Changes between Version 24 and Version 25 of changelog


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Timestamp:
Sep 23, 2011, 11:34:08 AM (15 years ago)
Author:
goddard
Comment:

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  • changelog

    v24 v25  
    99
    1010[[TicketQuery(max=500,status=closed,resolution=fixed,order=modified,desc=1,format=table,col=id|summary|type|owner|modified)]]
    11 
    12 {{{
    13 #!html
    14 
    15 <p>
    16 The following hand maintained list of changes was discontinued in Nov 2010,
    17 replaced by the above list generated from our Trac ticket database.
    18 </p>
    19 
    20 <p>
    21 This page lists changes to Chimera that are visible to users, including the
    22 date and Chimera version when the change was checked in, and who made the
    23 change (TG = Tom Goddard, AL = Andrew Ling).
    24 
    25 <p><b>November 18, 2010</b></p>
    26 <ul type=None>
    27 <li><p>Fixed center of rotation command when only bond selected.
    28 </ul>
    29 
    30 <p><b>November 17, 2010</b></p>
    31 <ul type=None>
    32 <li><p>Added memory error check in benchmark scene drawing.
    33 </ul>
    34 
    35 <p><b>November 16, 2010</b></p>
    36 <ul type=None>
    37 <li><p>Added mean and standard deviation density calc for segmentation regions.
    38 <li><p>Allowed fractional step in volume planes.
    39 </ul>
    40 
    41 <p><b>November 15, 2010</b></p>
    42 <ul type=None>
    43 <li><p>Fixed context help crash on mac, removed menu entry.
    44 <li><p>Added warning for invalid cell angles in mrc file.
    45 </ul>
    46 
    47 <p><b>November 12, 2010</b></p>
    48 <ul type=None>
    49 <li><p>Added volume flattening divide method, applied to termite gut.
    50 </ul>
    51 
    52 <p><b>November 10, 2010</b></p>
    53 <ul type=None>
    54 <li><p>Improved attribute table and orthoslice viewing.
    55 </ul>
    56 
    57 <p><b>November 9, 2010</b></p>
    58 <ul type=None>
    59 <li><p>Worked around netcdf volume reading bug, ScientificPython.
    60 </ul>
    61 
    62 <p><b>November 5, 2010</b></p>
    63 <ul type=None>
    64 <li><p>Added segment sliceview command to make montage images.
    65 <li><p>Added resize capability to segmentation image viewer.
    66 <li><p>Fixed pick blobs error when everything is clipped.
    67 <li><p>Fixed tiling order in orthoslice script, termite gut montages.
    68 <li><p>Added fill order option to vop tile command.
    69 </ul>
    70 
    71 <p><b>November 3, 2010</b></p>
    72 <ul type=None>
    73 <li><p>Made measure contactarea ignore outline boxes.
    74 </ul>
    75 
    76 <p><b>November 2, 2010</b></p>
    77 <ul type=None>
    78 <li><p>Improved measure contact area patch smoothness.
    79 <li><p>Added new color patterns for color by direction.
    80 <li><p>Added vop tile operation to make section image montages.
    81 </ul>
    82 
    83 <p><b>November 1, 2010</b></p>
    84 <ul type=None>
    85 <li><p>Fixed error reporting to include callback info.
    86 <li><p>Added segment directioncolor command.
    87 </ul>
    88 
    89 <p><b>October 29, 2010</b></p>
    90 <ul type=None>
    91 <li><p>Added measure distance command.
    92 </ul>
    93 
    94 <p><b>October 28, 2010</b></p>
    95 <ul type=None>
    96 <li><p>Fixed segmentation attribute table error for closed segmentation.
    97 </ul>
    98 
    99 <p><b>October 27, 2010</b></p>
    100 <ul type=None>
    101 <li><p>Implemented zone command.
    102 </ul>
    103 
    104 <p><b>October 26, 2010</b></p>
    105 <ul type=None>
    106 <li><p>Made segmentation attribute table remove unused columns.
    107 </ul>
    108 
    109 <p><b>October 22, 2010</b></p>
    110 <ul type=None>
    111 <li><p>Fixed morph map hang.
    112 </ul>
    113 
    114 <p><b>October 19, 2010</b></p>
    115 <ul type=None>
    116 <li><p>Debugged and fixed ScientificPython netcdf bindings code, 64-bit Windows.
    117 </ul>
    118 
    119 <p><b>October 11, 2010</b></p>
    120 <ul type=None>
    121 <li><p>Made mouse segmentation avoid showing all watershed regions.
    122 </ul>
    123 
    124 <p><b>October 6, 2010</b></p>
    125 <ul type=None>
    126 <li><p>Added measure command contact area operation.
    127 <li><p>Made contact area account for partial triangles.
    128 </ul>
    129 
    130 <p><b>October 5, 2010</b></p>
    131 <ul type=None>
    132 <li><p>Improved error message when fetch from emdb fails.
    133 <li><p>Fixed tube and ribbon shape ignoring specfied color with follow bonds.
    134 </ul>
    135 
    136 <p><b>October 4, 2010</b></p>
    137 <ul type=None>
    138 <li><p>Fixed shape tube followbonds option, ribbon band coloring.
    139 <li><p>Fixed multiscale colors, made 64-bit same as 32-bit.
    140 </ul>
    141 
    142 <p><b>October 1, 2010</b></p>
    143 <ul type=None>
    144 <li><p>Added images to region attribute table and segmentation files.
    145 <li><p>Added error handling when map size wrong when masking to region.
    146 </ul>
    147 
    148 <p><b>September 30, 2010</b></p>
    149 <ul type=None>
    150 <li><p>Added exporting region attributes as comma separated values.
    151 <li><p>Implemented read and write of segmentation region attributes in hdf5.
    152 <li><p>Simplified region attribute filter syntax, no more function calls.
    153 </ul>
    154 
    155 <p><b>September 29, 2010</b></p>
    156 <ul type=None>
    157 <li><p>Made measure spine region attributes appear in region list.
    158 <li><p>Fixed sym command bug, two models for coord sys arg.
    159 <li><p>Added filtering to region attribute list.
    160 </ul>
    161 
    162 <p><b>September 28, 2010</b></p>
    163 <ul type=None>
    164 <li><p>Made segmentation attribute browser using sortable table.
    165 </ul>
    166 
    167 <p><b>September 27, 2010</b></p>
    168 <ul type=None>
    169 <li><p>Checked in ribbon slice and curvature code.
    170 </ul>
    171 
    172 <p><b>September 24, 2010</b></p>
    173 <ul type=None>
    174 <li><p>Updated segger in chimera, segment unbin and show all fixes.
    175 </ul>
    176 
    177 <p><b>September 23, 2010</b></p>
    178 <ul type=None>
    179 <li><p>Fixed headless chimera movie recording.
    180 </ul>
    181 
    182 <p><b>September 22, 2010</b></p>
    183 <ul type=None>
    184 <li><p>Added curvature measurement to measure spine calculation.
    185 <li><p>Implemented shape ribbon command to show bacteria center slices.
    186 </ul>
    187 
    188 <p><b>September 21, 2010</b></p>
    189 <ul type=None>
    190 <li><p>Added rectangle to shape command.
    191 <li><p>Added connection failed error message, fit pdbs from emdb web service.
    192 <li><p>Fixed byte order of machst in mrc files written by chimera.
    193 <li><p>Made mac use immediate mode surf rendering for small surface pieces.
    194 </ul>
    195 
    196 <p><b>September 17, 2010</b></p>
    197 <ul type=None>
    198 <li><p>Fixed segment unbin so it shows region surfaces.
    199 </ul>
    200 
    201 <p><b>September 15, 2010</b></p>
    202 <ul type=None>
    203 <li><p>Fixed natural spline with single point, caused fly error.
    204 <li><p>Fixed bug where mask ijk to xyz transform wrong when map closed.
    205 <li><p>Fixed fit to segments closed mol, list reg number, transpar bugs.
    206 </ul>
    207 
    208 <p><b>September 14, 2010</b></p>
    209 <ul type=None>
    210 <li><p>Fixed fit to segments save fits menu entry.
    211 </ul>
    212 
    213 <p><b>September 13, 2010</b></p>
    214 <ul type=None>
    215 <li><p>Better error message when unable to write marker file.
    216 <li><p>Fixed emdb fetch error causing hang.
    217 <li><p>Fixed volume dialog session save with 2-d image stack.
    218 <li><p>Fixed multiscale bug deleting chains.
    219 <li><p>Fixed volume tracer bug opening marker set.
    220 </ul>
    221 
    222 <p><b>August 27, 2010</b></p>
    223 <ul type=None>
    224 <li><p>Allowed multiscale model creation without multiscale dialog existing,
    225 allows nogui or headless Chimera use.
    226 <li><p>Added surfaces keyword option to sym command for multiscale surfaces.
    227 <li><p>Added biological unit button to model panel.
    228 <li><p>Made multiscale use task manager when creating copies of molecules.
    229 </ul>
    230 
    231 <p><b>August 25, 2010</b></p>
    232 <ul type=None>
    233 <li><p>Fixed eman hdf file reading, python 2.7 / idle error.
    234 </ul>
    235 
    236 <p><b>August 6, 2010</b></p>
    237 <ul type=None>
    238 <li><p>Added list of fits to fit to segments dialog.
    239 <li><p>Made volume dialog show value type in balloon when mouse over "Range"
    240 dialog label (below histogram).
    241 <li><p>Made gaussian filter use original data value type by default.  Formerly
    242 it created a map with 32-bit float.
    243 </ul>
    244 
    245 <p><b>August 4, 2010</b></p>
    246 <ul type=None>
    247 <li><p>Fixed make transparent / opaque segment map menu entries when nothing selected.
    248 </ul>
    249 
    250 <p><b>August 3, 2010</b></p>
    251 <ul type=None>
    252 <li><p>Fixed fly command quaternion rotation interpolation.  Sometimes twirled
    253 360 degrees for close orientations.
    254 <li><p>Made fly command using natural cubic spline instead of Overhauser spline
    255 for smoother paths.
    256 <li><p>Made command file error halt processing and report error in reply log.
    257 Formerly command processing continued even after an error in a script.
    258 </ul>
    259 
    260 <p><b>August 2, 2010</b></p>
    261 <ul type=None>
    262 <li><p>Fixed saving masked region with segment map dialog, bounds were wrong.
    263 <li><p>Fixed render by attribute, numpy 1.4.1 int/long type problem.
    264 <li><p>Fixed show adjacent error in segment map when some regions have no contacts.
    265 <li><p>Fixed empty segmentation menu in segment map dialog.
    266 <li><p>Fixed segment map hide menu entry not working on grouped regions.
    267 <li><p>Fixed segger color density map error, numpy int/long problem.
    268 </ul>
    269 
    270 <p><b>July 27, 2010</b></p>
    271 <ul type=None>
    272 <li><p>Fixed watershed calc error 32-bit only, numpy 1.4 type error int/long.
    273 </ul>
    274 
    275 <p><b>July 22, 2010</b></p>
    276 <ul type=None>
    277 <li><p>Added movie crossfade command.
    278 </ul>
    279 
    280 <p><b>July 19, 2010</b></p>
    281 <ul type=None>
    282 <li><p>Fixed python 2.7 msms surface error on Windows.  Method for suppressing
    283 console window for mscalc program no longer valid in python 2.7.
    284 </ul>
    285 
    286 <p><b>July 15, 2010</b></p>
    287 <ul type=None>
    288 <li><p>Made segment mouse mode accept clicks on single-plane volume.
    289 <li><p>Fixed bug in solid coloring using mask, array size mismatch.
    290 <li><p>Made group/ungroup buttons work when grouped subregions selected.
    291 </ul>
    292 
    293 <p><b>July 13, 2010</b></p>
    294 <ul type=None>
    295 <li><p>Implemented segment command unbin operation to apply a mask computed
    296 on binned volume data to produce mask for the original full size volume data.
    297 <li><p>Fixed coordset holdSteady option when jumping to a single frame.
    298 </ul>
    299 
    300 <p><b>July 9, 2010</b></p>
    301 <ul type=None>
    302 <li><p>Made segmentation not keep grid indices for each region.  This reduces
    303 memory use of the segment map tool.
    304 </ul>
    305 
    306 <p><b>July 7, 2010</b></p>
    307 <ul type=None>
    308 <li><p>Added solid style volume coloring using a segmentation to the segment
    309 map dialog (color density menu entry).  Formerly only colored volume surfaces.
    310 </ul>
    311 
    312 <p><b>July 6, 2010</b></p>
    313 <ul type=None>
    314 <li><p>Optimized measure spine command using small c++ routine, 59x faster.
    315 </ul>
    316 
    317 <p><b>July 2, 2010</b></p>
    318 <ul type=None>
    319 <li><p>Made spine diameter report orthogonal diameters at mid-point along
    320 computed spine.
    321 </ul>
    322 
    323 <p><b>July 1, 2010</b></p>
    324 <ul type=None>
    325 <li><p>Made measure spine not need segmentation map open.
    326 </ul>
    327 
    328 <p><b>June 29, 2010</b></p>
    329 <ul type=None>
    330 <li><p>Fixed two bugs in fit to segments, neg corr, molmap replace
    331 </ul>
    332 
    333 <p><b>June 25, 2010</b></p>
    334 <ul type=None>
    335 <li><p>Improved imod seg file reader error message for non-IMOD files
    336 <li><p>Made render-by-attribute dialog handle segmentation regions
    337 </ul>
    338 
    339 <p><b>June 23, 2010</b></p>
    340 <ul type=None>
    341 <li><p>Fixed solid volume memory leak, Solid.matrix held reference
    342 <li><p>Made flatten filter use 64-bit float, needed for large maps
    343 <li><p>Added measure spine command to compute bacteria paths and lengths
    344 </ul>
    345 
    346 <p><b>June 22, 2010</b></p>
    347 <ul type=None>
    348 <li><p>Made masking to regions handle full res maps with binned masks
    349 </ul>
    350 
    351 <p><b>June 21, 2010</b></p>
    352 <ul type=None>
    353 <li><p>Fixed dbpuppet ac_key_error messages, Laura Morris
    354 <li><p>Implemented natural cubic spline, smoother than Overhauser spline
    355 <li><p>Added vop unbend operation, straighten bacteria
    356 <li><p>Wrote code to trace spine of bacteria automatically
    357 </ul>
    358 
    359 <p><b>June 17, 2010</b></p>
    360 <ul type=None>
    361 <li><p>Wrote code to unbend volume along path for straightening bacteria
    362 </ul>
    363 
    364 <p><b>June 1, 2010</b></p>
    365 <ul type=None>
    366 <li><p>Made segment mouse click on background show only ungrouped regions
    367 </ul>
    368 
    369 <p><b>June 14, 2010</b></p>
    370 <ul type=None>
    371 <li><p>Fixed cocoa open dialog nsscroller mouse click crashes
    372 <li><p>Added segger to chimera distribution
    373 </ul>
    374 
    375 <p><b>June 10, 2010</b></p>
    376 <ul type=None>
    377 <li><p>Added "3d" shortcut to toggle between sequential stereo and mono
    378 </ul>
    379 
    380 <p><b>June 2, 2010</b></p>
    381 <ul type=None>
    382 <li><p>Fixed region delete bug in segment map
    383 <li><p>Added flatten operation to volume filter dialog and vop command
    384 <li><p>Improved mouse segmentation grouping to avoid start of drag abrupt group size change
    385 </ul>
    386 
    387 <p><b>June 1, 2010</b></p>
    388 <ul type=None>
    389 <li><p>Added gui for enabling segment grouping mouse mode
    390 <li><p>Added ability to read old segger 1.4 regions files
    391 </ul>
    392 
    393 <p><b>May 28, 2010</b></p>
    394 <ul type=None>
    395 <li><p>Fixed mac universal build, tcltk docs not installed for debug version
    396 <li><p>Added menu entries to show grouped and ungrouped segmentation surfaces
    397 <li><p>Improved measure and color blobs to report sizes, boundary lengths
    398 </ul>
    399 
    400 <p><b>May 27, 2010</b></p>
    401 <ul type=None>
    402 <li><p>Allowed mouse mode grouping of single regions for blocking growth
    403 <li><p>Made segment command to group regions using a second segmentation
    404 <li><p>Fixed surface model front center, not ignoring hidden surface pieces
    405 </ul>
    406 
    407 <p><b>May 26, 2010</b></p>
    408 <ul type=None>
    409 <li><p>Made segmentation mouse mode detect clicked mask region, not density
    410 <li><p>Made seg mouse mode show contacting regions after changing a region
    411 <li><p>Added boundary region selection to find unclipped bacteria
    412 </ul>
    413 
    414 <p><b>May 21, 2010</b></p>
    415 <ul type=None>
    416 <li><p>Made mac ppc install debugging tcltk to avoid start-up crash
    417 </ul>
    418 
    419 <p><b>May 19, 2010</b></p>
    420 <ul type=None>
    421 <li><p>Made linux spacenavigator not print "connect error" to shell
    422 <li><p>Made connectivity mouse mode make region groups that can be saved
    423 </ul>
    424 
    425 <p><b>May 13, 2010</b></p>
    426 <ul type=None>
    427 <li><p>Fixed tix combobox menu behind dialog on cocoa
    428 <li><p>Fixed error deleting coord sys model during move command
    429 </ul>
    430 
    431 <p><b>May 12, 2010</b></p>
    432 <ul type=None>
    433 <li><p>Made debug graphics dialog not appear for new chimera version
    434 <li><p>Separated segger into separate segmentation and fitting dialogs
    435 </ul>
    436 
    437 <p><b>May 11, 2010</b></p>
    438 <ul type=None>
    439 <li><p>Fixed cocoa inactive menus not gray, tk_setPalette cocoa tk bug
    440 </ul>
    441 
    442 <p><b>May 10, 2010</b></p>
    443 <ul type=None>
    444 <li><p>Made all chimera builds use tk 8.6
    445 <li><p>Eliminated mac carbon builds
    446 </ul>
    447 
    448 <p><b>May 5, 2010</b></p>
    449 <ul type=None>
    450 <li><p>Made segger group and ungroup buttons change smoothing levels if nothing selected
    451 <li><p>Allowed small region removal after segmenting
    452 </ul>
    453 
    454 <p><b>May 4, 2010</b></p>
    455 <ul type=None>
    456 <li><p>Added density map surface coloring by segmentation region
    457 </ul>
    458 
    459 <p><b>May 3, 2010</b></p>
    460 <ul type=None>
    461 <li><p>Worked around ctrl double click atom in graphics not showing menu, Eric
    462 </ul>
    463 
    464 <p><b>April 29, 2010</b></p>
    465 <ul type=None>
    466 <li><p>Fixed segger minimum region size option
    467 <li><p>Made changing segger "max regions to display" have immediate effect
    468 </ul>
    469 
    470 <p><b>April 28, 2010</b></p>
    471 <ul type=None>
    472 <li><p>Optimized segger segmentation speed, about 5x speed-up
    473 <li><p>Changed segger hdf5 file format for faster read and write, smaller file
    474 </ul>
    475 
    476 <p><b>April 27, 2010</b></p>
    477 <ul type=None>
    478 <li><p>Made watershed segmentation use 26 neighbors for local maxima instead of 6
    479 <li><p>Added surface granularity parameter to segger
    480 </ul>
    481 
    482 <p><b>April 23, 2010</b></p>
    483 <ul type=None>
    484 <li><p>Preserved colors when using skeletons to edit a segmentation
    485 </ul>
    486 
    487 <p><b>April 21, 2010</b></p>
    488 <ul type=None>
    489 <li><p>Made segger read and write segmentation hdf5 file format
    490 <li><p>Fixed eman hdf reader, pixel size
    491 </ul>
    492 
    493 <p><b>April 19, 2010</b></p>
    494 <ul type=None>
    495 <li><p>Eliminated intel and ppc processor-specific mac daily builds from download page
    496 </ul>
    497 
    498 <p><b>April 16, 2010</b></p>
    499 <ul type=None>
    500 <li><p>Sped up segger grouping by adding track to maximum routine to _segment module
    501 <li><p>Avoided creating segger region surfaces unless needed.
    502 </ul>
    503 
    504 <p><b>April 15, 2010</b></p>
    505 <ul type=None>
    506 <li><p>Fixed linux space nav support, libspnav.so was not distributed
    507 </ul>
    508 
    509 <p><b>April 14, 2010</b></p>
    510 <ul type=None>
    511 <li><p>Made segger use new C++ module _segment for watershed calculation eliminating need for temporary file
    512 </ul>
    513 
    514 <p><b>April 13, 2010</b></p>
    515 <ul type=None>
    516 <li><p>Made transform coordinates dialog work with non-molecules
    517 <li><p>Added skeleton routines and menu to segger
    518 </ul>
    519 
    520 <p><b>April 6, 2010</b></p>
    521 <ul type=None>
    522 <li><p>Fixed bug in volume filter casting int16 -> uint16 bug where all values became 65535
    523 <li><p>Fixed wrong normals when contouring unsigned data
    524 <li><p>Made segger filtering small regions use connected size
    525 </ul>
    526 
    527 <p><b>March 29, 2010</b></p>
    528 <ul type=None>
    529 <li><p>Fixed fetch directory preference not saving, was requiring Enter key press
    530 </ul>
    531 
    532 <p><b>March 25, 2010</b></p>
    533 <ul type=None>
    534 <li><p>Fixed bug where center-of-view rotation not updating
    535 </ul>
    536 
    537 <p><b>March 17, 2010. Version 1.5</b></p>
    538 <ul type=None>
    539 <li><p>Fixed front-center to not move center during rotation.
    540 <li><p>Made opening pdb on command-line look for compressed local files.
    541 <li><p>Made opening python scripts not clear globals when finished.
    542 <li><p>Made turn keyword center accept "view", "models", "front".
    543 <li><p>Disabled silhouette outline drawing for volumetric rendering.
    544 </ul>
    545 
    546 <p><b>March 16, 2010. Version 1.5</b></p>
    547 <ul type=None>
    548 <li><p>Worked around cocoa bug unicode arrow keys in entry fields.
    549 <li><p>Fixed saxs profile calc to work with more than one molecule.
    550 </ul>
    551 
    552 <p><b>March 15, 2010. Version 1.5</b></p>
    553 <ul type=None>
    554 <li><p>Made saxs gui give better error if local execution fails.
    555 </ul>
    556 
    557 <p><b>March 9, 2010. Version 1.5</b></p>
    558 <ul type=None>
    559 <li><p>Put max number of regions to display in segger dialog.
    560 <li><p>Fixed segger bug, grouped regions remain displayed.
    561 </ul>
    562 
    563 <p><b>March 8, 2010. Version 1.5</b></p>
    564 <ul type=None>
    565 <li><p>Fixed arrow key menu shortcuts / cursor motion bug, cocoa.
    566 </ul>
    567 
    568 <p><b>March 5, 2010. Version 1.5</b></p>
    569 <ul type=None>
    570 <li><p>Made segger not accumulate smoothing when done twice.
    571 </ul>
    572 
    573 <p><b>March 3, 2010. Version 1.5</b></p>
    574 <ul type=None>
    575 <li><p>Remade segger dialog, added progress/cancel, menu reset, options pane...
    576 <li><p>Made segger save of region and map files show a file chooser dialog.
    577 </ul>
    578 
    579 <p><b>March 2, 2010. Version 1.5</b></p>
    580 <ul type=None>
    581 <li><p>Fixed missing cocoa menu check-marks, tk patch.
    582 <li><p>Made pdb personal directories try hierarchical layout.
    583 </ul>
    584 
    585 <p><b>March 1, 2010. Version 1.5</b></p>
    586 <ul type=None>
    587 <li><p>Added tk cocoa patch to fix option-e crash.
    588 </ul>
    589 
    590 <p><b>February 23, 2010. Version 1.5</b></p>
    591 <ul type=None>
    592 <li><p>Made default movie recording use variable bit rate, q = 8.
    593 <li><p>Debugged and fixed new ffmpeg bit rate in bits/sec instead of Kbits/sec.
    594 </ul>
    595 
    596 <p><b>February 21, 2010. Version 1.5</b></p>
    597 <ul type=None>
    598 <li><p>Worked around cocoa user interface lock-out on cocoa.
    599 </ul>
    600 
    601 <p><b>February 19, 2010. Version 1.5</b></p>
    602 <ul type=None>
    603 <li><p>Made close command accept multiple models.
    604 <li><p>Fixed reset command to work with now unhashable xform objects.
    605 </ul>
    606 
    607 <p><b>February 18, 2010. Version 1.5</b></p>
    608 <ul type=None>
    609 <li><p>Made write command allow "#" preceding model number.
    610 </ul>
    611 
    612 <p><b>February 17, 2010. Version 1.5</b></p>
    613 <ul type=None>
    614 <li><p>Made segger calculate sim map automatically for groups of regions.
    615 <li><p>Made measure inertia report center of ellipsoid.
    616 </ul>
    617 
    618 <p><b>February 8, 2010. Version 1.5</b></p>
    619 <ul type=None>
    620 <li><p>Changed segger to show pastel region colors.
    621 <li><p>Fixed segger axes alignment and normal direction.
    622 </ul>
    623 
    624 <p><b>February 5, 2010. Version 1.5</b></p>
    625 <ul type=None>
    626 <li><p>Included 32-bit / 64-bit info in benchmark submissions.
    627 <li><p>Made chimera About dialog report 32-bit or 64-bit.
    628 </ul>
    629 
    630 <p><b>February 4, 2010. Version 1.5</b></p>
    631 <ul type=None>
    632 <li><p>Added ppc mac cocoa and cocoa universal daily build targets.
    633 </ul>
    634 
    635 <p><b>February 3, 2010. Version 1.5</b></p>
    636 <ul type=None>
    637 <li><p>Fixed tk cocoa open/save double click by having no default button.
    638 <li><p>Made 17 small user interface improvments to segger.
    639 </ul>
    640 
    641 <p><b>February 1, 2010. Version 1.5</b></p>
    642 <ul type=None>
    643 <li><p>Added error checking in movie record command option values.
    644 </ul>
    645 
    646 <p><b>January 29, 2010. Version 1.5</b></p>
    647 <ul type=None>
    648 <li><p>Started 64-bit mac daily builds using Tk Cocoa and NSOPENGL.
    649 </ul>
    650 
    651 <p><b>January 22, 2010. Version 1.5</b></p>
    652 <ul type=None>
    653 <li><p>Made gaussian cube file reader handle skewed data axes.
    654 </ul>
    655 
    656 <p><b>January 20, 2010. Version 1.5</b></p>
    657 <ul type=None>
    658 <li><p>Fixed movie recorder dialog bug, director not initialized.
    659 </ul>
    660 
    661 <p><b>January 19, 2010. Version 1.5</b></p>
    662 <ul type=None>
    663 <li><p>Debugged cocoa actions/color menu not showing, images freed while in use.
    664 <li><p>Fixed cocoa application menu and wrong dock icon.
    665 </ul>
    666 
    667 <p><b>January 15, 2010. Version 1.5</b></p>
    668 <ul type=None>
    669 <li><p>Debugged cocoa model panel wrapped text, patched tix.
    670 </ul>
    671 
    672 <p><b>January 13, 2010. Version 1.5</b></p>
    673 <ul type=None>
    674 <li><p>Added color images to cocoa chimera color menu.
    675 <li><p>Fixed model panel scroll down-only, reported aqua tk bug, 2931538.
    676 <li><p>Allowed raytrace and supersample movie record options to change.
    677 </ul>
    678 
    679 <p><b>January 12, 2010. Version 1.5</b></p>
    680 <ul type=None>
    681 <li><p>SAX dialog fixes, raise dialog, remember empty executable pref.
    682 </ul>
    683 
    684 <p><b>January 11, 2010. Version 1.5</b></p>
    685 <ul type=None>
    686 <li><p>Started making cocoa daily builds with Tk 8.6.
    687 </ul>
    688 
    689 <p><b>January 6, 2010. Version 1.5</b></p>
    690 <ul type=None>
    691 <li><p>Added progress/cancel to gaussian filter using new task manager.
    692 </ul>
    693 
    694 <p><b>January 5, 2010. Version 1.4.1</b></p>
    695 <ul type=None>
    696 <li><p>Made side view cap clipped surfaces button only show dialog.
    697 <li><p>Made model panel focus button enable near/far clipping.
    698 </ul>
    699 
    700 <p><b>December 21, 2009. Version 1.5</b></p>
    701 <ul type=None>
    702 <li><p>Optimized gaussian filter to use efficient fft sizes.
    703 <li><p>Made gaussian filter not-cyclic wrap, 2x speed penalty.
    704 <li><p>Made gaussian filter more memory efficient, compute one plane at a time.
    705 </ul>
    706 
    707 <p><b>December 15, 2009. Version 1.4.1</b></p>
    708 <ul type=None>
    709 <li><p>Fixed movie recorder dialog size parsing error.
    710 </ul>
    711 
    712 <p><b>December 9, 2009. Version 1.5</b></p>
    713 <ul type=None>
    714 <li><p>Fixed keyboard shortcuts dialog to list all shortcuts.
    715 <li><p>Added filter entry to keyboard shortcut dialog.
    716 </ul>
    717 
    718 <p><b>December 8, 2009. Version 1.5</b></p>
    719 <ul type=None>
    720 <li><p>Made volume session not precede relative paths with './' or '.\'.
    721 </ul>
    722 
    723 <p><b>December 4, 2009. Version 1.5</b></p>
    724 <ul type=None>
    725 <li><p>Made shape command default coordinate system use surface model.
    726 </ul>
    727 
    728 <p><b>December 3, 2009. Version 1.5</b></p>
    729 <ul type=None>
    730 <li><p>Added rotation, qrotation, name arguments to shape command.
    731 <li><p>Added ellipsoid to shape command.
    732 </ul>
    733 
    734 <p><b>November 25, 2009. Version 1.5</b></p>
    735 <ul type=None>
    736 <li><p>Removed phantom force feedback tool from distribution.
    737 </ul>
    738 
    739 <p><b>November 24, 2009. Version 1.5</b></p>
    740 <ul type=None>
    741 <li><p>Made top view mode of side view dialog always show focal plane.
    742 <li><p>Fixed focal plane behind eye black-out bug.
    743 <li><p>Added movement mouse mode to structure editing menu.
    744 </ul>
    745 
    746 <p><b>November 23, 2009. Version 1.4</b></p>
    747 <ul type=None>
    748 <li><p>Made dialog auto-placement not override session restore placement.
    749 <li><p>Made session restore not place dialogs off-screen.
    750 </ul>
    751 
    752 <p><b>November 20, 2009. Version 1.4</b></p>
    753 <ul type=None>
    754 <li><p>Fixed aqua menu response by delaying menu post by 1 msec.
    755 </ul>
    756 
    757 <p><b>November 17, 2009. Version 1.4</b></p>
    758 <ul type=None>
    759 <li><p>Fixed front-center rotation updating too often.
    760 <li><p>Fixed morph map on volume subregion.
    761 </ul>
    762 
    763 <p><b>November 8, 2009. Version 1.4 and 1.5</b></p>
    764 <ul type=None>
    765 <li><p>Added use new plot window option to saxs dialog, default false (Chimera 1.5).
    766 <li><p>Added mw molecular weight shortcut (Chimera 1.4).
    767 </ul>
    768 
    769 <p><b>November 6, 2009. Version 1.4</b></p>
    770 <ul type=None>
    771 <li><p>Fixed uninitialized memory errors, no init of surfnet grid.
    772 </ul>
    773 
    774 <p><b>November 3, 2009. Version 1.4</b></p>
    775 <ul type=None>
    776 <li><p>Added Linux space navigator support.
    777 </ul>
    778 
    779 <p><b>November 2, 2009. Version 1.4</b></p>
    780 <ul type=None>
    781 <li><p>Fixed morph map error when volume closed during playback
    782 </ul>
    783 
    784 <p><b>October 30, 2009. Version 1.5</b></p>
    785 <ul type=None>
    786 <li><p>Added fit in map correlation about zero option, the default.
    787 <li><p>Made meshmol command produce model with new id number.
    788 </ul>
    789 
    790 <p><b>October 28, 2009. Version 1.5</b></p>
    791 <ul type=None>
    792 <li><p>Added msms warning message for wrong number of atom areas.
    793 <li><p>Optimized memory use in resampling maps.
    794 </ul>
    795 
    796 <p><b>October 16, 2009. Version 1.4</b></p>
    797 <ul type=None>
    798 <li><p>Made fit map gray out optimize and whole molecule options when not avail.
    799 </ul>
    800 
    801 <p><b>October 15, 2009. Version 1.4</b></p>
    802 <ul type=None>
    803 <li><p>Removed SAXS module.
    804 <li><p>Removed volume processing standalone programs from distribution.
    805 </ul>
    806 
    807 </p>
    808 <p><b>October 8, 2009.  Version 1.4</b></p>
    809 <ul type=None>
    810 <li><p>Made match command showMatrix argument print motion from current position
    811 in addition to motion from original file coordinates.
    812 <li><p>Don't print rotation when fitting only selected atoms with
    813 Fit in Map dialog.
    814 </ul>
    815 
    816 <p><b>October 7, 2009.  Version 1.4</b></p>
    817 <ul type=None>
    818 <li><p>Added fit dialog option to optimize correlation about zero instead of correlation about mean.
    819 <li><p>Made fit dialog option to move only selected atoms instead of whole
    820 molecules.
    821 <li><p>Added undo/redo motion buttons to fit dialog.
    822 </ul>
    823 
    824 <p><b>October 6, 2009.  Version 1.4</b></p>
    825 <ul type=None>
    826 <li><p>Made session merge not savepos session-start if that position already
    827 exists.
    828 <li><p>Replaced matrixcopy relativeTo keyword with "moving" keyword.
    829 <li><p>Made set light_quality command update quality in lighting dialog.
    830 <li><p>Added check for matching grid sizes in vop morph command.
    831 <li><p>Made vop cover update rendering options of source map -- was setting
    832 those options but failed to show them.
    833 <li><p>Fixed session merging error handling of old sessions.
    834 </ul>
    835 
    836 <p><b>October 2, 2009.  Version 1.4</b></p>
    837 <ul type=None>
    838 <li><p>Added hide command-line to bottom of command history menu.
    839 <li><p>Made session merge keep old window size and camera/viewer settings.
    840 </ul>
    841 
    842 <p><b>October 1, 2009.  Version 1.4</b></p>
    843 <ul type=None>
    844 <li><p>Made vrml models not use glossy shader, avoids black vrml objects.
    845 </ul>
    846 
    847 <p><b>September 30, 2009.  Version 1.4</b></p>
    848 <ul type=None>
    849 <li><p>Fixed glossy lighting fog so alpha is not used.  Needed so that
    850 100% transparent surfaces are invisible.
    851 <li><p>Added showSlabs option to measure rotation command.
    852 <li><p>Improved file fetch error on socket errors which are not IOError.
    853 <li><p>Added relativeXform option to matrixcopy to fix misaligned sessions.
    854 <li><p>Made session merging align old and new lowest id models.
    855 </ul>
    856 
    857 <p><b>September 29, 2009.  Version 1.4</b></p>
    858 <ul type=None>
    859 <li><p>Added update keyword to sym command, default false.
    860 <li><p>Added toggle outline box shortcut "ob".
    861 </ul>
    862 
    863 <p><b>September 28, 2009.  Version 1.4</b></p>
    864 <ul type=None>
    865 <li><p>Made selection object model order follow vertex order.  Allows
    866 vop add command to get correct model order.
    867 <li><p>Fixed surface zone session restore bug with molecular surfaces.
    868 <li><p>Added minRMS option to vop subtract for subtracting fit maps.
    869 <li><p>Made vop subtract operation use interpolation like vop add.
    870 </ul>
    871 
    872 <p><b>September 25, 2009.  Version 1.4</b></p>
    873 <ul type=None>
    874 <li><p>Made vop add not extend grid due to round-off if grids are identical.
    875 <li><p>Added multipliers arg to vop add.
    876 <li><p>Made open viper:1bbt fetch from viperdb instead of pdb.
    877 </ul>
    878 
    879 <p><b>September 18, 2009.  Version 1.4</b></p>
    880 <ul type=None>
    881 <li><p>Made ~surf command close molecular surfaces with closed molecules.
    882 </ul>
    883 
    884 <p><b>September 17, 2009.  Version 1.4</b></p>
    885 <ul type=None>
    886 <li><p>Fixed fit in map, with simulated map didn't move atoms.
    887 <li><p>Made measure buriedarea report buried areas for both atom sets.
    888 </ul>
    889 
    890 <p><b>September 16, 2009.  Version 1.4</b></p>
    891 <ul type=None>
    892 <li><p>Made mz shortcut place marker at origin in selected models local coords.
    893 <li><p>Added center and axis arguments to sym command.
    894 </ul>
    895 
    896 <p><b>September 15, 2009.  Version 1.4</b></p>
    897 <ul type=None>
    898 <li><p>Added symmetry group argument to sym command.
    899 </ul>
    900 
    901 <p><b>September 14, 2009.  Version 1.4</b></p>
    902 <ul type=None>
    903 <li><p>Improved color zone out-of-memory error message.
    904 </ul>
    905 
    906 <p><b>September 11, 2009.  Version 1.4</b></p>
    907 <ul type=None>
    908 <li><p>Added move molecule mouse mode.
    909 </ul>
    910 
    911 <p><b>September 10, 2009.  Version 1.4</b></p>
    912 <ul type=None>
    913 <li><p>Implemented vop cover operation for periodic map extension.
    914 </ul>
    915 
    916 <p><b>September 9, 2009.  Version 1.4</b></p>
    917 <ul type=None>
    918 <li><p>Fixed vanishing surface cap on Windows.
    919 </ul>
    920 
    921 <p><b>September 7, 2009.  Version 1.4</b></p>
    922 <ul type=None>
    923 <li><p>Fixed pseudobondgroup bounding box calculation, wrong coordinate system.
    924 <li><p>Added playDirection, playRange and addMode options to vop morph command.
    925 <li><p>Fixed front-center, was using mid-depth even when model intercepted.
    926 <li><p>Fixed color parsing error in measure inertia.
    927 </ul>
    928 
    929 <p><b>September 4, 2009.  Version 1.4</b></p>
    930 <ul type=None>
    931 <li><p>Added vop morph command.
    932 <li><p>Added number of cells option to unit cell dialog.
    933 <li><p>Made unit cell outline button toggle outline off.
    934 </ul>
    935 
    936 <p><b>September 3, 2009.  Version 1.4</b></p>
    937 <ul type=None>
    938 <li><p>Added options panel to unit cell dialog.
    939 </ul>
    940 
    941 <p><b>September 2, 2009.  Version 1.4</b></p>
    942 <ul type=None>
    943 <li><p>Made unit cell dialog handle inverting symmetries.
    944 </ul>
    945 
    946 <p><b>August 31, 2009.  Version 1.4</b></p>
    947 <ul type=None>
    948 <li><p>Made marker note labels set using actions label menu save in sessions.
    949 <li><p>Fixed bug where deleting marker did not delete residue.
    950 <li><p>Fixed split map by color bug, numpy array in sessions.
    951 </ul>
    952 
    953 <p><b>August 25, 2009.  Version 1.4</b></p>
    954 <ul type=None>
    955 <li><p>Added command "set light_quality glossy|normal".
    956 </ul>
    957 
    958 <p><b>August 24, 2009.  Version 1.4</b></p>
    959 <ul type=None>
    960 <li><p>Made surface color dialog show offset field only for electrostatics.
    961 </ul>
    962 
    963 <p><b>August 21, 2009.  Version 1.4</b></p>
    964 <ul type=None>
    965 <li><p>Translated mesh subdivision python to c++ for faster calculation.
    966 <li><p>Made error dialog not report full traceback, just a few lines.
    967 <li><p>Fixed shape command color parsing, was generating an error.
    968 <li><p>Made surface zone and color zone save arrays as strings in session files.
    969 <li><p>Fixed shape command, was adding to existing surface when none specified.
    970 </ul>
    971 
    972 <p><b>August 20, 2009.  Version 1.4</b></p>
    973 <ul type=None>
    974 <li><p>Saved surface data as strings in sessions, smaller files and faster
    975 save and restore.
    976 </ul>
    977 
    978 <p><b>August 19, 2009.  Version 1.4</b></p>
    979 <ul type=None>
    980 <li><p>Fixed aqua double menu posting bug.
    981 <li><p>Fixed shape command model id parsing error.
    982 <li><p>Added sop surface operation command. The finerMesh operation
    983 subdivides surface meshes to have uniform edge length.
    984 <li>Added offset keyword to scolor command to allow coloring by volume data
    985 or volume gradient at a position offset from a surface along the surface
    986 normals.  The offset can be a single signed float value, or a range given by
    987 two values start, end, and an integer N (e.g. offset 0,8.5,4) specifying that
    988 N offsets should be used and the average volume value used.  This is for
    989 coloring by projecting a slab of volume data.
    990 <li><p>Made mouse rotation center allow z and xy rotation when model
    991 rotation center is far off screen.  The xy-rotation region of the window now
    992 always includes a circle centered on the window with diameter half the window
    993 size (minimum of window width and height).
    994 </ul>
    995 
    996 <p><b>August 18, 2009.  Version 1.4</b></p>
    997 <ul type=None>
    998 <li><p>Fixed error when overwriting missing volume data file.
    999 <li><p>Fixed bug where volume selection outline box used new molecule
    1000 preferences.
    1001 </ul>
    1002 
    1003 <p><b>August 17, 2009.  Version 1.4</b></p>
    1004 <ul type=None>
    1005 <li><p>Added linux space navigator support contributed by Thomas Margraf.
    1006 </ul>
    1007 
    1008 <p><b>August 14, 2009.  Version 1.4</b></p>
    1009 <ul type=None>
    1010 <li><p>Made volume data contour calculation catch memory allocation exception
    1011 so Chimera does not crash.
    1012 </ul>
    1013 
    1014 <p><b>August 12, 2009.  Version 1.4</b></p>
    1015 <ul type=None>
    1016 <li><p>Made molmap command allow specifying map subid.
    1017 </ul>
    1018 
    1019 <p><b>August 11, 2009.  Version 1.4</b></p>
    1020 <ul type=None>
    1021 <li><p>Updated saxs profile calculation user interface, no longer requires
    1022 form factor file.
    1023 </ul>
    1024 
    1025 <p><b>August 10, 2009.  Version 1.4</b></p>
    1026 <ul type=None>
    1027 <li><p>Made initial molecule display style not apply to volume tracer
    1028 marker models.
    1029 </ul>
    1030 
    1031 <p><b>August 7, 2009.  Version 1.4</b></p>
    1032 <ul type=None>
    1033 <li><p>Fixed volume eraser error caused by new volume tracer api.
    1034 <li><p>Added surface color dialog offset option for electrostatic coloring.
    1035 <li><p>Fixed tile command argument parsing error.
    1036 </ul>
    1037 
    1038 <p><b>August 5, 2009.  Version 1.4</b></p>
    1039 <ul type=None>
    1040 <li><p>Added tube display to shape command.
    1041 </ul>
    1042 
    1043 <p><b>August 4, 2009.  Version 1.4</b></p>
    1044 <ul type=None>
    1045 <li><p>Made volume tracer tubes use surface model instead of vrml.
    1046 </ul>
    1047 
    1048 <p><b>August 3, 2009.  Version 1.4</b></p>
    1049 <ul type=None>
    1050 <li><p>Fixed volume outline box to avoid coloring and capping.
    1051 <li><p>Made volume flip normals for thresholds less than 0 default off.
    1052 <li><p>Added tile command.
    1053 <li><p>Made volume save command handle multifile save with %d index.
    1054 </ul>
    1055 
    1056 <p><b>July 31, 2009.  Version 1.4</b></p>
    1057 <ul type=None>
    1058 <li><p>Fixed subsampled grid data caching, caused blank histogram display.
    1059 <li><p>Added vop boxes operation to extract subregions around markers.
    1060 </ul>
    1061 
    1062 <p><b>July 29, 2009.  Version 1.4</b></p>
    1063 <ul type=None>
    1064 <li><p>Made volume tracer work without graphical user interface.
    1065 <li><p>Added vop median and scale filter operations.
    1066 </ul>
    1067 
    1068 <p><b>July 28, 2009.  Version 1.4</b></p>
    1069 <ul type=None>
    1070 <li><p>Replaced vop and volume command use_step/use_subregion arguments with step/subregion.
    1071 <li><p>Fixed imod reader bug, error reading point size records.
    1072 </ul>
    1073 
    1074 <p><b>July 24, 2009.  Version 1.4</b></p>
    1075 <ul type=None>
    1076 <li><p>Added measure inertia command for molecules and surfaces.
    1077 </ul>
    1078 
    1079 <p><b>July 22, 2009.  Version 1.4</b></p>
    1080 <ul type=None>
    1081 <li><p>Made scale filter clamp integer values to data type limits.
    1082 <li><p>Changed frame update timers to assure minimum event processing time.  Prevents some lock-outs during continuous rendering on aqua.
    1083 <li><p>Fixed broken mask command.
    1084 <li><p>Made mask command ignore hidden parts of surface.
    1085 </ul>
    1086 
    1087 <p><b>July 21, 2009.  Version 1.4</b></p>
    1088 <ul type=None>
    1089 <li><p>Made molmap accept a # character in the modelId argument.
    1090 </ul>
    1091 
    1092 <p><b>July 20, 2009.  Version 1.4</b></p>
    1093 <ul type=None>
    1094 <li><p>Fixed binning filter step size bug.
    1095 </ul>
    1096 
    1097 <p><b>July 17, 2009.  Version 1.4</b></p>
    1098 <ul type=None>
    1099 <li><p>Changed vop syntax, operation first arg, rejects invalid keywords.
    1100 <li><p>Fixed meshmol bug, error due to obsolete volume tracer call.
    1101 </ul>
    1102 
    1103 <p><b>July 16, 2009.  Version 1.4</b></p>
    1104 <ul type=None>
    1105 <li><p>Made session saving eliminate indent on long lists, smaller file size.
    1106 <li><p>Fixed emdb fetch bug where xml and web service used when not needed.
    1107 </ul>
    1108 
    1109 <p><b>July 15, 2009.  Version 1.4</b></p>
    1110 <ul type=None>
    1111 <li><p>Fixed bug in vop permute, permutation incorrect.
    1112 </ul>
    1113 
    1114 <p><b>July 14, 2009.  Version 1.4</b></p>
    1115 <ul type=None>
    1116 <li><p>Added vop add command.
    1117 <li><p>Added useGridStep, useGridSubregion, boundingGrid vop resample options.
    1118 <li><p>Made volumes with unicode filenames open.
    1119 </ul>
    1120 
    1121 <p><b>July 13, 2009.  Version 1.4</b></p>
    1122 <ul type=None>
    1123 <li><p>Added set/reset and cumulative transform to molecule transform dialog.
    1124 <li><p>Updated to pytables 2.1.1 to allow reading Chimera map format files with unicode file names.
    1125 </ul>
    1126 
    1127 <p><b>July 10, 2009.  Version 1.4</b></p>
    1128 <ul type=None>
    1129 <li><p>Made fit in map only use displayed subregion when counting points outside contour.
    1130 </ul>
    1131 
    1132 <p><b>June 23, 2009.  Version 1.4</b></p>
    1133 <ul type=None>
    1134 <li><p>Fixed non-orthogonal rotation errors in reading profec volume maps.
    1135 <li><p>Fixed gross memory inefficiency writing map file.  Was reading a full copy of map for every plane for formats that could not read submaps.
    1136 <li><p>Made mouse rotation virtual sphere center be the model center of rotation.
    1137 </ul>
    1138 
    1139 <p><b>June 22, 2009.  Version 1.4</b></p>
    1140 <ul type=None>
    1141 <li><p>Fixed incorrect default center for scolor command.
    1142 </ul>
    1143 
    1144 <p><b>June 19, 2009.  Version 1.4</b></p>
    1145 <ul type=None>
    1146 <li><p>Fixed per-pixel surface color bugs with transparent surfaces.
    1147 <li><p>Implemented scolor command for surface color dialog functionality.
    1148 </ul>
    1149 
    1150 <p><b>June 18, 2009.  Version 1.4</b></p>
    1151 <ul type=None>
    1152 <li><p>Fixed surface transparency color hierarchy problems.
    1153 </ul>
    1154 
    1155 <p><b>June 17, 2009.  Version 1.4</b></p>
    1156 <ul type=None>
    1157 <li><p>Added frames argument to surftransparency command.
    1158 <li><p>Made surftransparency command work on non-msms surfaces.
    1159 </ul>
    1160 
    1161 <p><b>June 12, 2009.  Version 1.4</b></p>
    1162 <ul type=None>
    1163 <li><p>Fixed session save error with empty marker set.
    1164 </ul>
    1165 
    1166 <p><b>June 10, 2009.  Version 1.4</b></p>
    1167 <ul type=None>
    1168 <li><p>Added bin operation to vop command.
    1169 </ul>
    1170 
    1171 <p><b>June 9, 2009.  Version 1.4</b></p>
    1172 <ul type=None>
    1173 <li><p>Implemented volume binning filter.
    1174 <li><p>Made per-pixel surface color use colormap end values instead of black.
    1175 <li><p>Fixed per-pixel surface color lighting.
    1176 </ul>
    1177 
    1178 <p><b>June 5, 2009.  Version 1.4</b></p>
    1179 <ul type=None>
    1180 <li><p>Made pick blobs and volume tracer work with per-model clipped surfaces.
    1181 </ul>
    1182 
    1183 <p><b>June 4, 2009.  Version 1.4</b></p>
    1184 <ul type=None>
    1185 <li><p>Added volume tracer mouse mode for marker placement on surfaces.
    1186 <li><p>Put each volume tracer marker in its own residue to allow specifying
    1187 numeric ranges in commands.
    1188 </ul>
    1189 
    1190 <p><b>June 3, 2009.  Version 1.4</b></p>
    1191 <ul type=None>
    1192 <li><p>Added mask command invertMask option.
    1193 <li><p>Added caps argument to shape command for cylinder caps.
    1194 </ul>
    1195 
    1196 <p><b>June 2, 2009.  Version 1.4</b></p>
    1197 <ul type=None>
    1198 <li><p>Made copy/paste work in aqua for bug report dialog "gathered info" field.
    1199 <li><p>Fixed morph map movie record bug, backslash t in file interpreted as tab.
    1200 </ul>
    1201 
    1202 <p><b>May 29, 2009.  Version 1.4</b></p>
    1203 <ul type=None>
    1204 <li><p>Added per pixel coloring to surface color dialog using textures.
    1205 <li><p>Made surface textures support luminance and border colors.
    1206 <li><p>Updated function names for emdb web service search.
    1207 </ul>
    1208 
    1209 <p><b>May 27, 2009.  Version 1.4</b></p>
    1210 <ul type=None>
    1211 <li><p>Made transparent texture coloring of surfaces work.
    1212 <li><p>Added texture coloring to surface color dialog.
    1213 <li><p>Fixed bug where 3d texture not updated when color mode changed.
    1214 <li><p>Fixed bug where volume color mode not updated when switching between 2d and 3d solid style.
    1215 </ul>
    1216 
    1217 
    1218 <p><b>May 20, 2009.  Version 1.4</b></p>
    1219 
    1220 <ul type=None>
    1221 <li><p>Fixed space navigator lag and poor response on aqua. TG
    1222 <li><p>Fixed actions missing some models with no selection when multiscale surfaces present. TG
    1223 </ul>
    1224 
    1225 <p><b>May 19, 2009.  Version 1.4</b></p>
    1226 
    1227 <ul type=None>
    1228 <li><p>Made emdb web search show citation and map release date. TG
    1229 <li><p>Made fetch panel show search field only for searchable databases. TG
    1230 </ul>
    1231 
    1232 <p><b>May 18, 2009.  Version 1.4</b></p>
    1233 
    1234 <ul type=None>
    1235 <li><p>Made volume save command handle "~" paths. TG
    1236 </ul>
    1237 
    1238 <p><b>May 11, 2009.  Version 1.4</b></p>
    1239 
    1240 <ul type=None>
    1241 <li><p>Made reply dialog text selectable and copyable on aqua. TG
    1242 <li><p>Made ~/Desktop/xxx paths work on windows. TG
    1243 </ul>
    1244 
    1245 <p><b>May 7, 2009.  Version 1.4</b></p>
    1246 
    1247 <ul type=None>
    1248 <li><p>Made movie encoding friendly error if output directory doesn't exist. TG
    1249 </ul>
    1250 
    1251 <p><b>May 1, 2009.  Version 1.4</b></p>
    1252 
    1253 <ul type=None>
    1254 <li><p>Added tilde expansion to movie encoding output path. TG
    1255 </ul>
    1256 
    1257 <p><b>April 30, 2009.  Version 1.4</b></p>
    1258 
    1259 <ul type=None>
    1260 <li><p>Fixed demo auto-play sometimes freezing Chimera.  Aqua Tk menu callback bug. TG
    1261 </ul>
    1262 
    1263 <p><b>April 27, 2009.  Version 1.4</b></p>
    1264 
    1265 <ul type=None>
    1266 <li><p>Added silhouette, depth cue, subdivision "set" command options. TG
    1267 <li><p>Added coordset command to play trajectories, for movie scripts. TG
    1268 </ul>
    1269 
    1270 <p><b>April 24, 2009.  Version 1.4</b></p>
    1271 
    1272 <ul type=None>
    1273 <li><p>Made command-` and shift-command-` cycle aqua windows. TG
    1274 <li><p>Removed aqua focus follows mouse code and preference setting. TG
    1275 <li><p>Made emdb fetch use web service to find fit pdbs, was using xml file. TG
    1276 </ul>
    1277 
    1278 <p><b>April 20, 2009.  Version 1.4</b></p>
    1279 
    1280 <ul type=None>
    1281 <li><p>Made multiscale copy isHet to avoid water chaining. TG
    1282 </ul>
    1283 
    1284 <p><b>April 15, 2009.  Version 1.4</b></p>
    1285 
    1286 <ul type=None>
    1287 <li><p>Made mac aqua tk use click-through. TG
    1288 </ul>
    1289 
    1290 <p><b>April 9, 2009.  Version 1.4</b></p>
    1291 
    1292 <ul type=None>
    1293 <li><p>Fixed fetch dialog to hide when return key pressed in id field. TG
    1294 </ul>
    1295 
    1296 <p><b>April 7, 2009.  Version 1.4</b></p>
    1297 
    1298 <ul type=None>
    1299 <li><p>Fixed export obj bug where wrong material file path written. TG
    1300 </ul>
    1301 
    1302 <p><b>March 30, 2009.  Version 1.4</b></p>
    1303 
    1304 <ul type=None>
    1305 <li><p>Added memory error check in volume filter. TG
    1306 </ul>
    1307 
    1308 <p><b>March 25, 2009.  Version 1.4</b></p>
    1309 
    1310 <ul type=None>
    1311 <li><p>Added emdb search capability to fetch by id dialog. TG
    1312 </ul>
    1313 
    1314 <p><b>March 24, 2009.  Version 1.4</b></p>
    1315 
    1316 <ul type=None>
    1317 <li><p>Fixed bug where last used data matrix for a volume not kept in cache. TG
    1318 <li><p>Increased volume data default cache size to 512 Mb, was 32 Mb. TG
    1319 </ul>
    1320 
    1321 <p><b>March 20, 2009.  Version 1.4</b></p>
    1322 
    1323 <ul type=None>
    1324 <li><p>Added slab option to shape command. TG
    1325 <li><p>Made mcopy copy bond properties, fixed label copy. TG
    1326 </ul>
    1327 
    1328 <p><b>March 19, 2009.  Version 1.4</b></p>
    1329 
    1330 <ul type=None>
    1331 <li><p>Fixed mcopy bug, coordinate copy did not work. TG
    1332 </ul>
    1333 
    1334 <p><b>March 16, 2009.  Version 1.4</b></p>
    1335 
    1336 <ul type=None>
    1337 <li><p>Fixed bug in dock grid error message. TG
    1338 <li><p>Made clip command give user-friendly near>far error message. TG
    1339 </ul>
    1340 
    1341 <p><b>March 13, 2009.  Version 1.4</b></p>
    1342 
    1343 <ul type=None>
    1344 <li><p>Made modbase and castp fetch use downlaod directory. TG
    1345 </ul>
    1346 
    1347 <p><b>March 12, 2009.  Version 1.4</b></p>
    1348 
    1349 <ul type=None>
    1350 <li><p>Made pubchem fetch use download directory. TG
    1351 </ul>
    1352 
    1353 <p><b>March 11, 2009.  Version 1.4</b></p>
    1354 
    1355 <ul type=None>
    1356 <li><p>Fixed fly command bug where an extra frame count was used. TG
    1357 <li><p>Made color command handle r,g,b,a numeric color arguments. TG
    1358 <li><p>Added fetching emdb maps to fetch-by-id dialog. TG
    1359 <li><p>Added button to fetch by id dialog shows download directory preferences. TG
    1360 <li><p>Added cancel link in progress messages to cancel fetch operation. TG
    1361 <li>Enabled uncompressing fetched data files. TG
    1362 <li>Made bondcolor and colordef handle r,g,b,a numeric arguments. TG
    1363 </ul>
    1364 
    1365 <p><b>March 10, 2009.  Version 1.4</b></p>
    1366 
    1367 <ul type=None>
    1368 <li><p>Added mcopy command to copy molecule settings. TG
    1369 <li><p>Added fetch-by-id download directory for eds, viperdb, pqs, pdb, cif, scop, ndb. TG
    1370 </ul>
    1371 
    1372 <p><b>March 6, 2009.  Version 1.4</b></p>
    1373 
    1374 <ul type=None>
    1375 <li><p>Made all command color arguments accept tk colors, comma-separated rgba. TG
    1376 </ul>
    1377 
    1378 <p><b>March 5, 2009.  Version 1.4</b></p>
    1379 
    1380 <ul type=None>
    1381 <li><p>Made volume scale filter respond when enter key pressed. TG
    1382 </ul>
    1383 
    1384 <p><b>March 4, 2009.  Version 1.4</b></p>
    1385 
    1386 <ul type=None>
    1387 <li><p>Made measure rotation mention coordinate system in reply log output. TG
    1388 <li><p>Made measure and vop keyword abbreviations work and case insensitive. TG
    1389 <li><p>Made rotation axis color be model color. TG
    1390 <li><p>Allowed markers/links to have no color, uses molecule color. TG
    1391 <li><p>Improved per-model clipping shorcuts cc, ca and removed tc. TG
    1392 <li><p>Made scale/shift volume filter update when filter settings changed. TG
    1393 </ul>
    1394 
    1395 <p><b>February 26, 2009.  Version 1.4</b></p>
    1396 
    1397 <ul type=None>
    1398 <li><p>Fixed saving markers as xml when atoms/bonds deleted. TG
    1399 </ul>
    1400 
    1401 <p><b>February 25, 2009.  Version 1.4</b></p>
    1402 
    1403 <ul type=None>
    1404 <li><p>Added showAxis option to measure rotation command. TG
    1405 </ul>
    1406 
    1407 <p><b>February 20, 2009.  Version 1.4</b></p>
    1408 
    1409 <ul type=None>
    1410 <li><p>Fixed molmap to work with molecules with different transforms. TG
    1411 <li><p>Made stl export for 3-d printing. TG
    1412 </ul>
    1413 
    1414 <p><b>February 17, 2009.  Version 1.4</b></p>
    1415 
    1416 <ul type=None>
    1417 <li><p>Made matrixcopy handle multiple destination models. TG
    1418 <li><p>Made shape command hide some mesh edges for icosahedron and cylinder. TG
    1419 <li><p>Added lighting attributes, normals, edge mask to surface session save. TG
    1420 <li><p>Made color zone with bond zone respect half-bond coloring. TG
    1421 </ul>
    1422 
    1423 <p><b>February 13, 2009.  Version 1.4</b></p>
    1424 
    1425 <ul type=None>
    1426 <li><p>Added silhouette edge drawing for transparent models. TG
    1427 <li><p>Added one layer and all layers transparency menu entries. TG
    1428 <li><p>Fixed multiscale bug where chain associated with original molecule
    1429 deleted, and other surfaces recalculated at new resolution. TG
    1430 <li><p>Fixed bug where volume session restore tried to set solid model
    1431 orientation when that model did not exist. TG
    1432 <li><p>Fixed bug where opening solid model did not set initial camera view. TG
    1433 </ul>
    1434 
    1435 <p><b>February 11, 2009.  Version 1.4</b></p>
    1436 
    1437 <ul type=None>
    1438 <li><p>Made session save include molecular surface attributes: smoothing,
    1439 lighting on/off, two-sided lighting, dot and line widths. TG
    1440 <li><p>Added one transparent layer surface option.  Added equivalent option
    1441 to volume dialog surface and mesh panel. TG
    1442 <li><p>Added shortcuts t5 and t0 to make surfaces 50% and 0% transparent. TG
    1443 </ul>
    1444 
    1445 
    1446 <p><b>February 10, 2009.  Version 1.4</b></p>
    1447 
    1448 <ul type=None>
    1449 <li><p>Made move/turn/rock/roll move inactive models when "models"
    1450 keyword used. TG
    1451 <li><p>Made open volumes use absolute paths even if specified with relative
    1452 paths so that data can be read later if current working directory changed. TG
    1453 </ul>
    1454 
    1455 <p><b>February 9, 2009.  Version 1.4</b></p>
    1456 
    1457 <ul type=None>
    1458 <li><p>Improved rendering of multiple transparent surface models so model
    1459 behind does not appear in front. TG
    1460 </ul>
    1461 
    1462 <p><b>January 28, 2009.  Version 1.4</b></p>
    1463 
    1464 <ul type=None>
    1465 <li><p>Made multiscale contacts not select chain surfaces when atoms of
    1466 chain are selected. TG
    1467 </ul>
    1468 
    1469 <p><b>January 21, 2009.  Version 1.4</b></p>
    1470 
    1471 <ul type=None>
    1472 <li><p>Wrote fly command to smoothly interpolate positions/camera. TG
    1473 </ul>
    1474 <p><b>January 20, 2009.  Version 1.4</b></p>
    1475 
    1476 <ul type=None>
    1477 <li><p>Fixed swapped buried ses/sas area atom attributes. TG
    1478 </ul>
    1479 
    1480 <p><b>January 19, 2009.  Version 1.4</b></p>
    1481 
    1482 <ul type=None>
    1483 <li><p>Fixed reset with frame count error when model closed. TG
    1484 <li><p>Made volume surface outline box unlit when using glossy lighting. TG
    1485 <li><p>Fixed bug where hide dust turned volume square mesh into triangles. TG
    1486 </ul>
    1487 
    1488 <p><b>January 18, 2009.  Version 1.4</b></p>
    1489 
    1490 <ul type=None>
    1491 <li><p>Made hdf map read use planes along smallest chunk shape axis. TG
    1492 <li><p>Added use step/subregion/zone options to volume save command. TG
    1493 <li><p>Added scale/shift/cast operation to volume filter dialog. TG
    1494 <li><p>Added permuteaxes operation to vop command. TG
    1495 </ul>
    1496 
    1497 <p><b>January 16, 2009.  Version 1.4</b></p>
    1498 
    1499 <ul type=None>
    1500 <li><p>Fixed bug in histogram calculation that caused slightly incorrect
    1501 volume threshold. TG
    1502 y<li><p>Added buried area to measure command. TG
    1503 </ul>
    1504 
    1505 <p><b>January 15, 2009.  Version 1.4</b></p>
    1506 
    1507 <ul type=None>
    1508 <li><p>Fixed matplotlib on windows, wasn't finding tcl/tk headers. TG
    1509 <li><p>Fixed turn/roll/rock bug, inactive models moved when center specified. TG
    1510 </ul>
    1511 
    1512 <p><b>January 14, 2009.  Version 1.4</b></p>
    1513 
    1514 <ul type=None>
    1515 <li><p>Fixed shader code to not throw error on compile/link info messages. TG
    1516 <li><p>Fixed esp coloring bug, coloring method not set. TG
    1517 <li><p>Fixed bright edges from glossy lighting, had diffuse light on
    1518 both sides of surface. TG
    1519 <li><p>Made correlation matplotlib plot use tk instead of native Mac window. TG
    1520 </ul>
    1521 
    1522 <p><b>January 13, 2009.  Version 1.4</b></p>
    1523 
    1524 <ul type=None>
    1525 <li><p>Fixed bug move,turn,roll,rock coordinateSystem arg not working. TG
    1526 <li><p>Fixed disappearing light arrows in light panel. TG
    1527 <li><p>Made turn/roll/rock/move use coord system of center or axis spec. TG
    1528 </ul>
    1529 
    1530 <p><b>January 9, 2009.  Version 1.4</b></p>
    1531 
    1532 <ul type=None>
    1533 <li><p>Added matplotlib 2d plotting library to distribution, used for showing
    1534 correlation of map with rotated map. TG
    1535 </ul>
    1536 
    1537 <p><b>January 8, 2009.  Version 1.4</b></p>
    1538 
    1539 <ul type=None>
    1540 <li><p>Added correlation for rotated map positions to measure command. TG
    1541 
    1542 </ul>
    1543 
    1544 <p><b>January 7, 2009.  Version 1.4</b></p>
    1545 
    1546 <ul type=None>
    1547 <li><p>Wrote measure command to show rotation axis connecting two models. TG
    1548 <li><p>Handle new delphi map format on mac with 64 bit floats. TG
    1549 <li><p>Made turn,roll,rock,move accept 2 atom or bond spec for axis. TG
    1550 <li><p>Added surface volume and area to measure command. TG
    1551 <li><p>Added map correlation to measure command. TG
    1552 <li><p>Made glossy lighting not apply to unlit lines, caused dim molecule
    1553 wires. TG
    1554 y</ul>
    1555 
    1556 <p><b>January 6, 2009.  Version 1.4</b></p>
    1557 
    1558 <ul type=None>
    1559 <li><p>Added median filtering to filter dialog. TG
    1560 <li><p>Added clip volume (cv), clip adjust (ca), glossy lighting (gl)
    1561 shortcuts. TG
    1562 <li><p>Made clip and cap shortcut act on selected model, not show dialogs. TG
    1563 <li><p>Fixed bug where single color volume solid dimmed by factor
    1564 of red component. TG
    1565 </ul>
    1566 
    1567 <p><b>January 2, 2009.  Version 1.4</b></p>
    1568 
    1569 <ul type=None>
    1570 <li><p>Fixed bug where surface cap not updated when mask changed. TG
    1571 <li><p>Added options panel to gaussian filter dialog, including
    1572 immediate update option. TG
    1573 <li><p>Made filter dialog adjust thresholds for constant volume
    1574 use the enclosed volume for the gaussian filtered volume rather than
    1575 the original volume. TG
    1576 <li><p>Made Filter button just update existing volume
    1577 if active volume is a gaussian filtered volume. TG
    1578 </ul>
    1579 
    1580 <p><b>December 30, 2008.  Version 1.4</b></p>
    1581 
    1582 <ul type=None>
    1583 <li><p>Moved per-pixel lighting option from effects panel to lighting panel. TG
    1584 <li><p>Fixed mac x11 start error when glossy lighting preference not supported. TG
    1585 <li><p>Fixed bug where glossy mode sometimes had no effect because
    1586 graphics context was not current when setting shader. TG
    1587 </ul>
    1588 
    1589 <p><b>December 29, 2008.  Version 1.4</b></p>
    1590 
    1591 <ul type=None>
    1592 <li><p>Allowed depth cue start >= 1 for back lighting effect. TG
    1593 <li><p>Made surface cap use only visible parts of surfaces, helps castp. TG
    1594 </ul>
    1595 
    1596 <p><b>December 19, 2008.  Version 1.4</b></p>
    1597 
    1598 <ul type=None>
    1599 <li><p>Added "glossy" lighting mode using an opengl shader providing
    1600 per-pixel lighting and angle-dependent transparency. TG
    1601 </ul>
    1602 
    1603 <p><b>December 18, 2008.  Version 1.4</b></p>
    1604 
    1605 <ul type=None>
    1606 <li><p>Replace depth cue yon intensity parameter with end depth. TG
    1607 </ul>
    1608 
    1609 <p><b>December 16, 2008.  Version 1.4</b></p>
    1610 
    1611 <ul type=None>
    1612 <li><p>Added slider to control width of gaussian filter. TG
    1613 </ul>
    1614 
    1615 <p><b>December 10, 2008.  Version 1.4</b></p>
    1616 
    1617 <ul type=None>
    1618 <li><p>Added hide dust tool that hides small connected surface blobs. TG
    1619 <li><p>Increased surface cap default offset 0.001 to 0.01 to avoid disappearing
    1620 caps. TG
    1621 <li><p>Made sum of gaussians routine (used by molmap) able to take
    1622 different standard deviations along 3 axes for PALM/STORM microscopy data. TG
    1623 </ul>
    1624 
    1625 <p><b>December 9, 2008.  Version 1.4</b></p>
    1626 
    1627 <ul type=None>
    1628 <li><p>Disabled used of Chimera user interface while volume data load is loaded,
    1629 allowing only cancel of data load. TG
    1630 <li><p>Moved volume auto display subregion option from data display panel to
    1631 subregion selection panel. TG
    1632 <li><p>Allowed volume auto-cropping (resampling) with rotated subregion box.
    1633 With solid style rendering this does a good job of showing slices that are not
    1634 parallel to the volume box faces. TG
    1635 </ul>
    1636 
    1637 <p><b>December 8, 2008.  Version 1.4</b></p>
    1638 
    1639 <ul type=None>
    1640 <li><p>Fixed subregion resampling box when source map has local rotation. TG
    1641 <li><p>Debugged blank volume histogram when session restored,
    1642 cache size not set before volume dialog created. TG
    1643 </ul>
    1644 
    1645 <p><b>December 5, 2008.  Version 1.4</b></p>
    1646 
    1647 <ul type=None>
    1648 <li><p>Added session saving for icosahedron tool. TG
    1649 </ul>
    1650 
    1651 <p><b>December 3, 2008.  Version 1.4</b></p>
    1652 
    1653 <ul type=None>
    1654 <li><p>Provide user-friendly error message when molecular surface calculation
    1655 produces truncated output. TG
    1656 <li><p>Suppress Mac 10.5 crash report dialog when molecular surface calculation
    1657 fails. TG
    1658 </ul>
    1659 
    1660 <p><b>November 25, 2008.  Version 1.4</b></p>
    1661 
    1662 <ul type=None>
    1663 <li><p>Made move selection mouse mode able to move surface pieces. TG
    1664 </ul>
    1665 
    1666 <p><b>November 21, 2008.  Version 1.2577.</b></p>
    1667 
    1668 <ul type=None>
    1669 <li><p>Made initial volume viewer thresholds symmetric about 0 for
    1670 electrostatic potential data and other polar data. TG
    1671 <li><p>Added gaussian and laplacian filters to vop command. TG
    1672 </ul>
    1673 
    1674 <p><b>November 20, 2008.  Version 1.2576.</b></p>
    1675 
    1676 <ul type=None>
    1677 <li><p>Made per-model clipping work with solid volume rendering where
    1678 projection mode is perpendicular to view (uses 3d textures).
    1679 </ul>
    1680 
    1681 <p><b>November 19, 2008.  Version 1.2576.</b></p>
    1682 
    1683 <ul type=None>
    1684 <li><p>Fixed error reading mrc file > 2 Gbytes. TG
    1685 </ul>
    1686 
    1687 <p><b>November 18, 2008.  Version 1.2575.</b></p>
    1688 
    1689 <ul type=None>
    1690 <li><p>Fixed hkcage command error when invoked second time with surface
    1691 capping enabled. TG
    1692 <li><p>Added planes keyword to volume command to show sequence of planes. TG
    1693 <li><p>Made turn, move, ... not raise error if model deleted during motion. TG
    1694 <li><p>Added volume outline box linewidth setting. TG
    1695 <li><p>Fixed reset command to preserve relative orientations. TG
    1696 </ul>
    1697 
    1698 <p><b>November 17, 2008.  Version 1.2575.</b></p>
    1699 
    1700 <ul type=None>
    1701 <li><p>Fixed bug that caused extra frames during movie capture scripts
    1702 that read volume data, caused by progress messages. TG
    1703 <li><p>Made movie encode command print status messages on main status line. TG
    1704 </ul>
    1705 
    1706 <p><b>November 14, 2008.  Version 1.2575.</b></p>
    1707 
    1708 <ul type=None>
    1709 <li><p>Fixed incorrect center of rotation when a model is closed where another
    1710 model has the same id. TG
    1711 <li><p>Made actions / focus with nothing selected turn of near/far clipping. TG
    1712 </ul>
    1713 
    1714 <p><b>November 13, 2008.  Version 1.2574.</b></p>
    1715 
    1716 <ul type=None>
    1717 <li><p>Suppress Mac 10.5 crash report dialog when molecular surface
    1718 calculation mscalc program crashes. TG
    1719 <li><p>Fixed volume command bug setting color of solid rendering. TG
    1720 </ul>
    1721 
    1722 <p><b>November 12, 2008.  Version 1.2574.</b></p>
    1723 
    1724 <ul type=None>
    1725 <li><p>Fixed bugs writing image stacks as single hdf (*.cmap) files. TG
    1726 </ul>
    1727 
    1728 <p><b>November 11, 2008.  Version 1.2574.</b></p>
    1729 
    1730 <ul type=None>
    1731 <li><p>Made molecule bounds include atom radii to avoid clipping atom spheres
    1732 when near/far clipping is turned off. TG
    1733 
    1734 <li><p>Fixed error closing volumes when new session opened. TG
    1735 <li><p>Fixed bug where distant opaque solid volume models appeared in front of
    1736 closer opaque soild volume models. TG
    1737 <li><p>Fixed bug where restored traced surface not saved in subsequent sessions.
    1738 TG
    1739 </ul>
    1740 
    1741 <p><b>November 10, 2008.  Version 1.2574.</b></p>
    1742 
    1743 <ul type=None>
    1744 <li><p>Added warning when restoring a session file written by a newer chimera
    1745 version. TG
    1746 <li><p>Fixed bug restoring volume / surface coloring from session files written
    1747 by Chimera version more than 1 year old. TG
    1748 </ul>
    1749 
    1750 <p><b>November 6, 2008.  Version 1.2573.</b></p>
    1751 
    1752 <ul type=None>
    1753 
    1754 <li><p>Fixed volume eraser bug introduce Sept 30. TG
    1755 </ul>
    1756 
    1757 <p><b>November 4, 2008.  Version 1.2573.</b></p>
    1758 
    1759 <ul type=None>
    1760 <li><p>Made surface capping on by default. TG
    1761 <li><p>Made space navigator preserve front-center rotation point during
    1762 rotation. TG
    1763 </ul>
    1764 
    1765 <p><b>November 3, 2008.  Version 1.2573.</b></p>
    1766 
    1767 <ul type=None>
    1768 <li><p>Made near/far clip planes off by default. TG
    1769 </ul>
    1770 
    1771 <p><b>October 31, 2008.  Version 1.2572.</b></p>
    1772 
    1773 <ul type=None>
    1774 <li><p>Made surface bounds calculation use bounding sphere instead of box
    1775 resulting in tighter bounds for sphere-like surfaces. Effects amount of camera
    1776 zoom when the first model show is a surface. TG
    1777 </ul>
    1778 
    1779 <p><b>October 29, 2008.  Version 1.2572.</b></p>
    1780 
    1781 <ul type=None>
    1782 <li><p>Changed default surface transparency blend model to dim (alpha,1-alpha).
    1783 TG
    1784 <li><p>Added center of rotation mode name options "fixed", "front", "models",
    1785 and "independent" to cofr command. TG
    1786 <li><p>Made coordinateSystem arguments to movement commands work without '#'. TG
    1787 </ul>
    1788 
    1789 <p><b>October 28, 2008.  Version 1.2571.</b></p>
    1790 
    1791 <ul type=None>
    1792 <li><p>Fixed failure to hide clicked triangle using pick blobs tool. TG
    1793 <li><p>Cleared surface visibility/color atom attributes when surface closed. TG
    1794 </ul>
    1795 
    1796 <p><b>October 27, 2008.  Version 1.2571.</b></p>
    1797 
    1798 <ul type=None>
    1799 <li><p>Fixed bug where hiding a molecular surface piece made subsequent surface
    1800 show not work. TG
    1801 </ul>
    1802 
    1803 <p><b>October 24, 2008.  Version 1.2571.</b></p>
    1804 
    1805 <ul type=None>
    1806 <li><p>Changed the default center of rotation mode to front-center. TG
    1807 <li><p>Fixed multiscale session save error that happened after chain deleted. TG
    1808 </ul>
    1809 
    1810 <p><b>October 22, 2008.  Version 1.2569.</b></p>
    1811 
    1812 <ul type=None>
    1813 <li><p>Added front-center center of rotation mode. TG
    1814 <li><p>Added coordinate system, center, models arguments to turn, roll, rock,
    1815          and move commands. TG
    1816 <li><p>Made benchmark dialog show warning if models are open. TG
    1817 <li><p>Allowed move command to move along all 3 axes at once. TG
    1818 <li><p>Made cofr command accept point coordinates and coord sys arguments. TG
    1819 <li><p>Added center, coord system, model id args to shape command. TG
    1820 </ul>
    1821 
    1822 <p><b>October 20, 2008.  Version 1.2567.</b></p>
    1823 
    1824 <ul type=None>
    1825 <li><p>Made options panel for morph map and added roundtrip option. TG
    1826 </ul>
    1827 
    1828 <p><b>October 15, 2008.  Version 1.2566.</b></p>
    1829 
    1830 <ul type=None>
    1831 <li><p>Fixed actions menu entries focus, set pivot, surface
    1832 hide/show/repr/tranparency and color when a molecular surface is selected
    1833 but not its atoms. TG
    1834 </ul>
    1835 
    1836 <p><b>October 14, 2008.  Version 1.2566.</b></p>
    1837 
    1838 <ul type=None>
    1839 <li><p>Made focus command and action use center-of-models when nothing selected.
    1840 TG
    1841 <li><p>Fixed session saving error after closing traced surface model. TG
    1842 </ul>
    1843 
    1844 <p><b>October 10, 2008.  Version 1.2566.</b></p>
    1845 
    1846 <ul type=None>
    1847 <li><p>Fixed model panel configure dialog bug, pmw tabs not raising in
    1848 Mac Aqua Chimera. TG
    1849 </ul>
    1850 
    1851 <p><b>October 1, 2008.  Version 1.2561.</b></p>
    1852 
    1853 <ul type=None>
    1854 
    1855 <li><p>Made molecular surface show "all components" false in selection
    1856 inspector if all-component calculation failed and instead used single-component.
    1857 TG
    1858 <li><p>Fixed volume show/hide icon update error on model close. TG
    1859 </ul>
    1860 
    1861 <p><b>September 29, 2008.  Version 1.2561.</b></p>
    1862 
    1863 <ul type=None>
    1864 <li><p>Added memory checking to c++ python array allocation used in volume
    1865 and surface calculations. TG
    1866 </ul>
    1867 
    1868 <p><b>September 25, 2008.  Version 1.2561.</b></p>
    1869 
    1870 <ul type=None>
    1871 <li><p>Added ls keyboard shortcut to open last session file. TG
    1872 </ul>
    1873 
    1874 <p><b>September 23, 2008.  Version 1.2560.</b></p>
    1875 
    1876 <ul type=None>
    1877 <li><p>Fixed volume solid color mode and projection mode bugs. TG
    1878 </ul>
    1879 
    1880 <p><b>September 19, 2008.  Version 1.2559.</b></p>
    1881 
    1882 <ul type=None>
    1883 <li><p>Added out-of-memory test for large surfaces. TG
    1884 <li><p>Turn off mesh lighting for single plane volume display. TG
    1885 <li><p>Made volume planes switch to solid style only when "one" button pressed.
    1886 TG
    1887 <li><p>Made single plane volume contour surface without capping render with
    1888 mesh to show 2d contours. TG
    1889 </ul>
    1890 
    1891 <p><b>September 12, 2008.  Version 1.2558.</b></p>
    1892 
    1893 <ul type=None>
    1894 <li><p>Added fourier transform to vop command, removed fourier transform
    1895 menu entry. TG
    1896 </ul>
    1897 
    1898 <p><b>September 11, 2008.  Version 1.2558.</b></p>
    1899 
    1900 <ul type=None>
    1901 <li><p>Made volume square mesh option show box cap diagonals.
    1902 The square mesh code that excluded box cap diagonals also excluded all
    1903 contours for single data planes. TG
    1904 <li><p>Added volume planes cycle option with plane count and speed control.
    1905 Replaces "play" button. TG
    1906 <li><p>Added button to volume planes panel to preload data. Allows faster
    1907 moving through planes. TG
    1908 </ul>
    1909 
    1910 <p><b>September 10, 2008.  Version 1.2558.</b></p>
    1911 
    1912 <ul type=None>
    1913 <li><p>Fixed volume tracer bug where first marker on empty space mispositioned
    1914 if no models are opened. TG
    1915 </ul>
    1916 
    1917 <p><b>September 9, 2008.  Version 1.2558.</b></p>
    1918 
    1919 <ul type=None>
    1920 <li><p>Changed volume dialog origin field to show index of xyz origin instead
    1921 of xyz coordinates of index 0,0,0. Allows changing voxel size without altering
    1922 xyz origin position within array. TG
    1923 <li><p>Added originIndex keyword to volume command for specifying the xyz origin
    1924 in grid index units.  Changing voxelSize with volume command now preserves
    1925 index of xyz 0,0,0 rather than xyz of index 0,0,0. TG
    1926 <li><p>Added single volume plane surface and mesh display.  Allows drawing
    1927 2d contour lines.  Formerly surface and mesh style volume display showed
    1928 nothing for single planes. TG
    1929 </ul>
    1930 
    1931 <p><b>September 8, 2008.  Version 1.2557.</b></p>
    1932 
    1933 <ul type=None>
    1934 <li><p>Made solid volume rendering status messages about color appear
    1935 only once per frame. Were showing for every data plane. TG
    1936 <li><p>Fixed erratic incorrect use of x or y projection axes in solid
    1937 rendering. TG
    1938 <li><p>Fixed netcdf out of memory error message. TG
    1939 <li><p>Fixed bugs where volume dialog did not update display style and
    1940 hide/show icon when solid style hidden (and hence solid model closed). TG
    1941 </ul>
    1942 
    1943 <p><b>September 5, 2008.  Version 1.2557.</b></p>
    1944 
    1945 <ul type=None>
    1946 <li><p>Added luminance color for volume rendering so single color modes need
    1947 not display white. TG
    1948 <li><p>Added auto projection mode that chooses 2d z planes rendering volume
    1949 slabs with aspect 4:1 or greater, otherwise xyz planes (using more memory). TG
    1950 </ul>
    1951 
    1952 <p><b>September 3, 2008.  Version 1.2554.</b></p>
    1953 
    1954 <ul type=None>
    1955 <li><p>Removed colormap mode from solid style volume rendering. TG
    1956 </ul>
    1957 
    1958 <p><b>September 2, 2008.  Version 1.2554.</b></p>
    1959 
    1960 <ul type=None>
    1961 <li><p>Changed electrostatic surface coloring to be opaque red/white/blue. TG
    1962 </ul>
    1963 
    1964 <p><b>August 29, 2008.  Version 1.2554.</b></p>
    1965 
    1966 <ul type=None>
    1967 <li><p>Added volume projection mode option for tomogram viewing using solid
    1968 style.  Allows only showing z planes.  3x less memory use versus xyz mode
    1969 where planes most parallel to screen used. More memory efficient. TG
    1970 
    1971 <li><p>Change volume solid style rendering to not make full 3-d temporary color
    1972 array. Instead computes only 2-d color planes at a time.  Reduces memory use. TG
    1973 </ul>
    1974 
    1975 <p><b>August 28, 2008.  Version 1.2554.</b></p>
    1976 
    1977 <ul type=None>
    1978 <li><p>Added support for volume color pixel formats (opengl texture
    1979 format): RGB, luminance/alpha, luminance, 4,8,12 or 16-bit.  Formerly
    1980 only RGBA 8-bit used.  More memory efficient, faster transfer to
    1981 graphics card, allows display of larger maps.
    1982 </ul>
    1983 
    1984 <p><b>August 27, 2008.  Version 1.2554.</b></p>
    1985 
    1986 <ul type=None>
    1987 <li><p>Fixed color zone session restore bug on msms surfaces. TG
    1988 </ul>
    1989 
    1990 <p><b>August 26, 2008.  Version 1.2553.</b></p>
    1991 
    1992 <ul type=None>
    1993 <li><p>Updated surface model programmer's guide documentation. TG
    1994 <li><p>Made morph map not report error on reset/cancel movie recording. TG
    1995 </ul>
    1996 
    1997 <p><b>August 25, 2008.  Version 1.2552.</b></p>
    1998 
    1999 <ul type=None>
    2000 <li><p>Sped up volume plane display solid rendering 2x by reusing color array. TG
    2001 </ul>
    2002 
    2003 <p><b>August 22, 2008.  Version 1.2552.</b></p>
    2004 
    2005 <ul type=None>
    2006 <li><p>Delayed volume dialog histogram and range updates to speed up
    2007 cycling through volume planes. TG
    2008 <li>Optimized speed of volume plane display. TG
    2009 </ul>
    2010 
    2011 <p><b>August 21, 2008.  Version 1.2552.</b></p>
    2012 
    2013 <ul type=None>
    2014 <li><p>Added Chimera video documentation to web site. AL
    2015 <li><p>Changed implementation of solid style volume rendering with
    2016 colormaps to not use opengl pixel transfer. Avoids graphics driver
    2017 bug on GeForce 7300 Mac graphics. TG
    2018 <li><p>Made solid volume colormap use 8-bit color values instead of float,
    2019 more memory efficient. TG
    2020 </ul>
    2021 
    2022 <p><b>August 20, 2008.  Version 1.2552.</b></p>
    2023 
    2024 <ul type=None>
    2025 <li><p>Made imod file reader to correctly handle open vs closed contours. TG
    2026 <li><p>Added support uint8 rgba color values in solid rendering, more
    2027 memory efficient. TG
    2028 </ul>
    2029 
    2030 <p><b>August 19, 2008.  Version 1.2552.</b></p>
    2031 
    2032 <ul type=None>
    2033 <li><p>Removed broken spotlight help/search menu entry on aqua mac 10.5. TG
    2034 <li><p>Fixed color_by_volume() routine used in scripts. TG
    2035 </ul>
    2036 
    2037 <p><b>August 15, 2008.  Version 1.2550.</b></p>
    2038 
    2039 <ul type=None>
    2040 <li><p>Added 8-bit color indices for solid volume rendering, more
    2041 memory efficient.  Formerly only 16-bit indices used. TG
    2042 </ul>
    2043 
    2044 <p><b>August 14, 2008.  Version 1.2550.</b></p>
    2045 
    2046 <ul type=None>
    2047 <li><p>Made surface color tool ignore volume outline boxes. TG
    2048 </ul>
    2049 
    2050 <p><b>August 13, 2008.  Version 1.2550.</b></p>
    2051 
    2052 <ul type=None>
    2053 <li><p>Making imod file reader properly skip unused records. TG
    2054 <li><p>Updated tomoplane extension to new surface model api. TG
    2055 
    2056 </ul>
    2057 
    2058 <p><b>August 12, 2008.  Version 1.2549.</b></p>
    2059 
    2060 <ul type=None>
    2061 <li><p>Fixed bug where closing volume series removed wrong entry from menu. TG
    2062 </ul>
    2063 
    2064 <p><b>August 1, 2008.  Version 1.2549.</b></p>
    2065 
    2066 <ul type=None>
    2067 <li><p>Fixed black covering status line on aqua when graphics window
    2068 resized smaller. TG
    2069 </ul>
    2070 
    2071 <p><b>July 31, 2008.  Version 1.2548.</b></p>
    2072 
    2073 <ul type=None>
    2074 <li><p>Added focus follows mouse preference, only shown and used on aqua. TG
    2075 </ul>
    2076 
    2077 <p><b>July 30, 2008.  Version 1.2547.</b></p>
    2078 
    2079 <ul type=None>
    2080 <li><p>Fixed pif map bug where integer file values scaled by floating point
    2081 scale factor remained as an integer map.  Caused sparse histograms. TG
    2082 <li><p>Made volume cap facing initially off for PIF maps since they are
    2083 most often inverted. TG
    2084 <li><p>Made marker resize mouse mode use caps lock instead of alt key. TG
    2085 <li><p>Added option to hide in-window menus on aqua. TG
    2086 </ul>
    2087 
    2088 
    2089 <p><b>July 29, 2008.  Version 1.2546.</b></p>
    2090 
    2091 <ul type=None>
    2092 <li><p>Moved create color key button to options panel. TG
    2093 </ul>
    2094 
    2095 
    2096 <p><b>July 28, 2008.  Version 1.2546.</b></p>
    2097 
    2098 <ul type=None>
    2099 <li><p>Put new movie making tutorial on chimera tutorials and
    2100 animations web pages. TG
    2101 </ul>
    2102 
    2103 <p><b>July 23, 2008.  Version 1.2544.</b></p>
    2104 
    2105 <ul type=None>
    2106 
    2107 <li><p>Made volume series update histograms for all series.  Was only updating
    2108 one when multiple series played simultaneosly. TG
    2109 <li><p>
    2110 </ul>
    2111 
    2112 <p><b>July 22, 2008.  Version 1.2544.</b></p>
    2113 
    2114 <ul type=None>
    2115 <li><p>Made volume series tool handle multiwavelength priism data. TG
    2116 <li><p>Made volume series tool allow playing all series at once. TG
    2117 <li><p>Fixed memory leak when volumes created and closed. Data array
    2118 was deallocated but not surface model and volume python object. TG
    2119 <li><p>Added showDialog option to molmap command to suppress display of
    2120 volume dialog (useful in MD trajectory per-frame scripts). TG
    2121 <li><p>Made fetch eds able to set model id on command-line. TG
    2122 </ul>
    2123 
    2124 <p><b>July 21, 2008.  Version 1.2544.</b></p>
    2125 
    2126 <ul type=None>
    2127 <li><p>Fixed bug when volume data read canceled on opening,
    2128 session save failed. TG
    2129 </ul>
    2130 
    2131 <p><b>July 18, 2008.  Version 1.2544.</b></p>
    2132 
    2133 <ul type=None>
    2134 <li><p>Made volume series tool copy changes in voxel size and volume origin. TG
    2135 <li><p>Fixed bug saving volume over original file on a different file system
    2136 than /tmp (file move didn't work). TG
    2137 <li><p>Fixed bug where msms calculation says it succeeded but actually returns
    2138 an incorrect empty surface. TG
    2139 <li><p>Fixed movie recorder ffmpeg encoding on aqua, trouble reporting status
    2140 from non-gui thread.  Disabled status reporting on aqua. TG
    2141 <li><p>Made movie recorder not raise main window when doing image capture. TG
    2142 </ul>
    2143 
    2144 <p><b>July 15, 2008.  Version 1.2542.</b></p>
    2145 
    2146 <ul type=None>
    2147 <li><p>Fixed bug, surface color wrong if volume moved while data is being
    2148 read. TG
    2149 <li><p>Fixed space navigator lag on aqua. TG
    2150 </ul>
    2151 
    2152 <p><b>July 9, 2008.  Version 1.2540.</b></p>
    2153 
    2154 <ul type=None>
    2155 <li><p>Production release Chimera 1.2540.
    2156 </ul>
    2157 
    2158 <p><b>July 8, 2008.  Version 1.2540.</b></p>
    2159 
    2160 <ul type=None>
    2161 
    2162 <li><p>Fixed bug where NaN volume normals caused raytracing failure. TG
    2163 </ul>
    2164 
    2165 <p><b>July 7, 2008.  Version 1.2540.</b></p>
    2166 
    2167 <ul type=None>
    2168 <li><p>Made vop resample command undisplay original instead of
    2169 grid volume. TG
    2170 <li><p>Fixed volume dialog shown/hidden indicator updating for new volumes. TG
    2171 <li><p>Made crash report dialog on mac not appear for
    2172 mscalc crashes (msms surface calculation). TG
    2173 </ul>
    2174 
    2175 <p><b>July 2, 2008.  Version 1.2540.</b></p>
    2176 
    2177 <ul type=None>
    2178 <li><p>Fixed aqua bug: patched pmw to make open dialog history popup menus
    2179 appear on top. TG
    2180 
    2181 </ul>
    2182 
    2183 <p><b>July 1, 2008.  Version 1.2537.</b></p>
    2184 
    2185 <ul type=None>
    2186 <li><p>Made volume solid style coloring properly color min/max data values. In
    2187 some cases the data values corresponding to the end nodes on the volume
    2188 histogram were not colored. TG
    2189 <li><p>Fixed molecule copies behavior of crystal contacts tool
    2190 and added command version. TG
    2191 </ul>
    2192 
    2193 <p><b>June 30, 2008.  Version 1.2537.</b></p>
    2194 
    2195 <ul type=None>
    2196 <li><p>Optimized morph map, 8x faster linear combination on 256^3 array. TG
    2197 <li><p>Made vop resample command use better name for new volume. TG
    2198 <li><p>Fixed aqua bug: patched pmw notebook bubble buttons and borders for
    2199 aqua tk 8.5.2. TG
    2200 
    2201 </ul>
    2202 
    2203 <p><b>June 27, 2008.  Version 1.2537.</b></p>
    2204 
    2205 <ul type=None>
    2206 <li><p>Fixed aqua bug: clipped volume plane button text and feature buttons. TG
    2207 <li><p>Fixed volume show/hide icon in volume dialog in solid mode. Sometimes
    2208 showed incorrect display state. TG
    2209 </ul>
    2210 
    2211 <p><b>June 26, 2008.  Version 1.2537.</b></p>
    2212 
    2213 <ul type=None>
    2214 <li><p>Added mS shortcut to place markers on selected atoms. TG
    2215 </ul>
    2216 
    2217 <p><b>June 25, 2008.  Version 1.2537.</b></p>
    2218 
    2219 <ul type=None>
    2220 <li><p>Added aqua in-window menubars for all dialogs: castp,
    2221 selection workbench, modbase, rotamers, render by attr, viewdock, demo, movie,
    2222 multalign. TG
    2223 </ul>
    2224 
    2225 <p><b>June 24, 2008.  Version 1.2535.</b></p>
    2226 
    2227 <ul type=None>
    2228 <li><p>Fixed aqua bug: disappearing bonds (stick style) and vrml cylinders
    2229 when zooming. TG
    2230 <li><p>Fixed aqua bug: playing morph map gave volume dialog focus
    2231 prevented stopping morph playback. TG
    2232 <li><p>Fixed aqua bug: mouse scroll wheel zooming very insensitive. TG
    2233 </ul>
    2234 
    2235 <p><b>June 19, 2008.  Version 1.2534.</b></p>
    2236 
    2237 <ul type=None>
    2238 <li><p>Fixed volume dialog surface brightness and transparency sliders.
    2239 They were producing color component values > 1 causing error messages. TG
    2240 <li><p>Made command-q and the main window close button show the quit
    2241 confirmation dialog on aqua. TG
    2242 </ul>
    2243 
    2244 <p><b>June 18, 2008.  Version 1.2532.</b></p>
    2245 
    2246 <ul type=None>
    2247 <li><p>Added in-window menu bars to volume and tracer dialog windows in aqua. TG
    2248 <li><p>Added vop subtract operation for making difference maps. TG
    2249 <li><p>Fixed volume histogram flickering on aqua. TG
    2250 </ul>
    2251 
    2252 <p><b>June 17, 2008.  Version 1.2531.</b></p>
    2253 
    2254 <ul type=None>
    2255 <li><p>Fixed divide by zero warning message appearing in shell when
    2256 using volume solid style rendering with opacity = 1. TG
    2257 </ul>
    2258 
    2259 <p><b>June 16, 2008.  Version 1.2531.</b></p>
    2260 
    2261 <ul type=None>
    2262 <li><p>Fixed error when deleting volumes caused by trying to update
    2263 volume shown indicator (dash icon) after deletion. TG
    2264 <li><p>Added option/command key 3-button mouse emulation in aqua. TG
    2265 </ul>
    2266 
    2267 <p><b>June 13, 2008.  Version 1.2531.</b></p>
    2268 
    2269 <ul type=None>
    2270 
    2271 <li><p>Added MacMolPlt/Gamess quantum orbitals volume file reader. TG
    2272 </ul>
    2273 
    2274 <p><b>June 12, 2008.  Version 1.2531.</b></p>
    2275 
    2276 <ul type=None>
    2277 <li><p>Made volume viewer and volume tracer show menu bar at top of screen
    2278 on aqua. TG
    2279 </ul>
    2280 
    2281 <p><b>June 11, 2008.  Version 1.2529.</b></p>
    2282 
    2283 <ul type=None>
    2284 <li><p>Fixed display of headings in preferences tools pane on aqua. TG
    2285 <li><p>Added focus follow mouse mode for aqua. TG
    2286 </ul>
    2287 
    2288 <p><b>June 10, 2008.  Version 1.2527.</b></p>
    2289 
    2290 <ul type=None>
    2291 <li><p>Made opening electrostatic potential file formats (delphi, apbs, uhbd)
    2292 and molecular orbital file formats (gaussian, gopenmol) turn of box face
    2293 surface capping so that negative threshold levels do not result in box surface.
    2294 TG
    2295 <li><p>Fixed actions menu surface transparency on molecular surfaces colored
    2296 by molecule. TG
    2297 <li><p>Made in-memory writable volumes created by volume eraser have names
    2298 ending in "copy" to distinguish them from original volumes. TG
    2299 <li><p>Made opening volume file not use data from already opened writable
    2300 volume since that data may be modified later. TG
    2301 <li>Fixed aqua 60% cpu usage when showing model panel, but in tix
    2302 scrolledhlist with headers. TG
    2303 </ul>
    2304 
    2305 <p><b>June 9, 2008.  Version 1.2527.</b></p>
    2306 
    2307 <ul type=None>
    2308 <li><p>Made model menus use multiple columns on x11 if they have more than
    2309 35 entries to avoid inaccessible entries off bottom of screen. TG
    2310 
    2311 <li><p>Made saving volume data update the volume name in volume dialog
    2312 and menus. TG
    2313 </ul>
    2314 
    2315 <p><b>June 6, 2008.  Version 1.2525.</b></p>
    2316 
    2317 <ul type=None>
    2318 <li><p>Made surface display use opengl vertex buffer objects instead of display
    2319 lists, leading to 2x faster rendering on two tested graphics cards. TG
    2320 </ul>
    2321 
    2322 <p><b>June 5, 2008.  Version 1.2525.</b></p>
    2323 
    2324 <ul type=None>
    2325 <li><p>Made priism volume file reader set correct voxel size. TG
    2326 <li><p>Made molecular surface display for a set of atoms not override
    2327 partial surface display done with surface zone tool. TG
    2328 <li><p>Made active volume name highlighting on aqua use blue color. Was using
    2329 white which was identical to inactive background. TG
    2330 
    2331 <li><p>Made main window have focus at startup on aqua. TG
    2332 </ul>
    2333 
    2334 <p><b>June 3, 2008.  Version 1.2525.</b></p>
    2335 
    2336 <ul type=None>
    2337 <li><p>Fixed hang on aqua caused by benchmark dialog horizontal scrollbar
    2338 display/undisplay. TG
    2339 <li><p>Fixed aqua bug where movie recorder could not be stopped because
    2340 graphics window was given focus at each frame preventing pressing the Stop
    2341 button. TG
    2342 <li><p>Fixed aqua bug where movie recorder could not find ffmpeg executable. TG
    2343 </ul>
    2344 
    2345 <p><b>June 2, 2008.  Version 1.2525.</b></p>
    2346 
    2347 <ul type=None>
    2348 <li><p>Made priism volume file reader handle xywzt and xyzwt data orders
    2349 (w = wavelength, t = time). TG
    2350 
    2351 </ul>
    2352 
    2353 <p><b>May 30, 2008.  Version 1.2524.</b></p>
    2354 
    2355 <ul type=None>
    2356 <li><p>Fixed molecular surface bug where closing surface model and then
    2357 reshowing surface for subset of atoms showed entire surface. TG
    2358 <li><p>Made toolbar and model panel balloons not take focus in aqua. TG
    2359 </ul>
    2360 
    2361 <p><b>May 28, 2008.  Version 1.2523.</b></p>
    2362 
    2363 <ul type=None>
    2364 <li><p>Padded selection button in lower right corner of main window so that
    2365 text is not clipped on aqua. TG
    2366 <li><p>Made atom spec balloons on aqua not have window frame, and not take
    2367 focus. TG
    2368 <li><p>Added apple application menu entries for About Chimera... and
    2369 Preferences... on aqua. TG
    2370 
    2371 <li><p>Made model panel Select button work on molecular surfaces. TG
    2372 </ul>
    2373 
    2374 <p><b>May 27, 2008.  Version 1.2522.</b></p>
    2375 
    2376 <ul type=None>
    2377 <li><p>Fixed volume image stack session saving bug. TG
    2378 <li><p>Fixed recently introduced bug where color byatom with a surface shown
    2379 generated an error. TG
    2380 <li><p>Fixed aqua chimera crash when any dialog shown by disabling apple event
    2381 handling code. TG
    2382 </ul>
    2383 
    2384 <p><b>May 26, 2008.  Version 1.2522.</b></p>
    2385 
    2386 <ul type=None>
    2387 <li><p>Made actions atom/ribbon/surface menus work with multiscale models. TG
    2388 
    2389 </ul>
    2390 
    2391 <p><b>May 22, 2008.  Version 1.2517.</b></p>
    2392 
    2393 <ul type=None>
    2394 <li><p>Made space navigator work with independent center of rotation mode. TG
    2395 <li><p>Made select command on surfaces select all the surface pieces. TG
    2396 </ul>
    2397 
    2398 <p><b>May 21, 2008.  Version 1.2517.</b></p>
    2399 
    2400 <ul type=None>
    2401 <li><p>Fixed recently introduced bug where cofr command did not work on
    2402 undisplayed selected surfaces. TG
    2403 </ul>
    2404 
    2405 <p><b>May 20, 2008.  Version 1.2514.</b></p>
    2406 
    2407 <ul type=None>
    2408 <li><p>Made selecting molecular surface select atoms and bonds. TG
    2409 <li><p>Made action menu set pivot work on selected surfaces. TG
    2410 <li><p>Made volume viewer detect surface color/style changes made from Actions menu or by other means. TG
    2411 </ul>
    2412 
    2413 <p><b>May 19, 2008.  Version 1.2511.</b></p>
    2414 
    2415 <ul type=None>
    2416 <li><p>Fixed fit map error when no atoms selected and simulated map enabled. TG
    2417 </ul>
    2418 
    2419 <p><b>May 15, 2008.  Version 1.2511.</b></p>
    2420 
    2421 <ul type=None>
    2422 <li><p>Made Actions / Focus menu entry work for selected surfaces. TG
    2423 <li><p>Fixed volume series error when playing series when active volume
    2424 in not in series. TG
    2425 <li><p>Fixed volume series bug undisplaying surfaces when caching off. TG
    2426 </ul>
    2427 
    2428 <p><b>May 13, 2008.  Version 1.2510.</b></p>
    2429 
    2430 <ul type=None>
    2431 <li><p>Made Actions menu entries work when molecular surfaces are selected.
    2432 Formerly they only worked when atoms were selected. TG
    2433 <li><p>Made selecting a surface in mesh or dot style require clicking on
    2434 a mesh line or dot.  Formerly any area of the surface could be clicked.
    2435 The new behavior allows selecting molecules within surfaces. TG
    2436 <li><p>Made volume surfaces selectable. TG
    2437 <li><p>Made Actions / Surface and Actions / Color menu entries work on
    2438 non-molecular surfaces. TG
    2439 <li><p>Removed Actions / Target menu. TG
    2440 </ul>
    2441 
    2442 <p><b>May 12, 2008.  Version 1.2510.</b></p>
    2443 
    2444 <ul type=None>
    2445 <li><p>Fixed crash at startup on mac when remote displaying caused by
    2446 space navigator tool. Same problem when --nogui mode used and the user
    2447 is not logged in to the mac console. TG
    2448 </ul>
    2449 
    2450 <p><b>May 9, 2008.  Version 1.2510.</b></p>
    2451 
    2452 <ul type=None>
    2453 <li><p>Made molecular surface calculation report the number of surface
    2454 components and the solvent excluded and solvent accessible surface areas. TG
    2455 <li><p>Fixed error in surface color tool when surface is colored by volume
    2456 value and the volume is closed and then the surface is changed. TG
    2457 </ul>
    2458 
    2459 <p><b>May 8, 2008.  Version 1.2510.</b></p>
    2460 
    2461 <ul type=None>
    2462 <li><p>Removed accelerators on/off menu entries from Tools / General Controls
    2463 menu and renamed Accelerators List entry to Keyboard Shortcuts.  Keyboard
    2464 shortcuts are now enabled with a switch on the dialog and that setting is now
    2465 saved in preferences automatically. TG
    2466 </ul>
    2467 
    2468 <p><b>May 7, 2008.  Version 1.2510.</b></p>
    2469 
    2470 <ul type=None>
    2471 <li><p>Made Fetch Structure by ID report download progress in status line. TG
    2472 </ul>
    2473 
    2474 <p><b>May 6, 2008.  Version 1.2510.</b></p>
    2475 
    2476 <ul type=None>
    2477 <li><p>Fixed recently introduced bug in model panel Tile button where models
    2478 were placed in random order on screen.  Fixed ordering is by model id number. TG
    2479 
    2480 </ul>
    2481 
    2482 <p><b>May 5, 2008.  Version 1.2510.</b></p>
    2483 
    2484 <ul type=None>
    2485 <li><p>Put least used controls of surface color dialog in options panel. TG
    2486 <li><p>Made surface color dialog use a separate volume menu that is displayed
    2487 when color method is by volume data value. Formerly every volume appeared as
    2488 an entry in the coloring method menu. TG
    2489 <li><p>Added electrostatic coloring method to surface color dialog. This is
    2490 the same as coloring by volume data value, only with dialog text specialized
    2491 to save "electrostatic potential" to reduce confusion. TG
    2492 <li><p> Fixed session saving bug with custom colored molecular surface models.
    2493 Bug introduced in past month.  TG
    2494 </ul>
    2495 
    2496 <p><b>May 2, 2008.  Version 1.2510.</b></p>
    2497 
    2498 <ul type=None>
    2499 
    2500 <li><p>Made benchmark tool draw models on screen to avoid inflated frame rates.
    2501 Formerly drawing was done in an internal buffer and not shown and newer drivers
    2502 shortcut the rendering leading to frame rates sometimes 2x higher than in
    2503 actual use.  TG
    2504 <li><p>Added "report scores" button to benchmark tool to send scores to
    2505 RBVI for posting on web. TG
    2506 <li><p>Simplified benchmark dialog to show only the commonly used controls,
    2507 with others hidden in an options panel. TG
    2508 <li><p>Fixed bug in benchmark tool with solid rendering where volume was not
    2509 in field of view so some graphics drivers rendered nothing leading to very
    2510 large test cases which caused memory errors. TG
    2511 </ul>
    2512 
    2513 <p><b>April 30, 2008.  Version 1.2508.</b></p>
    2514 
    2515 <ul type=None>
    2516 <li><p>Fixed bug in crystal contacts tool where contacts between a crystal
    2517 asymmetric unit and copies translated by unit cell translations were not
    2518 detected. TG
    2519 <li><p>Added option to crystal contacts tool to create moleucule models for
    2520 contacting copies. TG
    2521 </ul>
    2522 
    2523 <p><b>April 28, 2008.  Version 1.2506.</b></p>
    2524 
    2525 <ul type=None>
    2526 <li><p>Made volume eraser radius slider resize when the dialog is resized. TG
    2527 </ul>
    2528 
    2529 <p><b>April 25, 2008.  Version 1.2506.</b></p>
    2530 
    2531 <ul type=None>
    2532 <li><p>Made model panel Tile button highlight when non-molecule models selected. TG
    2533 </ul>
    2534 
    2535 <p><b>April 24, 2008.  Version 1.2506.</b></p>
    2536 
    2537 <ul type=None>
    2538 <li><p>Made model panel Tile button work with all models, not just molecules. TG
    2539 </ul>
    2540 
    2541 <p><b>April 18, 2008.  Version 1.2505.</b></p>
    2542 
    2543 <ul type=None>
    2544 <li><p>Made phantom force feedback tool volume aligned cross-hair display
    2545 correctly when local volume coordinates are rotated. TG
    2546 </ul>
    2547 
    2548 <p><b>April 17, 2008.  Version 1.2504.</b></p>
    2549 
    2550 <ul type=None>
    2551 <li><p>Added color palette option menu and a button to reverse color order
    2552 to surface color tool. TG
    2553 </ul>
    2554 
    2555 <p><b>April 16, 2008.  Version 1.2503.</b></p>
    2556 
    2557 <ul type=None>
    2558 <li><p>Made multiscale tool with surface resolution = 0 (solvent excluded
    2559 surface) use probe radius, vertex density and disjoint component preference
    2560 settings.  Formerly it used values that could not be changed. TG
    2561 <li><p>Made relative orientation schematic shortcut "ai" not give an error
    2562 when rotation angle is zero. TG
    2563 </ul>
    2564 
    2565 <p><b>April 15, 2008.  Version 1.2503.</b></p>
    2566 
    2567 <ul type=None>
    2568 <li><p>Made phantom force feedback tool handle volume step change, and
    2569 made move marker warn if no marker is under cursor. TG
    2570 </ul>
    2571 
    2572 <p><b>April 11, 2008.  Version 1.2503.</b></p>
    2573 
    2574 <ul type=None>
    2575 
    2576 <li><p>Simplified Phantom Force Feedback dialog.  Made key commands work from
    2577 main Chimera window.  Changed move models, zoom, contour level, move marker
    2578 keyboard commands to press once to activate, again to deactivate.  Formerly key
    2579 had to be held down. TG
    2580 <li><p>Included Phantom force feedback OpenHaptics event handling in Windows
    2581 Chimera distribution. User is required to install OpenHaptics driver. TG
    2582 </ul>
    2583 
    2584 <p><b>April 10, 2008.  Version 1.2503.</b></p>
    2585 
    2586 <ul type=None>
    2587 <li><p>Fixed bug where molecular surface calculation for zero atoms failed. TG
    2588 </ul>
    2589 
    2590 <p><b>April 8, 2008.  Version 1.2503.</b></p>
    2591 
    2592 <ul type=None>
    2593 <li><p>Made "ac" command accept arguments which are keyboard shortcuts to run.
    2594 Without arguments it still enables typing keyboard shortcuts to main window. TG
    2595 </ul>
    2596 
    2597 <p><b>April 7, 2008.  Version 1.2503.</b></p>
    2598 
    2599 <ul type=None>
    2600 <li><p>Added support for Space Navigator six degree-of-freedom input device
    2601 to Windows Chimera versions. TG
    2602 </ul>
    2603 
    2604 <p><b>April 4, 2008.  Version 1.2503.</b></p>
    2605 
    2606 <ul type=None>
    2607 <li><p>Made molecular surface calculation not show a console window on Windows.
    2608 TG
    2609 </ul>
    2610 
    2611 <p><b>April 3, 2008.  Version 1.2503.</b></p>
    2612 
    2613 <ul type=None>
    2614 <li><p>Fixed molecular surface calculation on Windows. Was interpreting ctrl-z
    2615 as end of input. Also mscalc program was not started correctly. TG
    2616 </ul>
    2617 
    2618 <p><b>April 2, 2008.  Version 1.2502.</b></p>
    2619 
    2620 <ul type=None>
    2621 <li><p>Added support for Space Navigator six degree-of-freedom input device
    2622 to Mac Chimera versions. TG
    2623 </ul>
    2624 
    2625 <p><b>April 1, 2008.  Version 1.2502.</b></p>
    2626 
    2627 <ul type=None>
    2628 <li><p>Fixed bug where enabling surface capping and surface coloring caused
    2629 continuous recalculation of cap and colors. TG
    2630 
    2631 <li><p>Made surface cap color not flicker to solid color when moving cap. TG
    2632 </ul>
    2633 
    2634 <p><b>March 27, 2008.  Version 1.2502.</b></p>
    2635 
    2636 <ul type=None>
    2637 <li><p>Made multiscale dialog use stand-alone program molecular surface
    2638 calculation when resolution set to zero for solvent excluded surface. TG
    2639 </ul>
    2640 
    2641 <p><b>March 26, 2008.  Version 1.2501.</b></p>
    2642 
    2643 <ul type=None>
    2644 <li><p>Optimized surface distance calculation (keyboard shortcut "sd") by
    2645 translating Python code to C++.  Several hundred times faster.  TG
    2646 </ul>
    2647 
    2648 <p><b>March 25, 2008.  Version 1.2501.</b></p>
    2649 
    2650 <ul type=None>
    2651 <li><p>Changed solvent excluded/accessible surface area calculation to use
    2652 analytical values instead of approximate values calculated from the triangulated
    2653 surface (which depended on vertex density). TG
    2654 <li><p>Added per-residue solvent excluded/accessible surface area (areaSES,
    2655 areaSAS) attributes viewable with Render by Attribute tool. TG
    2656 <li><p>Added solvent excluded/accessible surface area in Reply Log
    2657 output when molecular surface is calculated.
    2658 <li><p>Made up and down arrow keys work with selected surface pieces. TG
    2659 <li><p>Fixed bug in IMOD mesh file reader where normal vectors appeared in
    2660 the surface vertex array resulting in wrong inertia calculation. TG
    2661 <li><p>Added "ra" keyboard shortcut for showing render-by-attribute dialog. TG
    2662 <li><p>Added "se" keyboard shortcut for toggling silhouette edge display. TG
    2663 <li><p>Fixed bug in surface distance calculation where distance to an
    2664 edge was used when the closest distance was actually to a vertex. TG
    2665 </ul>
    2666 
    2667 <p><b>March 20, 2008.  Version 1.2501.</b></p>
    2668 
    2669 <ul type=None>
    2670 <li><p>Fixed meshmol command on molecular surfaces, "truth value ambiguous"
    2671 error. TG
    2672 <li><p>Fixed error in Measure and Color Blobs, "array cannot be safely
    2673 cast to required type" on 64-bit Chimera versions. TG
    2674 <li><p>Made Color Zone, Surface Zone and Surface Color work on MSMS surface
    2675 caps. TG
    2676 </ul>
    2677 
    2678 <p><b>March 18, 2008.  Version 1.2500.</b></p>
    2679 
    2680 <ul type=None>
    2681 <li><p>Made Chimera calculate solvent excluded molecular surfaces using a
    2682 standalone application so crashes do not crash Chimera.  TG
    2683 <li><p>Made molecular surface calculation assign per-atom solvent excluded
    2684 surface area (areaSES) and solvent accessible surface area (areaSAS) values
    2685 that can be used with Render by Attribute dialog or the "select" command. TG
    2686 <li><p>Molecular surfaces now are implemented using SurfaceModel.  Some
    2687 new attributes of this type of model are visible in the selection and model
    2688 attribute inspector dialogs. TG
    2689 <li><p>Eliminated warning messages that appeared in the Chimera reply log
    2690 on Mac OS 10.5 about an unhandled apple event.  TG
    2691 <li><p>Changed Benchmark molecule tests to only time one molecule instead of
    2692 six.
    2693 <li><p>Fixed ribbon benchmark timing, previous scores invalid.  TG
    2694 </ul>
    2695 
    2696 <p><b>March 17, 2008.  Version 1.2500.</b></p>
    2697 
    2698 <ul type=None>
    2699 <li><p>Fixed a triangle template allocation bug in MSMS molecular surface
    2700 calculation reducing number of crash cases in half.  Also changed to allow
    2701 surface calculation when one atom is entirely inside of another.  TG
    2702 <li><p>Made Movie Recorder respect preference for saving POVray files. TG
    2703 <li><p>Fixed InterSurf to use new SurfaceModel Python names. TG
    2704 </ul>
    2705 
    2706 <p><b>March 11, 2008.  Version 1.2500.</b></p>
    2707 
    2708 <ul type=None>
    2709 <li><p>Renamed Surface_Model to SurfaceModel and changed Python method
    2710 names and attributes to eliminated underscore characters.  TG
    2711 </ul>
    2712 
    2713 <p><b>March 5, 2008.  Version 1.2499.</b></p>
    2714 
    2715 <ul type=None>
    2716 <li><p>Added dot surface display and dot size setting to surface models,
    2717 settable with selection inspector. TG
    2718 </ul>
    2719 
    2720 <p><b>March 4, 2008.  Version 1.2498.</b></p>
    2721 
    2722 <ul type=None>
    2723 <li><p>Reduced memory use of volume solid style rendering in color map
    2724 mode.  Was unnecessarily making floating point copy of map. TG
    2725 </ul>
    2726 
    2727 <p><b>February 29, 2008.  Version 1.2497.</b></p>
    2728 
    2729 <ul type=None>
    2730 <li><p>Removed setting to flip surface lighting normals visible in
    2731 selection inspector dialog. TG
    2732 </ul>
    2733 
    2734 <p><b>February 28, 2008.  Version 1.2496.</b></p>
    2735 
    2736 <ul type=None>
    2737 <li><p>Added consistency checking (valid record size) in delphi map
    2738 file reader. TG
    2739 </ul>
    2740 
    2741 <p><b>February 27, 2008.  Version 1.2495.</b></p>
    2742 
    2743 <ul type=None>
    2744 <li><p>Added checkbuttons to volume tracer mouse mode panel that match
    2745 those in the Mouse menu. TG
    2746 <li><p>Fixed volume tracer session restore bug where a second traced surfaces
    2747 model was created after restoring a session containing traced surfaces. TG
    2748 
    2749 <li><p>Made volume tracer delete surface panel only delete selected
    2750 traced surfaces.  Was deleting any selected surface. TG
    2751 <li><p>Made volume tracer continuous marker placement while dragging
    2752 work with "on spot", "on plane", or "outside data" mouse mode.  Was ignoring
    2753 those settings and always dropping markers on plane. TG
    2754 </ul>
    2755 
    2756 <p><b>February 26, 2008.  Version 1.2495.</b></p>
    2757 
    2758 <ul type=None>
    2759 <li><p>Fixed volume tracer bug where traceback given if "marker color
    2760 matches volume color" enabled and marker is placed. TG
    2761 <li><p>Made crash dump detection for bug reporting work on Mac OS 10.5.
    2762 Mac OS 10.5 uses separate file for each crash, while 10.4 used one file
    2763 for all crashes of the same application. TG
    2764 </ul>
    2765 
    2766 <p><b>February 22, 2008.  Version 1.2495.</b></p>
    2767 
    2768 <ul type=None>
    2769 <li><p>Modified per-model clipping command to not modify existing clip
    2770 plane axis or origin unless explicit options are given. TG
    2771 
    2772 </ul>
    2773 
    2774 <p><b>February 21, 2008.  Version 1.2495.</b></p>
    2775 
    2776 <ul type=None>
    2777 <li><p>Added option to create simulated map (uses molmap command)
    2778 to the fit map dialog. TG
    2779 </ul>
    2780 
    2781 <p><b>February 20, 2008.  Version 1.2495.</b></p>
    2782 
    2783 <ul type=None>
    2784 <li><p>Added per-model clipping command mclip. TG
    2785 <li><p>Fixed volume eraser bug that gave traceback when erasing done
    2786 with eraser sphere entirely outside of volume. TG
    2787 <li><p>Fixed bug on movement mouse mode where no translation was possible
    2788 if near clip plane was at or in front of eye position.  Changed behavior
    2789 so amount of translation is based on dragging center of rotation of object.
    2790 TG
    2791 </ul>
    2792 
    2793 <p><b>February 19, 2008.  Version 1.2494.</b></p>
    2794 
    2795 <ul type=None>
    2796 <li><p>Added zflip option to vop (volume operation) command to change
    2797 the hand of a map by reversing the order of the z planes. TG
    2798 </ul>
    2799 
    2800 <p><b>February 15, 2008.  Version 1.2493.</b></p>
    2801 
    2802 <ul type=None>
    2803 <li><p>Added IMOD map file reader, file suffix ".rec". These are MRC maps
    2804 but signed 8-bit mode is interpreted as unsigned. TG
    2805 <li><p>Changed volume solid style transparency modulation from
    2806 t -&gt; t ** (1.0/planes) to t -&gt; t ** (1.0/(planes*t)). Here planes
    2807 = minimum number of planes along each axis times the transparency factor
    2808 and the initial transparency t is the height of the transfer function on
    2809 the histogram (0-1 range). For transparent voxels the change is minor.
    2810 For opaque voxels it makes the effective thickness smaller and avoids
    2811 a large brightness jump between opacity 0.99 and 1.0. TG
    2812 
    2813 </ul>
    2814 
    2815 <p><b>February 13, 2008.  Version 1.2493.</b></p>
    2816 
    2817 <ul type=None>
    2818 <li><p>Fixed bug where deleting volume tracer links by means other than
    2819 the "delete links" menu entry would later cause session saving to fail.  TG
    2820 <li><p>Made session saving for volume opens put paths in the session file
    2821 that are relative to the session file directory if the volume data lies
    2822 within or below that directory. This allows restoring the session file after
    2823 moving a directory containing session files and volume data. TG
    2824 <li><p>Added linewidth option to shape command for meshes. TG
    2825 <li><p>Made shape command show mesh by default only for icosahedron
    2826 (not sphere) with lattice option specified. TG
    2827 <li><p>Changed shape command default color to "gray". TG
    2828 </ul>
    2829 
    2830 <p><b>February 12, 2008.  Version 1.2493.</b></p>
    2831 
    2832 <ul type=None>
    2833 
    2834 <li><p>Added displayThreshold option to molmap command to set the initial
    2835 contour level of the new map so that the specified fraction of total mass
    2836 is contained within the contour.  Default value 0.95.  TG
    2837 <li><p>Changed effect of volume solid style transparency slider so that
    2838 it modulates transparency even when factor times depth in planes is less
    2839 than 1.  This allows making completely opaque single planes. TG
    2840 </ul>
    2841 
    2842 <p><b>February 8, 2008.  Version 1.2493.</b></p>
    2843 
    2844 <ul type=None>
    2845 <li><p>Reduced memory use when saving a volume zone. For maps larger than
    2846 16 Mvoxels the map mask is computed plane by plane.  Smaller maps use 12
    2847 bytes per voxel overhead.  TG
    2848 </ul>
    2849 
    2850 <p><b>February 7, 2008.  Version 1.2493.</b></p>
    2851 
    2852 <ul type=None>
    2853 <li><p>Fixed split map button in color zone dialog. TG
    2854 </ul>
    2855 
    2856 <p><b>January 31, 2008.  Version 1.2492.</b></p>
    2857 
    2858 <ul type=None>
    2859 <li><p>Combined "fit model in map" and "fit map in map" dialogs into a single
    2860 dialog, and combined menu entries into one entry.  Dialog has new layout but
    2861 same functionality as original two dialogs. TG
    2862 <li><p>Added option for real-time updating of correlation and average map
    2863 value to fit map dialog. TG
    2864 </ul>
    2865 
    2866 <p><b>January 30, 2008.  Version 1.2486.</b></p>
    2867 
    2868 <ul type=None>
    2869 <li><p>Added ability to create surfaces from stacks of loops and curves
    2870 with the volume path tracer tool.  Uses the new Surface panel of the volume
    2871 path tracer dialog. TG
    2872 <li><p>Renamed "volume path tracer" to "volume tracer".  TG
    2873 <li><p>Reordered volume tools menu to put more frequently useful tools near
    2874 the top and group them by functionality. TG
    2875 <li><p>Added split map button to color zone dialog and eliminated separate
    2876 volume tools menu entry for split map. TG
    2877 
    2878 <li><p>Changed molmap ratio of resolution to Gaussian standard deviation
    2879 to be 1/(pi*sqrt(2)) (~0.225) from former value of 1/(2*sqrt(pi)) (~0.282). TG
    2880 <li>Made split map by color zone give proper alignment when map coordinates
    2881 involve a rotation.
    2882 </ul>
    2883 
    2884 <p><b>January 29, 2008.  Version 1.2485.</b></p>
    2885 
    2886 <ul type=None>
    2887 <li><p>Added keyboard shortcut "or" to toggle orthographic projection. TG
    2888 </ul>
    2889 
    2890 <p><b>January 25, 2008.  Version 1.2485.</b></p>
    2891 
    2892 <ul type=None>
    2893 <li><p>Added ability to export surfaces in Wavefront OBJ format using
    2894 File / Export Scene.  TG
    2895 <li><p>Optimized "split map by color zone" to use less memory.  Operates
    2896 plane by plane for maps larger than 16 Mvoxels.  TG
    2897 
    2898 <li><p>Added mouse mode to resize a selected surface by dragging.  Enabled
    2899 for one drag use by keyboard shortcut sz.  TG
    2900 <li><p>Added keyboard shortcut "ao" to activate only selected surfaces. TG
    2901 <li><p>Added keyboard shortcut "oc" to allow typing one command and then
    2902 automatically return to entering keyboard shortcuts. TG
    2903 <li><p>Allowed resizing volume path tracer markers by dragging the mouse
    2904 while holding the Alt key down if the move/resize mode is enabled. TG
    2905 </ul>
    2906 
    2907 <p><b>January 24, 2008.  Version 1.2485.</b></p>
    2908 
    2909 <ul type=None>
    2910 <li><p>Added "resample" operation to vop command to resample one volume
    2911 data set on the grid of a second volume data set.  TG
    2912 </ul>
    2913 
    2914 <p><b>January 23, 2008.  Version 1.2485.</b></p>
    2915 
    2916 <ul type=None>
    2917 
    2918 <li><p>Fixed incorrect rainbow colormap direction for volumes with
    2919 rotated local coordinates. TG
    2920 <li><p>Made "measure and color blobs" dialog and mask command ignore
    2921 outline boxes around volume data. TG
    2922 <li><p>Added "shape" command that makes surfaces having standard geometric
    2923 shapes.  Handles cylinder, sphere, and icosahedron.  Includes icosahedral
    2924 mesh capabilities of hkcage command.  Includes interpolating icosahedron
    2925 with sphere and alternate coordinates systems as in the Icosahedron surface
    2926 dialog. TG
    2927 <li><p>Changed vm keyboard shortcut to mask active volume using selected
    2928 surfaces.  Formerly it masked volume using volume contour surface.  TG
    2929 </ul>
    2930 
    2931 <p><b>January 22, 2008.  Version 1.2485.</b></p>
    2932 
    2933 <ul type=None>
    2934 <li><p>Made volume contour surfaces have correct lighting when the voxel
    2935 size along an axis is made negative to flip the hand of the map.  Formerly
    2936 two sided lighting gave dark surface in this case. TG
    2937 <li><p>Made image stack volume reader handle multi-page tiff images. TG
    2938 <li><p>Fixed surface capping bug when new surface created while capping is
    2939 enabled.  TG
    2940 </ul>
    2941 
    2942 <p><b>January 18, 2008.  Version 1.2485.</b></p>
    2943 
    2944 <ul type=None>
    2945 <li><p>Added molmap command to make volume from a molecule by summing
    2946 Gaussians at each atom position. TG
    2947 </ul>
    2948 
    2949 <p><b>January 16, 2008.  Version 1.2483.</b></p>
    2950 
    2951 <ul type=None>
    2952 <li><p>Made opening tiff image stacks work by selecting all images in the
    2953 open dialog.  Formerly only one image was selected and others that had the
    2954 same prefix and different numeric suffix were inferred. TG
    2955 <li><p>Made image stack reader handle image types other than TIFF.  Can
    2956 handle any image format understood by the Python image library (e.g. png,
    2957 jpeg). TG
    2958 </ul>
    2959 
    2960 <p><b>January 15, 2008.  Version 1.2483.</b></p>
    2961 
    2962 <ul type=None>
    2963 
    2964 <li><p>Fixed chimera "--send" startup option on mac.  Was always starting
    2965 a new instance of chimera. TG
    2966 </ul>
    2967 
    2968 <p><b>January 11, 2008.  Version 1.2483.</b></p>
    2969 
    2970 <ul type=None>
    2971 <li><p>Removed marker set models closed with the file menu entry in
    2972 the volume path tracer dialog.  Formerly the models were just emptied
    2973 of markers. TG
    2974 <li><p>Changed mask command sandwich option default value to true. TG
    2975 <li><p>Changed mask command fullmap option to require a true/false value.
    2976 Formerly the option took no value. TG
    2977 </ul>
    2978 
    2979 <p><b>January 10, 2008.  Version 1.2483.</b></p>
    2980 
    2981 <ul type=None>
    2982 <li><p>Made default projection axis for mask command y instead of z. TG
    2983 
    2984 <li><p>Renamed "pick surface pieces" dialog and menu entry to the more
    2985 descriptive "measure and color blobs". TG
    2986 <li><p>Added slab option to mask command to mask using a slab of specified
    2987 thickness created by thickening a surface. TG
    2988 </ul>
    2989 
    2990 <p><b>January 9, 2008.  Version 1.2483.</b></p>
    2991 
    2992 <ul type=None>
    2993 <li><p>Added selection inspector attributes for surface pieces:
    2994 surface piece count, line thickness, line smoothing, lighting, two
    2995 sided lighting, lighting normal direction, transparency brightness. TG
    2996 <li><p>Made selection inspector attributes for surface models and pieces
    2997 update when changed using other dialogs or commands. TG
    2998 </ul>
    2999 
    3000 <p><b>January 8, 2008.  Version 1.2481.</b></p>
    3001 
    3002 <ul type=None>
    3003 <li><p>Added attributes to selection inspector dialog for surfaces and
    3004 surface pieces.  Attributes: color, display style (mesh/solid), displayed,
    3005 triangle count, active, selectable with mouse.  TG
    3006 
    3007 <li><p>Made selected surfaces show green outline even when "selectable with
    3008 mouse" is turned off.  TG
    3009 <li><p>Made keyboard shortcuts work on surfaces selected with select command.
    3010 The select command selects the surface model but not the surface components.
    3011 TG
    3012 </ul>
    3013 
    3014 <p><b>January 7, 2008.  Version 1.2481.</b></p>
    3015 
    3016 <ul type=None>
    3017 <li><p>Made surfnet tool create a surface model instead of a vrml model.
    3018 Allows measuring enclosed volume, coloring, splitting disjoint components,
    3019 ....  TG
    3020 <li><p>Eliminated _cubes contour calculation module.  TG
    3021 </ul>
    3022 
    3023 <p><b>January 2, 2008.  Version 1.2481.</b></p>
    3024 
    3025 <ul type=None>
    3026 <li><p>Added fill value option to vop command.  Large negative fill values
    3027 can produce flat cut faces when erasing an octant.  TG
    3028 
    3029 </ul>
    3030 
    3031 <p><b>December 21, 2007.  Version 1.2480.</b></p>
    3032 
    3033 <ul type=None>
    3034 <li><p>Made help command show documentation for commands volume, topo, sym,
    3035 bondzone, split, msc, meshmol, mask, hkcage, crystalcontacts.  TG
    3036 <li><p>Added vop (volume operation command) to erase an octant.  Plan to
    3037 support many other volume modifying operations (gaussian filter, erase
    3038 outside sphere, interpolate, ...) as options to this command in the future.
    3039 TG
    3040 <li><p>Changed volume suffixes from <N> format (e.g. "map.mrc <1>")
    3041 to instead append model id number.  Previous suffix number was not the
    3042 model id number.  TG
    3043 </ul>
    3044 
    3045 <p><b>December 20, 2007.  Version 1.2480.</b></p>
    3046 
    3047 <ul type=None>
    3048 <li><p>Made meshmol command work when surface has the same model id number
    3049 as an existing molecule.  TG
    3050 <li><p>Fixed bug in multiscale tool where molecule copies were not closed
    3051 when multiscale model deleted.  TG
    3052 </ul>
    3053 
    3054 <p><b>December 18, 2007.  Version 1.2479.</b></p>
    3055 
    3056 <ul type=None>
    3057 <li><p>Made changing volume step size with step menu not turn off automatic
    3058 step size adjustment.  Now the voxel limit for automatic step adjustment is
    3059 instead changed to the number of voxels shown with the chosen step.  TG
    3060 <li><p>Changed default volume solid threshold brightness at 99% rank data
    3061 value from 1.0 to 0.99 to avoid completely opaque voxels.  TG
    3062 <li><p>Reduced memory allocation used to zero volume solid 3-d texture from
    3063 4*(number of voxels) bytes to 4*(number of voxels in one xy plane).  TG
    3064 <li><p>Optimized pick surface piece tool.  About 10x faster in typical case.
    3065 TG
    3066 <li><p>Added Tools / Volume Data menu entry that adds Volume menu to main
    3067 window menu bar, and remembers this setting for future sessions.  TG
    3068 </ul>
    3069 
    3070 <p><b>December 14, 2007.  Version 1.2476.</b></p>
    3071 
    3072 <ul type=None>
    3073 <li><p>Fixed toggle surface selectability keyboard shortcut ts.  TG
    3074 </ul>
    3075 
    3076 <p><b>December 12, 2007.  Version 1.2476.</b></p>
    3077 
    3078 <ul type=None>
    3079 <li><p>Made topography command work with yz and xz planes.  Formerly only
    3080 handled xy planes.  TG
    3081 <li><p>Added topography command "replace" option to replace the existing
    3082 topography surface rather than create a new one.  TG
    3083 <li><p>Made volume planes show the correct depth after All planes button is
    3084 pressed when step size is greater than 1.  TG
    3085 <li><p>Fixed volume command writing brix, mrc and netcdf formats.
    3086 Was giving an error message and not writing file. TG
    3087 </ul>
    3088 
    3089 <p><b>December 11, 2007.  Version 1.2476.</b></p>
    3090 
    3091 <ul type=None>
    3092 <li><p>Made volume solid rendering model have same id number as volume
    3093 surface model.  Wasn't doing that when solid was shown first.  TG
    3094 </ul>
    3095 
    3096 <p><b>December 7, 2007.  Version 1.2476.</b></p>
    3097 
    3098 <ul type=None>
    3099 <li>Fixed bug where volume data set menu and list box contained deleted
    3100 volumes. TG
    3101 <li><p>Fixed error in session restore where multiscale models of volume
    3102 path tracer marker sets were present.  TG
    3103 </ul>
    3104 
    3105 <p><b>December 5, 2007.  Version 1.2476.</b></p>
    3106 
    3107 <ul type=None>
    3108 
    3109 <li><p>Removed checkbutton volume planes panel of volume dialog and added
    3110 "one", "all" buttons to control display of single plane or all planes.
    3111 New interface makes it clearer that plane display is not a mode, and makes
    3112 display of all planes more reliable. TG
    3113 <li><p>Made sessions include derived maps (e.g. Gaussian filter) that have
    3114 been saved to a separate volume file. TG
    3115 </ul>
    3116 
    3117 <p><b>December 4, 2007.  Version 1.2476.</b></p>
    3118 
    3119 <ul type=None>
    3120 <li><p>Fixed bug that caused volume histogram to be off by a few percent
    3121 in number of voxels counts per value bin.  TG
    3122 <li><p>Added threshold normalization to morph map dialog.  Adjusts volume
    3123 threshold to keep a fixed number of grid points within the contour surface
    3124 for all interpolated maps.  TG
    3125 </ul>
    3126 
    3127 <p><b>November 30, 2007.  Version 1.2475.</b></p>
    3128 
    3129 <ul type=None>
    3130 <li><p>Added key shortcuts to create a new volume using the zone display of
    3131 the active volume (zv), and the region outside the zone (ez, erase zone). TG
    3132 
    3133 </ul>
    3134 
    3135 <p><b>November 29, 2007.  Version 1.2475.</b></p>
    3136 
    3137 <ul type=None>
    3138 <li><p>Added topography command which creates a surface corresponding to
    3139 a volume data plane.  The surface height above the volume plane is
    3140 proportional to the volume data value.  TG
    3141 </ul>
    3142 
    3143 <p><b>November 27, 2007.  Version 1.2473.</b></p>
    3144 
    3145 <ul type=None>
    3146 <li><p>Made Chimera compatible with 2 year old Chimera 1.2154 preferences files.
    3147 Showing volume with new Chimera and old preferences file caused error.  TG
    3148 <li><p>Made restoring a session that uses the Surface Color tool not display
    3149 the Surface Color dialog unless it was displayed when the session was saved.
    3150 TG
    3151 <li><p>Added TIFF volume file reader support for 16-bit unsigned integer,
    3152 32 bit floating point, and 32 bit integer pixel values.  TG
    3153 <li><p>Added volume file writing in BRIX  format (used by crystallography
    3154 program O). TG
    3155 
    3156 </ul>
    3157 
    3158 <p><b>November 15, 2007.  Version 1.2470.</b></p>
    3159 
    3160 <ul type=None>
    3161 <li><p>Chimera production release 1.2470.
    3162 </ul>
    3163 
    3164 <p><b>November 13, 2007.  Version 1.2469.</b></p>
    3165 
    3166 <ul type=None>
    3167 <li><p>Made Gaussian filter copy the local coordinate rotation of original
    3168 map. TG
    3169 <li><p>Made volume subregion resampling pad by half a voxel between the
    3170 displayed outline box and the resampling grid.  This allows resampling on
    3171 the exact grid of a second map by clicking outside that map to outline it
    3172 (which includes a half voxel padding).  TG
    3173 <li><p>Added display full volume keyboard shortcut fv.  Useful after
    3174 showing a subregion for returning to full map display.  TG
    3175 </ul>
    3176 
    3177 <p><b>November 8, 2007.  Version 1.2468.</b></p>
    3178 
    3179 <ul type=None>
    3180 <li><p>Fixed priism volume file reader byte order detection code.  Did
    3181 not work correctly with 8-bit data values.  TG
    3182 </ul>
    3183 
    3184 <p><b>November 7, 2007.  Version 1.2468.</b></p>
    3185 
    3186 <ul type=None>
    3187 <li><p>Added options to the Gaussian filter dialog to use only the displayed
    3188 subsampling, and to use only the displayed subregion. TG
    3189 <li><p>Fixed volume caching bug that sometimes caused single plane volume
    3190 data display to be blank.  TG
    3191 <li><p>Fixed bug in morph map where the first map was modified instead of
    3192 creating a new interpolated map when the first map was writable. TG
    3193 </ul>
    3194 
    3195 <p><b>November 6, 2007.  Version 1.2468.</b></p>
    3196 
    3197 <ul type=None>
    3198 <li><p>Made Chimera start correctly on Mac OS 10.5 (Leopard) by preventing
    3199 Chimera from trying to automatically start the X server, since that is now
    3200 done by the operating system.  TG
    3201 <li><p>Fixed bug in error message displayed when reading truncated XPLOR
    3202 volume files.  TG
    3203 </ul>
    3204 
    3205 <p><b>November 5, 2007.  Version 1.2468.</b></p>
    3206 
    3207 <ul type=None>
    3208 <li><p>Made BRIX/DSN6 (O map) volume file reader apply scale and shift from
    3209 file header to 8-bit values to produce floating point values.  TG
    3210 </ul>
    3211 
    3212 <p><b>October 31, 2007.  Version 1.2467.</b></p>
    3213 
    3214 <ul type=None>
    3215 <li><p>Made mask command handle degenerate cases where projected grid lines
    3216 exactly intersect surface vertices or edges.  TG
    3217 </ul>
    3218 
    3219 <p><b>October 29, 2007.  Version 1.2466.</b></p>
    3220 
    3221 <ul type=None>
    3222 <li><p>Added "sandwich" option to mask command for extracting the volume
    3223 between two surfaces along a projection axis.  Without this option regions
    3224 between one surface and the volume box boundary are also included.  TG
    3225 </ul>
    3226 
    3227 <p><b>October 26, 2007.  Version 1.2466.</b></p>
    3228 
    3229 <ul type=None>
    3230 <li><p>Changed hkcage command which makes icosahedral cages use keyword
    3231 options instead of requiring options to be in fixed order.  Added "replace"
    3232 keyword option to replace the existing cage instead of creating a new model.
    3233 TG
    3234 
    3235 </ul>
    3236 
    3237 <p><b>October 24, 2007.  Version 1.2465.</b></p>
    3238 
    3239 <ul type=None>
    3240 <li><p>Made MRC volume files written by Chimera contain the Chimera version
    3241 and date. TG
    3242 <li><p>Made split command which places chains of an atomic model in separate
    3243 models do nothing when applied to a single chain. TG
    3244 </ul>
    3245 
    3246 <p><b>October 23, 2007.  Version 1.2465.</b></p>
    3247 
    3248 <ul type=None>
    3249 <li><p>Added mask command which creates a volume data set containing
    3250 only the values within a surface. TG
    3251 <li><p>Fixed bug in close points calculation used by Find Clashes,
    3252 Color Zone and Surface Zone tools which in rare cases may have led to
    3253 incorrect neighbor calculation or hanging. TG
    3254 </ul>
    3255 
    3256 <p><b>October 22, 2007.  Version 1.2465.</b></p>
    3257 
    3258 <ul type=None>
    3259 <li><p>Fixed bug where meshmol command would create a model aligned
    3260 with the model with lowest id number instead of the original mesh model. TG
    3261 <li><p>Fixed bug where resampled volume had no name in volume dialog and
    3262 model panel. TG
    3263 <li><p>Made volume display tolerate externally deleted contour surface groups,
    3264 for example with Ds keyboard shortcut. TG
    3265 </ul>
    3266 
    3267 <p><b>October 18, 2007.  Version 1.2463.</b></p>
    3268 
    3269 <ul type=None>
    3270 <li><p>Fixed volume series bug opening priism format data. TG
    3271 </ul>
    3272 
    3273 <p><b>October 17, 2007.  Version 1.2463.</b></p>
    3274 
    3275 <ul type=None>
    3276 <li><p>Made morph map volume browse button display the opened data. TG
    3277 </ul>
    3278 
    3279 <p><b>October 11, 2007.  Version 1.2458.</b></p>
    3280 
    3281 <ul type=None>
    3282 <li><p>Made calculation of volume enclosed in a surface handle surface holes
    3283 but placing a point at the center of each boundary curve and making a triangle
    3284 fan to cover the hole. TG
    3285 <li><p>Add split map and fourier transform menu entries (Tools / Volume Data).
    3286 TG
    3287 </ul>
    3288 
    3289 <p><b>October 10, 2007.  Version 1.2456.</b></p>
    3290 
    3291 <ul type=None>
    3292 <li><p>Added several tools from experimental features web page to the
    3293 distribution: morph map, transform molecule coordinates, mesh to molecule,
    3294 icosahedral cage (hkcage command), surface distance, crystal contacts, volume
    3295 series, movement mouse mode, flatten icosahedron, split molecule, multiscale
    3296 color command, pick surface pieces, symmetry copies command (sym).  TG
    3297 <li><p>Added Tools menu to volume dialog. TG
    3298 <li><p>Optimized speed of Find Clashes tool. TG
    3299 <li><p>Added version number to Chimera HDF map file format. TG
    3300 </ul>
    3301 
    3302 <p><b>October 9, 2007.  Version 1.2455.</b></p>
    3303 
    3304 <ul type=None>
    3305 <li><p>Added "cap high values at box faces" volume surface rendering option. TG
    3306 <li><p>Made popup balloons for IMOD object surfaces give object name.
    3307 Mousing over other selectable surfaces will also show names.  TG
    3308 <li>Add keyboard shortcut Ds to delete selected surfaces and Sc to split
    3309 selected surfaces into one surface for each connected component. TG
    3310 </ul>
    3311 
    3312 <p><b>October 6, 2007.  Version 1.2454.</b></p>
    3313 
    3314 <ul type=None>
    3315 <li><p>Made volume contour surfaces use lighting normals parallel to data
    3316 gradient instead of averaged surface triangle normals.  Gives less faceted
    3317 apperance.  TG
    3318 <li><p>Made multiscale model tool use surface lighting normals based on
    3319 gradient of atom density rather than average normal of surface triangles.
    3320 Small improvement in surface smoothness.  TG
    3321 </ul>
    3322 
    3323 <p><b>October 5, 2007.  Version 1.2454.</b></p>
    3324 
    3325 <ul type=None>
    3326 <li><p>Added IMOD mesh file reader. TG
    3327 <li><p>Added Gaussian filter tool to smooth volume data by convolving with
    3328 a gaussian. TG
    3329 <li><p>Added Fourier transform keyboard shortcut FT to display 3-dimensional
    3330 Fourier transform of volume data. TG
    3331 <li><p>Added keyboard shortcut sm to split a volume data set into multiple
    3332 data sets, one for each color of the original volume, as colored by the
    3333 color zone tool. TG
    3334 <li><p>Made multiscale model tool not change the display style of the original
    3335 molecule used in building multimeric assembly.  Only displays new copies as
    3336 surfaces.  TG
    3337 
    3338 </ul>
    3339 
    3340 <p><b>October 4, 2007.  Version 1.2454.</b></p>
    3341 
    3342 <ul type=None>
    3343 <li><p>Made surface capping not show a cap for a clipped unit cell outline box.
    3344 (Bug 4605). TG
    3345 <li><p>Made unit cell tool pack asymmetric unit in single unit cell even when
    3346 molecule atoms/ribbon is undisplayed (as when using Multiscale).  Now uses
    3347 center of all atoms rather than center of displayed atoms for packing.
    3348 (Bug 4606). TG
    3349 </ul>
    3350 
    3351 <p><b>October 3, 2007.  Version 1.2454.</b></p>
    3352 
    3353 <ul type=None>
    3354 <li><p>Added tool to print mean, standard deviation and RMS for volume data
    3355 (Tools / Volume Data / Volume Mean, SD, RMS). TG
    3356 <li><p>Made color zone slider range equal to diagonal size of surface bounding
    3357 box.  Formerly maximum slider value was always 30.  TG
    3358 <li><p>Made surface capping not create a cap for clipped volume outline box. TG
    3359 
    3360 </ul>
    3361 
    3362 <p><b>October 2, 2007.  Version 1.2451.</b></p>
    3363 
    3364 <ul type=None>
    3365 <li><p>Made volume contour surfaces cover volume box faces where high
    3366 density is exposed.  TG
    3367 </ul>
    3368 
    3369 <p><b>September 26, 2007.  Version 1.2450.</b></p>
    3370 
    3371 <ul type=None>
    3372 <li><p>Made volume contour calculation work on volumes up to size 4 Gvoxels.
    3373 Formerly the limit was 4/3 Gvoxels.  TG
    3374 </ul>
    3375 
    3376 <p><b>September 20, 2007.  Version 1.2448.</b></p>
    3377 
    3378 <ul type=None>
    3379 <li><p>Added series of 10 initial volume colors to volume data display
    3380 options panel.  Opened data sets are shown in different colors.  TG
    3381 </ul>
    3382 
    3383 <p><b>September 19, 2007.  Version 1.2448.</b></p>
    3384 
    3385 <ul type=None>
    3386 <li><p>Made volume data saving use a temporary file if map is written back
    3387 over itself.  Formerly this would cause an error if the map was not entirely
    3388 cached in memory because the source file would be erased before all the
    3389 needed data was obtained.  TG
    3390 </ul>
    3391 
    3392 <p><b>September 18, 2007.  Version 1.2448.</b></p>
    3393 
    3394 <ul type=None>
    3395 <li><p>Added "compress" option to volume command to compress data when
    3396 saving in Chimera map format.  Useful for mask files.  TG
    3397 
    3398 <li><p>Made volume command region option accept "all" or "full" value
    3399 to set region display to show the full data set.  TG
    3400 <li><p>Fixed bug where volume command did not accept upper case boolean values
    3401 True, TRUE, False, .... TG
    3402 <li><p>Fixed volume command so that model id numbers of "solid" models can
    3403 be used.  Formerly the model id of the volume surface model was required.  TG
    3404 <li><p>Made default solid volume rendering thresholds use only 2 nodes for
    3405 mask data sets having just two values 0/1.  TG
    3406 <li><p>Made Chimera map file include original file names with suffix stripped
    3407 off when multiple maps are written to one file.  TG
    3408 </ul>
    3409 
    3410 <p><b>September 17, 2007.  Version 1.2448.</b></p>
    3411 
    3412 <ul type=None>
    3413 <li><p>Added "symmetry" option to volume command that assigns symmetry
    3414 matrices to a volume data set.  It takes an argument "icos,XXX" where XXX
    3415 is one of 222, 2n5, n25, 2n3, 222r, 2n5r, n25r, 2n3r to specify icosahedral
    3416 symmetry in one of the standard coordinate frames as in the icosahedron
    3417 tool.  Future additions will support space and point group and screw symmetries
    3418 and BIOMT PDB matrices.  TG
    3419 </ul>
    3420 
    3421 <p><b>September 15, 2007.  Version 1.2448.</b></p>
    3422 
    3423 <ul type=None>
    3424 <li><p>Made experimental "sym" command use symmetries associated with volume
    3425 data set.  If there are none it uses BIOMT matrices from PDB model as
    3426 previously.  Not yet on web. TG
    3427 <li><p>Added "contact" and "range" options to "sym" command to make molecule
    3428 copies only when it is near the original copy.  Both parameters take a
    3429 distance.  Contact requires a pair of atoms within the threshold distance
    3430 while range requires the center of the molecule bounding boxes to be within
    3431 the specified range.  Not yet on web. TG
    3432 <li>Added keyboard shortcut "ic" to assign icosahedral 222 symmetry to the
    3433 active volume data set. TG
    3434 </ul>
    3435 
    3436 <p><b>September 12, 2007.  Version 1.2446.</b></p>
    3437 
    3438 <ul type=None>
    3439 <li><p>Added volume command chunkShape option for writing map files that
    3440 allow fast access to yz planes.  TG
    3441 </ul>
    3442 
    3443 <p><b>September 11, 2007.  Version 1.2445.</b></p>
    3444 
    3445 <ul type=None>
    3446 
    3447 <li><p>Made CCP4 and MRC separate file formats in File / Open dialog.
    3448 Formerly they were treated as one format.  CCP4 reader now will not
    3449 incorrectly interpret xorigin, yorigin, zorigin parameters found only
    3450 in MRC2000 files.  TG
    3451 <li><p>Changed CCP4 and MRC file readers heuristic for deciding whether
    3452 origin header values (ncstart, nrstart, nsstart) are valid.  Now requires
    3453 that they have magnitude no larger than 10 times the maximum data size along
    3454 the 3 axes.  Formerly use limit of 1 times original axis data size for each
    3455 axis.  Fixes bug 4473. TG
    3456 <li><p>Replaced HDF file reader with two file readers that use HDF: 1) EMAN HDF
    3457 and 2) Chimera map format.  TG
    3458 <li><p>Added Chimera map file writer.
    3459 <li><p>Made movie recorder encode from jpeg images.  Fixes bug 4284.  TG
    3460 <li><p>Made surface color properly handle volume data set that is closed
    3461 while it is being used for automatic color updates.  TG
    3462 </ul>
    3463 
    3464 <p><b>September 10, 2007.  Version 1.2445.</b></p>
    3465 
    3466 <ul type=None>
    3467 <li><p>Clamped colormap size for solid rendering of volumes to maximum
    3468 reported by OpenGL.  Fixed bug 4324. TG
    3469 <li><p>Fixed volume path tracer bug where adding third marker set sometimes
    3470 caused dialog to go into infinite resizing loop adding and removing a
    3471 scrollbar.  Fixes bug 3305. TG
    3472 </ul>
    3473 
    3474 <p><b>September 7, 2007.  Version 1.2445.</b></p>
    3475 
    3476 <ul type=None>
    3477 <li><p>Made opening volume data set with a Chimera command or on the Chimera
    3478 command-line give a explanatory error message instead of a Python traceback.
    3479 Fixes bug 4450. TG
    3480 </ul>
    3481 
    3482 <p><b>September 5, 2007.  Version 1.2445.</b></p>
    3483 
    3484 <ul type=None>
    3485 <li><p>Made volume command keywords not have underscores, and not be
    3486 case sensitive, and allow unique prefix abbreviations. TG
    3487 <li><p>Made volume command color
    3488 options accept values "colorpanel", "fromeditor", or "editor" in which
    3489 case color is taken from color dialog.  Also can now use color names
    3490 defined with Chimera colordef command. TG
    3491 <li><p>Made volume command save path option accept
    3492 "browse" or "browser" in which case a modal save file dialog is opened
    3493 to choose the file. TG
    3494 <li><p>Fixed bug saving sessions when volume dialog shown but no volumes
    3495 are opened. TG
    3496 <li><p>Made volume crop button use a circumscribing data axis aligned box
    3497 when selection box has been rotated.  TG
    3498 </ul>
    3499 
    3500 <p><b>September 4, 2007.  Version 1.2443.</b></p>
    3501 
    3502 <ul type=None>
    3503 <li><p>Added subregion selection panel controls to copy subregions that
    3504 are not aligned with the data axes.  New controls are "rotate selection box"
    3505 switch, "resample voxel size" entry, and "resample" button. TG
    3506 <li><p>Made mrc, netcdf and hdf file reader and writer code save and
    3507 restore data rotation. TG
    3508 <li><p>Made solid style volume rendering correctly display skewed data,
    3509 common with crystallographic density maps. TG
    3510 <li><p>Eliminated "double" and "half" button on subregion selection panel
    3511 to reduce crowding.  Rarely used. TG
    3512 <li><p>Allow unicode volume files names. Fixes bug 4433. TG
    3513 </ul>
    3514 
    3515 <p><b>August 24, 2007.  Version 1.2442.</b></p>
    3516 
    3517 <ul type=None>
    3518 <li><p>Added "volume" command to change all rendering settings of volume
    3519 data, that can be changed with the volume dialog. TG
    3520 <li><p>Made volume object a subclass of surface model.  This allows
    3521 extension code to more easily obtain the volume object from the list
    3522 of open models with chimera.openModels.list(). TG
    3523 </ul>
    3524 
    3525 <p><b>August 23, 2007.  Version 1.2441.</b></p>
    3526 
    3527 <ul type=None>
    3528 <li><p>Changed volume code so that Chimera "open" command can assign model
    3529 id numbers when opening volume data. TG
    3530 <li><p>Simplified volume data python interface so extensions do not need
    3531 to use volume viewer dialog. TG
    3532 </ul>
    3533 
    3534 <p><b>August 10, 2007.  Version 1.2437.</b></p>
    3535 
    3536 <ul type=None>
    3537 <li><p>Made volume dialog display histograms for multiple data sets.
    3538 A single line above each histogram shows the data name, size, step menu,
    3539 visibility (eye icon) and close map button (dash icon).  Up to 3 histograms
    3540 are shown, and this limit can be changed with a new display options setting.
    3541 The "active" data set has a white background behind its name.  The level
    3542 entry field and color button and rendering options shown in the dialog
    3543 effect only the active data set.  There is no provision for changing the
    3544 settings for multiple data sets at the same time. TG
    3545 <li><p>Removed Show and Unshow buttons from bottom of dialog.  Replaced
    3546 by "eye" icon button above each data histogram to show/unshow data.
    3547 Eye icon has white background when data is shown. TG
    3548 <li><p>Eliminated data menu panel which also showed data size and step.  Added a
    3549 Data menu to the dialog menu bar.  The size and step is now shown above each
    3550 histogram. TG
    3551 <li><p>Moved display style panel (surface/mesh/solid) below histograms.  Formerly
    3552 it was above histograms.  Better to put the most useful data sets info at
    3553 the top.  Display style is now closer to color and threshold settings. TG
    3554 
    3555 <li><p>Changed display stye heading from "Show: *surface  *mesh  *solid" to
    3556 "Style: *surface  *mesh  *solid".
    3557 <li><p>Fixed newly introduced bug in UHBD volume file reader.  TG
    3558 </ul>
    3559 
    3560 <p><b>August 9, 2007.  Version 1.2436.</b></p>
    3561 
    3562 <ul type=None>
    3563 <li><p>Made volume data size show as a single number with superscript 3
    3564 if size is the same along all three axes. TG
    3565 <li><p>Made moving volume plane slider or changing plane axis not automatically
    3566 activate plane display.  Avoids unintended switch into plane mode. TG
    3567 <li><p>Made sample grid points always have indices that are multiples of
    3568 step size.  Formerly if a volume subregion had an origin that was not a
    3569 multiple of the step size then the sample point included that origin.
    3570 This change makes precomputed subsamples behave the same way as
    3571 subsamples extracted from full resolution arrays. TG
    3572 </ul>
    3573 
    3574 <p><b>August 8, 2007.  Version 1.2436.</b></p>
    3575 
    3576 <ul type=None>
    3577 
    3578 <li><p>Made volume plane display checkbutton update when volume region
    3579 changed using other interfaces such as subregion selection "Full"
    3580 button. TG
    3581 <li><p>Made volume dialog File / Open map dialog close as soon as file
    3582 is chosen.  Formerly it waited to see if the open succeeded.  TG
    3583 </ul>
    3584 
    3585 <p><b>August 6, 2007.  Version 1.2434.</b></p>
    3586 
    3587 <ul type=None>
    3588 <li><p>Made volume plane display to respect auto step size adjustment to
    3589 achieve the user-requested voxel limit.  Formerly plane display did not adjust
    3590 the step size. TG
    3591 <li><p>Fixed newly introduce volume data caching bug seen when requested
    3592 data and cache data have different origins and step sizes. TG
    3593 </ul>
    3594 
    3595 <p><b>August 3, 2007.  Version 1.2434.</b></p>
    3596 
    3597 <ul type=None>
    3598 <li><p>Added volume file reader for HDF5 format used by EMAN and SPARX. TG
    3599 
    3600 <li><p>Added third party HDF5 library and PyTables 2.0 python module
    3601 (interface to hdf5) to the Chimera distribution. TG
    3602 </ul>
    3603 
    3604 <p><b>August 2, 2007.  Version 1.2434.</b></p>
    3605 
    3606 <ul type=None>
    3607 <li><p>Changed volume solid rendering transparency so that voxel brightness
    3608 is now multiplied by opacity.  This makes more transparent voxels dimmer.
    3609 This mode is now the default.  The former mode can be enabled by turning off
    3610 the new "Dim transparent voxels" setting under "Solid rendering options". TG
    3611 <li><p>Changed the effect of the transparency slider for solid volume
    3612 rendering.  It now is a fraction of displayed data thickness while formerly
    3613 it was a thickness value.  The fraction times the number of planes (minimum
    3614 for 3 axes) gives a depth in planes that is used as an exponent to modulate
    3615 transparency.  Transfer function (1-alpha) is mapped to (1-alpha)**(1/planes).
    3616 If the planes values is 2 this means that the new transparency will require
    3617 2 planes to block as much light as the same amount of light as one plane
    3618 using the unmodified transfer function. TG
    3619 <li>Changed default solid rendering transfer function ramp.  Now
    3620 starts at rank 10% data value ramping up to full brightness at rank
    3621 99% and continuing to the maximum data value at full brightness.
    3622 With new default transparency mode this provides reasonable
    3623 brightness views of single planes or full maps. TG
    3624 <li><p>Renamed volume viewer "Transparency Factor" (surface rendering) and
    3625 "Transparency Depth" (solid rendering) slider headings to "Transparency". TG
    3626 </ul>
    3627 
    3628 <p><b>July 31, 2007.  Version 1.2430.</b></p>
    3629 
    3630 <ul type=None>
    3631 
    3632 <li><p>Made reading volume data with step size greater than 1 only allocate
    3633 space for the subsampled data.  Formerly the full size data set would be
    3634 read into memory.  The new behavior permits display of data sets larger than
    3635 will fit in memory. TG
    3636 <li><p>Made reading binary volume files report progress every 0.2 seconds
    3637 or every data z plane read, which ever is longer.  Previously used a less
    3638 reliable estimate for frequency of messages based on bytes of data read.  TG
    3639 <li><p>Fixed bug where scale bar value-changed callback occurs when scale
    3640 limits are updated if the old scale value does not lie within the limits.
    3641 Observed for volume z plane slider when switching between data sets. TG
    3642 </ul>
    3643 
    3644 <p><b>July 27, 2007.  Version 1.2430.</b></p>
    3645 
    3646 <ul type=None>
    3647 <li><p>Made movie recorder turn off raytrace preview overriding the
    3648 user preference. TG
    3649 <li><p>Made "movie encode" command implicitly do a "movie stop" before
    3650 encoding.  Formerly, frame capture continued while encoding was done.  TG
    3651 </ul>
    3652 
    3653 <p><b>July 26, 2007.  Version 1.2430.</b></p>
    3654 
    3655 <ul type=None>
    3656 
    3657 <li><p>Added z plane panel to volume viewer.  Allows quick switching between
    3658 individual data z planes shown using solid rendering by moving a slider. TG
    3659 <li><p>Added volume viewer option to initially display a single z plane when
    3660 opening data sets larger than 256 Mvoxels. TG
    3661 </ul>
    3662 
    3663 <p><b>July 25, 2007.  Version 1.2430.</b></p>
    3664 
    3665 <ul type=None>
    3666 <li><p>Made volume dialog not transiently resize when displayed for the first
    3667 time. TG
    3668 <li><p>Made volume "show data when opened if smaller than X Mvoxels" use
    3669 size of subsampled data if a precomputed subsample file is being read. TG
    3670 </ul>
    3671 
    3672 <p><b>July 24, 2007.  Version 1.2430.</b></p>
    3673 
    3674 <ul type=None>
    3675 <li><p>Made volume step size menu add entries for new step sizes that are
    3676 entered using the region bounds panel. TG
    3677 
    3678 <li><p>Made volume region bounds panel not deactivate auto-step adjustment
    3679 when new bounds are entered by step values are left the same.  TG
    3680 <li><p>Added user-friendly error message when allocating an array for
    3681 reading a volume data set fails.  TG
    3682 </ul>
    3683 
    3684 <p><b>July 23, 2007.  Version 1.2430.</b></p>
    3685 
    3686 <ul type=None>
    3687 <li><p>Made each volume have its own auto-adjust step size setting.  Formerly
    3688 all volumes used the dialog setting. TG
    3689 <li><p>Made newly opened volumes use the default rendering options instead
    3690 of the options currently set in the volume dialog. Definitely want this
    3691 behavior for auto-adjust step, but no so clear for smoothing, outline box,
    3692 others. TG
    3693 <li><p>Fixed bug where canceling volume file read disabled updates of volume
    3694 display when threshold or step size changed. TG
    3695 </ul>
    3696 
    3697 <p><b>July 21, 2007.  Version 1.2430.</b></p>
    3698 
    3699 <ul type=None>
    3700 
    3701 <li><p>Added volume file reader for stacks of TIFF images. TG
    3702 <li><p>Added progress report status-line messages when reading volume files.
    3703 <li><p>Added cancel link (in blue) in volume progress status messages. TG
    3704 <li><p>Added support for multi-color status-line messages and detecting
    3705 mouse clicks on parts of status-line messages. TG
    3706 <li><p>Made writing MRC or NetCDF volume file read and write one z-plane
    3707 at a time to allow writing files larger than can fit in memory. TG
    3708 <li><p>Changed volume viewer dialog "step" menu entries to be just a single
    3709 number instead of 3 numbers if steps along all 3 axes are the same
    3710 (e.g. 2 instead of 2 2 2). TG
    3711 <li><p>Eliminated parentheses around volume size shown in volume dialog. TG
    3712 <li><p>Eliminated "ctrl-click on histogram to add or delete thresholds" message
    3713 from volume dialog.  Not worth the dialog space.  TG
    3714 <li><p>Multi-component volume data files are now appear as separate data sets
    3715 for each component.  This effects multi-wavelength optical microscopy files
    3716 in Priism format.  One histogram is displayed in the volume dialog instead
    3717 of multiple histograms. TG
    3718 </ul>
    3719 
    3720 <p><b>July 17, 2007.  Version 1.2430.</b></p>
    3721 
    3722 <ul type=None>
    3723 <li><p>Fixed movie recorder bug when using raytracing and encoding with
    3724 "play forward and backward".  GNAT 4208. TG
    3725 </ul>
    3726 
    3727 <p><b>July 7, 2007.  Version 1.2425.</b></p>
    3728 
    3729 <ul type=None>
    3730 <li><p>Made single plane volume data sets display using "solid" rendering
    3731 style even if dialog is set to surface or mesh.  Helpful for looking at EM
    3732 micrographs. TG
    3733 </ul>
    3734 
    3735 <p><b>July 2, 2007.  Version 1.2425.</b></p>
    3736 
    3737 <ul type=None>
    3738 <li><p>Made volume and multiscale surface models allow variable thickness
    3739 silhouette edges. TG
    3740 </ul>
    3741 
    3742 <p><b>June 1, 2007.  Version 1.2417.</b></p>
    3743 
    3744 <ul type=None>
    3745 <li><p>Fixed volume path tracer marker placement when per-model clipping
    3746 and solid rendering used.  Was ignoring per-model clip plane. TG
    3747 <li><p>Made volume path tracer marker placement with solid rendering use
    3748 threshold level given by the lowest node in the solid transfer function
    3749 with brightness > 0.  Formerly was using surface threshold. TG
    3750 <li><p>Made volume gOpenMol file reader provide a user-friendly error
    3751 message when reading an empty file.  GNAT 3952.  TG
    3752 </ul>
    3753 
    3754 <p><b>May 24, 2007.  Version 1.2416.</b></p>
    3755 
    3756 <ul type=None>
    3757 <li><p>Fixed volume path tracer test suite test.  Use of deprecated Python
    3758 os.tmpnam() on Windows Vista gave unwritable file.  TG
    3759 </ul>
    3760 
    3761 <p><b>May 17, 2007.  Version 1.2412.</b></p>
    3762 
    3763 <ul type=None>
    3764 <li><p>Fixed mesh benchmark divide by zero that occured with defective
    3765 graphics driver that could not render mesh. TG
    3766 </ul>
    3767 
    3768 <p><b>May 15, 2007.  Version 1.2411.</b></p>
    3769 
    3770 <ul type=None>
    3771 <li><p>Fixed 64-bit Linux dependency on system lapack / blas libraries. TG
    3772 </ul>
    3773 
    3774 <p><b>May 14, 2007.  Version 1.2410.</b></p>
    3775 
    3776 <ul type=None>
    3777 <li><p>Fixed movie command bug where (unnecessary) movie reset command
    3778 issued after movie encode command which was still working in background.
    3779 GNAT 3873.  TG
    3780 </ul>
    3781 
    3782 <p><b>May 9, 2007.  Experimental feature.</b></p>
    3783 
    3784 <ul type=None>
    3785 <li><p>Enhanced IMOD segmentation file reader to read contours and points,
    3786 creating a volume path tracer model. TG
    3787 </ul>
    3788 
    3789 <p><b>May 8, 2007.  Version 1.2399.</b></p>
    3790 
    3791 <ul type=None>
    3792 <li><p>Made closing volume path tracer dialog turn off the marker placement
    3793 mouse mode.  Reshowing the dialog turns the mouse mode back on. TG
    3794 <li><p>Renamed button on movie recorder output path browse dialog
    3795 from Save to Set Movie Path.  Bug #2270. TG
    3796 <li><p>Fixed bug #3833 where volume menu it fit map in map tool did not update
    3797 after a volume was closed.  Made volume menus in fit map, values at atom
    3798 positions, and morph map dialog automatically update as soon as a volume data
    3799 set is opened or closed. TG
    3800 </ul>
    3801 
    3802 <p><b>May 1, 2007.  Version 1.2392.</b></p>
    3803 
    3804 <ul type=None>
    3805 <li><p>Fixed bug in bondzone command where "if array:" construct used to
    3806 test if array is non-empty.  Bug introduced with switch from Numeric to
    3807 Numpy library.  TG
    3808 </ul>
    3809 
    3810 <p><b>April 30, 2007.  Version 1.2388.</b></p>
    3811 
    3812 <ul type=None>
    3813 <li><p>Fixed bug opening biological unit model from PQS database using
    3814 id on command-line (e.g. "open pqsID:104l") TG
    3815 </ul>
    3816 
    3817 <p><b>April 27, 2007.  Version 1.2388.</b></p>
    3818 
    3819 <ul type=None>
    3820 <li><p>Added code to check the Mac Python crash log to see if the last
    3821 invocation of Chimera ended in a crash.  If so, a dialog appears the next
    3822 time they run Chimera allowing them to report the crash including the
    3823 crash log. TG
    3824 <li><p>Added xray fo-fc difference maps from the Uppsala Electron
    3825 Density Server to File / Fetch by Id. TG
    3826 <li><p>Added biological unit PDB files from the Probably Quaternary Structure
    3827 (PQS) server to File / Fetch by Id. TG
    3828 </ul>
    3829 
    3830 <p><b>April 26, 2007.  Version 1.2388.</b></p>
    3831 
    3832 <ul type=None>
    3833 <li><p>Fixed bug #3808 where movie recorder "play forward then backward"
    3834 option caused error on Windows. TG
    3835 <li><p>Fixed bug #3812 where default movie recorder output movie file location
    3836 is unwritable on Windows Vista. TG
    3837 </ul>
    3838 
    3839 <p><b>April 25, 2007.  Version 1.2384.</b></p>
    3840 
    3841 <ul type=None>
    3842 <li><p>Made opening APBS, DelPhi, or UBHD electrostatic potential files
    3843 show surface color dialog instead of volume viewer. TG
    3844 </ul>
    3845 
    3846 <p><b>April 11, 2007.  Version 1.2375.</b></p>
    3847 
    3848 <ul type=None>
    3849 <li><p>Changed movie recorder default image file format to PPM.  Typically 3x faster image capture than with PNG image format, probably because of time spent compressing image. TG
    3850 <li><p>Bug fix.  Nucleic acid blobs reschains.py error when scale bar shown. TG
    3851 <li><p>Bug #3775 fixed.  Fit model in map when map not shown. TG
    3852 </ul>
    3853 
    3854 <p><b>April 9, 2007.  Version 1.2373.</b></p>
    3855 
    3856 <ul type=None>
    3857 
    3858 <li><p>Added button to movie recorder to show raytracing preferences. TG
    3859 <li><p>Suppressed image saving status messages when capturing with movie recorder. TG
    3860 <li><p>Change movie command "loop" keyword to "roundtrip". TG
    3861 </ul>
    3862 
    3863 <p><b>April 6, 2007.  Version 1.2372.</b></p>
    3864 
    3865 <ul type=None>
    3866 <li><p>Included C++ header files in Chimera distributions. TG
    3867 <li><p>Restricted movie recorder to PNG image format when raytracing. TG
    3868 </ul>
    3869 
    3870 <p><b>April 5, 2007.  Version 1.2370.</b></p>
    3871 
    3872 <ul type=None>
    3873 
    3874 <li><p>Added movie recorder option to play frames forward then backward when encoding. Also added movie command "loop" option to permit this. TG
    3875 <li><p>Added raytracing option to movie recorder. TG
    3876 </ul>
    3877 
    3878 <p><b>April 3, 2007.  Version 1.2369.</b></p>
    3879 
    3880 <ul type=None>
    3881 <li><p>Added supersampling option to movie recorder. TG
    3882 </ul>
    3883 
    3884 <p><b>March 28, 2007.  Version 1.2366.</b></p>
    3885 
    3886 <ul type=None>
    3887 <li><p>Made volume viewer, scale bar, path tracer, and multiscale use model number offset when restoring a session an merging an already opened session.  TG
    3888 <li><p>Made scale bar, path tracer, and multiscale preserve model numbers when
    3889 session is restored. TG
    3890 
    3891 </ul>
    3892 
    3893 <p><b>March 27, 2007.  Version 1.2365.</b></p>
    3894 
    3895 <ul type=None>
    3896 <li><p>Made measure volume/area tool automatically update as surface changes. TG
    3897 </ul>
    3898 
    3899 <p><b>March 9, 2007.  Version 1.2354.</b></p>
    3900 
    3901 <ul type=None>
    3902 <li><p>Made session restore of volume data sets use original model numbers. TG
    3903 </ul>
    3904 
    3905 }}}