEAR command nonfunctional
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
2753 # bug fix: data "model"...end "model" saves state without first line if first line is empty
2754 # bug fix: "show data types" putting comma in wrong location
2768 # bug fix: draw adds extra circle in 11.5.25
2769 # bug fix: minimization out-of-plane energy calculation error
2770 # bug fix: better initial minimization parameters
2771 # bug fix: (applet) script termination callback should not be sent to message queue
2772 # bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window
2773 # bug fix: draw width -1 or draw mesh nofill with very short cylinders creates odd jumpy effect
2774 # bug fix: draw CIRCLE for multiple model sets
2842 # bug fix: UFF torsion calculation incorrect
2843 # bug fix: UFF.prm not properly recognizing sp2 N in N-oxides
2844 # bug fix: minimizer for compounds containing isotopes D and T
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
2893 # bug fix: null surfaceGenerator causes MO exception
2894 # bug fix: isosurface reading/writing JVXL files having insideout keyword
2900 # bug fix: zap x.y additional work -- connections, isosurfaces
2901 # bug fix: zap x.y not correcting Eval variables
2902 # bug fix: isosurface user VolumeData not properly loading
2910 # bug fix: zap x.y for dots
2911 # bug fix: zap {atom expression} for not including all atoms in a model in the selection
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
2939 # bug fix: mol2 reader cannot read files with single-line comments
2945 # bug fix: CAChe CSF reader not reading partial charges
2946 # bug fix: WebExport with http:// files fails to save file
2947 # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
2950 # bug fix: state saving with rotateSelected spinning spins entire model
2951 # bug fix: getproperty("chaininfo") for non-biological model causes null pointer exception
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}"
2959 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
2962 # bug fix: write PDB format incorrectly writes atoms with 4-length names
2963 # bug fix: Spartan SMOL directory reader doesn't assign bonds
2970 # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
2973 # bug fix: write PDB format incorrectly writes atoms with 4-length names
2974 # bug fix: Spartan SMOL directory reader doesn't assign bonds
3040 # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propert…
3041 # bug fix: functions, save/restore state were disabled by bug in 1.5.8
3042 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error
3043 # bug fix: undocumented .vdw atom property was equivalent to .valence
3044 # bug fix: GAMESS reading of F orbital order incorrect
3057 # bug fix: ISOSURFACE LIST command requires current isosurface
3058 # bug fix: JVXL writing does not properly save pocket cavities or minsets
3059 # bug fix: DATA command assigning property to last atom in structure fails
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
3074 # bug fix: lines starting with @{ redefine "{"
3075 # bug fix: echo offsets do not correct for window position
3076 # bug fix: menu reports too many chains
3085 # bug fix: explicit "SELECT NONE" must be given for label defaults to be set
3087 # bug fix: menu select element missing SELECT command
3088 # bug fix: for delayed font scaling animation using the font command and antialias display
3094 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms
3095 # bug fix: setParameterValue("perspectiveDepth",perspectiveDepth);
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
3104 # bug fix: fixes applet memory leak in relation to consoles
3110 # bug fix: fixes applet memory leak due to
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
3136 # bug fix: default label offsets mangled by default Front/Group
3149 # bug fix: PDB files with missing amino acid carbonyl O cause exception
3155 # bug fix: check if the file is CIF before PDB
3156 # bug fix: color hbonds translucent
3157 # bug fix: state: calculate hbonds not saved
3158 # bug fix: state: calculate surfaceDistance WITHIN (({....}))
3160 # bug fix: state: selection state "end function" missing semicolon
3161 # bug fix: isosurface lcaoCartoon "pz" translucent not setting both lobes translucent
3162 # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe
3163 # bug fix: save state for "color SelectionHalos"
3175 # bug fix: unclosed InputStream readers in zip file accessing
3180 # bug fix: unclosed readers in Pmesh, FileManager, Jvxl
3206 # bug fix: quaternion for nucleic acids
3212 # bug fix: wing vectors for biopolymers
3215 # bug fix: translateSelected/rotateSelected does not move cartoons
3216 # bug fix: tainted occupancy not saved in state
3217 # bug fix: biopolymers have wrong wing vectors (from 11.3.62)
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
3226 # bug fix: explicit format LOAD "XXX::whatever" extended to XML variants
3236 # bug fix: pmesh test1 "inline" "1 {2. 0. 0.} 0" disallowed, but that should be OK
3237 # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already map…
3238 # bug fix: isosurface lcaoCartoon "type" {atomExpression}
3246 # bug fix: better checking of scripts involving full run of all scripts
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
3254 # bug fix: version integer missing sometimes
3255 # bug fix: isosurface with trajectories
3260 # bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL
3261 # bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range
3270 # bug fix: draw/isosurface/etc. on/off/delete should operate on all objects
3271 # bug fix: display within(plane...)
3272 # bug fix: select site=n broken
3273 # bug fix: quaternion/ramachandran/model can show up together if user issues FRAME ALL
3274 # bug fix: frame 1.2 when file 1 only has one model displaying all files
3275 # bug fix: quaternion x reports wrong frame number
3276 # bug fix: selectionHalo status and color not in state
3277 # bug fix: color selectionHalos none
3278 # bug fix: polyhedra .... translucent 0.3 green
3279 # bug fix: moveto alternative format missing necessary 0 rotationRadius requirement
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"
3286 # bug fix: print {atomSet}.color -- .color returning bounding box!
3287 # bug fix: multiframe draw with labels different for each frame not properly saved in state
3288 # bug fix: within upgrade for boundbox: within(boundbox), within(boundbox,atomExpression)
3294 # bug fix: calculate hbonds for trajectories
3296 # bug fix: calculate hbonds broken in 11.3.58 (missing model field in BioPolymer)
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
3299 # bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected ato…
3300 # webexport help instructions fix to be consistent for local testing.
3306 # bug fix: multifile cartoons improperly rendering in all frames
3307 # bug fix: dipoleScale not saved in state
3308 # bug fix: quaternions broken in 11.3.58
3312 # bug fix: select 1.5 in trajectory context should switch to that set of coordinates
3313 # bug fix: draw not colored
3314 # bug fix: mousewheel too low power
3315 # bug fix: select */4 when "4" is inappropriate returns all instead of none
3316 # bug fix: memory leak in applet due to mouse/hoverwatcher listeners
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
3324 # bug fix: more work on trajectories in a multimodel context
3326 # bug fix: quick fix for disabling popup menu under Java 7 where permissions are not granted
3328 # bug fix: load trajectory extended to multifile context
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
3345 # bug fix: 11.3.58 can't set bond diameters
3346 # bug fix: with set syncMouse, target applet sets syncMouse off inappropriately
3352 # bug fix: set mouseSync with sync * ON disabling sync but not reenabling it
3353 # bug fix: spin on missing in final state function.
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
3366 # bug fix: revised sync commands
3373 # bug fix: "load trajectory" broken
3379 # bug fix: isosurface map of properties lost in 11.3.54
3389 # bug fix: axes/unitcell improperly slabbing on internal slab
3390 # bug fix: XOR returning OR when not a bitset
3391 # bug fix: unary minus for planes and points
3395 # bug fix: slab/depth planes not properly constructed
3399 # bug fix: applet.loadInline(String[] models) messes up
3412 # bug fix: scroll wheel with synchronization does not track properly
3418 # bug fix: JVXL writing/reading of simple plane writes precision color flag
3422 # bug fix: reinstating "insideout" isosurface option
3423 # bug fix: JVXL writing of lobe, sphere, ellipsoid, hydrogenOrbital
3424 # bug fix: loadInline not properly autobonding -- causes null pointer error
3425 # bug fix: data ... end model instead of end "model" causes null pointer exception
3431 # bug fix: symop=0NNN not returning all atoms with translation NNN
3437 # bug fix: no special atom checks for PDB symmetry files
3439 # bug fix: HallInfo --- Hall term miscalculation OUCH! -- mistken commenting out of code in 11.1.28…
3440 # bug fix: set measures 0.1 --- solid line does not move.
3442 # bug fix: completion of set parameter clean up
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
3455 # bug fix: default connections include proper PDB CONECT records
3464 # bug fix: write FILE not handling binary file formats properly
3466 # bug fix: PDB CONECT records not creating bonds for ALL models
3467 # bug fix: load =xxxx broken in 11.3.50
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
3484 # bug fix: setting perspective model resets unit cell on
3485 # bug fix: debug comment in TransformManager
3486 # bug fix: hideNotSelected not in state.
3492 # bug fix: set perspectiveDepth off broken in 11.3.48
3493 # bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth
3494 # bug fix: scaleAngstromsPerInch not in state
3495 # bug fix: _firstFrame/_lastFrame variables mess up state
3496 # bug fix: calculate surfaceDistance broken for 11.3.48
3507 # bug fix: scale3D not working
3590 # bug fix: multimodel files could have connected atoms between different models.
3592 # bug fix: application animation frame button reset always goes to frame 1
3598 # bug fix: antialiasDisplay changes during spinning (or any rendering) causes null pointer error
3623 # bug fix: "isosurface select() map property xxxx" array out of bounds error
3624 # bug fix: color bonds CPK not working
3628 # bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers
3629 # bug fix: Jmol math getProperty() doesn't pass parameter in some cases
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
3633 # bug fix: Jmol math (x[2])[3] indistinguishable from x[2][3]
3639 # bug fix: new boundbox command with small numbers of 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
3676 # bug fix: POVRAY and other buttons aren't enabled when there are no atoms but instead draw objects…
3677 # bug fix: new label fonts not loaded when labels resized
3679 # bug fix: nuisance "render mesh error" console report
3695 # bug fix for bioshapes visible outside of current visible frame set
3697 # bug fix for selecting atoms of atomsets using [-n] or [0]
3702 # bug fix: more natural mouse SHIFT-RIGHT behavior.
3715 # bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes …
3720 # bug fix: Strings too long in state can cause Eclipse "infinite loop" bug
3726 # bug fix: assigning a negative value to a dataAtomNumberField value caused BitSet.set() exception
3728 # bug fix: Jmol parameter setting syntax too loose
3753 # bug fix: antialias with translucent but antialiasTranslucent = false; labels, text, echos, hover,…
3754 # bug fix: negative formal charges
3762 # bug fix: write coord mol not working
3771 # bug fix: connect (..) (..) # with implicit "single" causes state to use "partial 0"
3779 # bug fix: new frame title and state
3783 # bug fix: select by itself not working; oy. Since at least 11.0
3785 # bug fix: ramachandran/quaternion fix for assignment of structure
3786 # bug fix: isosurfaces not taking their default name properly
3790 # bug fix: small fix for povray cap at back side
3791 # bug fix: overly long titles now again substringed in the popup menu.
3793 # bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
3794 # bug fix: quaternion
3797 # bug fix: set xxxCallback not allowed
3806 # bug fix: math operations with bond bitsets; % and + operating on arrays
3807 # bug fix: _set variable definition removed
3843 # bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms.
3845 # bug fix: @{} for within(1.0,point,@{....})
3852 # POV-Ray fix for number formatting width > 999
3860 # bug fix: draw @{x - {1 0 0}}
3861 # bug fix: antialias with set picking draw
3862 # bug fix: draw object text not selective for frame
3868 # bug fix: noninteger MO occupancies
3869 # bug fix: antialias labels not fully bitmapped
3870 # bug fix: RPN processor too limited in nesting level
3871 # bug fix: MO processing for Gaussian and PSI3 errors
3876 # bug fix: slabbed atoms are now capped in povray output.
3880 # bug fix: povray output of translucent objects now have reduced glare, for
3887 # bug fix: antialias causing image to be partial size.
3888 # bug fix: hover state not properly showing specific-atom hover labels.
3897 # bug fix: antialias adjustments for hover text and background box
3898 # bug fix: antialias fix for text color same as background and in front of translucent surface appe…
3899 # bug fix: antialias fix for applet
3902 # bug fix: webexport scriptbutton template had erroneous script names.
3908 # bug fix: antialiasing with translucent/POV-ray
3930 # bug fix: -- adds antialiasing for translucent objects
3931 # bug fix: error in state for connect DELETE
3932 # bug fix: 0-diameter atoms displayed as single pixels when perspectiveDepth = false
3940 # bug fix: inline loading not working
3955 # bug fix: getproperty atominfo returning string to Integer()
3971 # bug fix: select [SET] or [2MO] or [DB']
3972 # bug fix: app -c flag errors not going to Logger.Error
3973 # bug fix: no partial charges!
3974 # bug fix: 11.3.14+ does not write colormapped JVXL files
3975 # bug fix: Using isosurface within 1.0 @pt1 where pt1 is a draw point save state cannot be restored…
3986 # bug fix: insertion codes stored incorrectly in 11.3.32
4013 # bug fix: rockets color incorrect for head groups
4019 # bug fix: vibration disabled in 11.3.31
4020 # bug fix: zoomto cancels slabbing
4021 # bug fix: zoomto (atomExpression) 0 # zooms to 2x
4036 # bug fix: backbone not in state
4047 # bug fix: dipoles moved back into shape from shapespecial
4048 # bug fix: semi missing in show orientation message, second part (zyz text)
4049 # bug fix: select 0 selects all instead of PDB group 0
4050 # bug fix: write t.xxx
4056 # bug fix: calculate aromatic for N and O refined
4092 # bug fix: unitcell missing some lines when axes turned off
4101 # bug fix: menu for UNITCELL
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
4161 # bug fix within(chain,xxx) not working
4162 # bug fix for() as first command in script or line
4163 # bug fix we were not exporting error free xhtml 1.1.
4164 # bug fix for WebPageMaker not writing files
4165 # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(…
4173 # bug fix compiler not recognizing "axes =" or "measures = "
4174 # bug fix for WebPageMaker creating uncompressed PNG
4175 # bug fix for WebPageMaker not stripping \ in load file names
4181 # critical bug fix for 11.3.23 compiler not recognizing line endings
4182 # bug fix for show state for draw in multi-model environment
4183 # bug fix? for background model not available for multiple frame range (e.g. frame 2.0) or after in…
4249 # Bug? fix: update the page templates to XHTML 1.1
4259 # bug fix: isosurface of MOs not properly displaying color in saved state
4260 # bug fix: state saving of @ definitions has extra = sign.
4316 # bug fix for arrows way too fat (introduced in 11.3.19) :(
4322 # bug fix: critical arrow fix of 11.3.17 for 2-point arrows
4323 # bug fix: write PNG default was 0 compression. -q flag was OK for setting 0-9
4324 # bug fix: ragged arrow tip
4330 # critical bug fix for 11.3.17 in regard to serialization of arrays
4342 # bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point.
4343 # bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter
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}
4523 # bug fix: -g ignored on -n option, even if -w is present
4524 # bug fix: unknown color palette could cause error
4617 # bug fix: zoomTo 100%
4618 # bug fix: set language fr needs quotes but should not
4619 # bug fix: load multiple files inline causes null pointer exception
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
4639 # bug fix: state of multi-polymer protein cannot be restored
4640 # bug fix: dots nn% not operational
4641 # bug fix: molecular dipole and multiple frames
4659 # bug fix for isosurface mapping of planes by MEP (see 11.3.2)
4709 # bug fix: isosurface color -- not operating for some isosurface types
4710 # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
4711 # bug fix: gamess reader MO fix
4712 # bug fix: state save of STRUCTURE misplaced
4720 # bug fix: reading of JVXL files for orbitals loses phase information
4721 # bug fix: ACD/Labs nonstandard cml "builtin" property reader
4722 # bug fix: isosurface interior cavity was not setting meshdata surfaceSet null
4723 # bug fix: select dna can select rna if chain is mixed hybrid dna+rna
4729 # bug fix: inappropriate draw pick spinning for single point
4730 # bug fix: dots not available in multimodel mode
4731 # bug fix: multiple isosurface cavities incorrect in a multimodel environment
4732 # bug fix: isosurface cavity not filled completely
4733 # bug fix: nested ifs can cause last endif to throw error
4734 # bug fix: compiler bug working with very small real numbers
4735 # bug fix: Support for mol2 files with blank line after comments.
4741 # bug fix: ACD/Labs nonstandard cml "builtin" property reader
4743 # bug fix: odydata fix for files with \r\n for line ending
4744 # bug fix for PDB remediated T/DT difference of C5M/C7
4745 # bug fix: set spin X was case-selective
4746 # bug fix: echo text not re-orienting on resize of applet or application
4747 # bug fix: multiple isosurface cavities in a multimodel environment
4748 # bug fix: missing set picking ident in popup window
4749 # bug fix: popup menu set picking label not working
4765 # bug fix pmesh not working
4766 # bug fix for state after calculate surface, calculate hbonds, configuration, dynamic variable defi…
4785 # bug fix: set picking label
4786 # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation
4787 # bug fix: state for phased atomic orbitals does not preserve red/blue color
4788 # bug fix: mo opaque causing "invalid argument" when no MOs
4789 # bug fix: isosurface cavity molecular caused exception
4796 # bug fix: debugscript on;center 3-5; "-" missing
4797 # bug fix: zoomTo (5-7) read as "5 to -7"
4798 # bug fix: move with time < 0.03 seconds causes molecule to disappear
4799 # bug fix: hover interruption
4800 # bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag
4807 # bug fix for 3D text echo staying in window
4808 # bug fix for draw text+translucency
4809 # bug fix for draw text not hovering for points
4810 # bug fix for multiple draw objects in show state
4811 # bug fix for spin save reversed direction
4812 # bug fix for CdkAdapter not having auxiliaryInfo data
4825 # bug fix for Gaussian file reader fix for very large negative MO coefficients
4826 # bug fix for move not releasing isInMotion
4827 # bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t"…
4828 # bug fix for select {*}[0], {*}[-1], etc., which now counts from the end back
4836 # bug fix for gamess reader MO fix
4837 # bug fix for mopac GRAPHF file fix (resolver thought MOL)
4838 # bug fix for lcaocartoon "lp" fix for AX3E and AX2E
4844 # bug fix for compound document reader not reading enough short segment pointers
4845 # bug fix for Spartan reader not recognizing 5D orbital problem
4846 # bug fix for animation skipping frames
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)
4863 # bug fix for retaining the last-saved file type selected for Image export (app)
4864 # bug fix for "wait" not recognizing if it is just a syntax check (app)
4870 # bug fix for inability to specify fractional coordinates: adds fx, fy, fz as
4873 # bug fix for inability to use x,y,z,fx,fy,fz with cartesian points
4874 # bug fix for select BONDS ({...}) not preserved in state
4875 # bug fix for geosurface not always restored from saved state
4876 # bug fix for strandcount saved explicitly forces bioshape load
4882 # bug fix for labels mysteriously disappearing. Also probably taking up HUGE amounts of hashtable s…
4883 # bug fix for hydrogen bond calculation with incomplete nucleic acid definitions.
4884 # bug fix for "set picking draw" crashing Jmol
4885 # bug fix for strandCount not carrying over to meshRibbon
4886 # bug fix for geosurface/dots save/restore state exception
4887 # bug fix for save state using "measurements off" instead of "set measurements off"
4893 # bug fix for lack of updating of certain variable predefined expressions
4894 # bug fix for smiles nonfunctional
4896 # bug fix for load append and structure commands
4897 # bug fix for load files losing structure and cartoons
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"
4900 # bug fix for {atom expression}.ident nonfunctional
4914 # bug fix for load with explicit spacegroup not respecting normalization choice
4915 # bug fix for symop=nijk selecting base atoms when not appropriate
4916 # bug fix for select specialposition non-functional
4917 # bug fix for adding atoms but mads[] going stale
4919 # bug fix for structure loss on load append. (structure is supposed to be recalculated).
4928 # bug fix for backgroundModel and save state
4929 # bug fix for load append with spacegroups causing atoms to be repositioned
4930 # bug fix for anim playrev in loop mode causing animation to stall
4938 # bug fix for mo data misreading in smol files
4939 # bug fix for lcaoCartoon "s" giving incomplete spheres
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.
4942 # bug fix in frame range 1.0 when file 1 has only one model.
4948 # bug fix for opaque triangles missing one pixel on right side when translucent objects are present.
4949 # bug fix for label alignments sometimes not being saved properly in the state
4950 # bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now
4972 # bug fix and additional work in relation to translations
4994 # app fix for Edit...preferences not properly refreshing for axes and boundbox
5000 # fix for x = {...}.resno and {...}.groupID
5001 # fix for select resno=-1
5156 # bug fix in isosurface contour -n going WAY back to before 10.9.60
5883 # app fix for console entry messing up cursor position;
5886 # fix for "draw off" not recorded in save state
5887 # fix for within(integer,...) bug using RasMol units
5888 # fix for _modelnumber showing up as 2001