Changes between Initial Version and Version 1 of oldchangelog


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Timestamp:
Sep 23, 2011, 11:37:20 AM (15 years ago)
Author:
goddard
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  • oldchangelog

    v1 v1  
     1= 2007 - 2010 Chimera Change Log =
     2
     3The following hand maintained list of changes was discontinued in Nov 2010,
     4replaced by a new [wiki:changelog change log] generated from our Trac ticket database.
     5
     6{{{
     7#!html
     8
     9<p>
     10This page lists changes to Chimera that are visible to users, including the
     11date and Chimera version when the change was checked in, and who made the
     12change (TG = Tom Goddard, AL = Andrew Ling).
     13
     14<p><b>November 18, 2010</b></p>
     15<ul type=None>
     16<li><p>Fixed center of rotation command when only bond selected.
     17</ul>
     18
     19<p><b>November 17, 2010</b></p>
     20<ul type=None>
     21<li><p>Added memory error check in benchmark scene drawing.
     22</ul>
     23
     24<p><b>November 16, 2010</b></p>
     25<ul type=None>
     26<li><p>Added mean and standard deviation density calc for segmentation regions.
     27<li><p>Allowed fractional step in volume planes.
     28</ul>
     29
     30<p><b>November 15, 2010</b></p>
     31<ul type=None>
     32<li><p>Fixed context help crash on mac, removed menu entry.
     33<li><p>Added warning for invalid cell angles in mrc file.
     34</ul>
     35
     36<p><b>November 12, 2010</b></p>
     37<ul type=None>
     38<li><p>Added volume flattening divide method, applied to termite gut.
     39</ul>
     40
     41<p><b>November 10, 2010</b></p>
     42<ul type=None>
     43<li><p>Improved attribute table and orthoslice viewing.
     44</ul>
     45
     46<p><b>November 9, 2010</b></p>
     47<ul type=None>
     48<li><p>Worked around netcdf volume reading bug, ScientificPython.
     49</ul>
     50
     51<p><b>November 5, 2010</b></p>
     52<ul type=None>
     53<li><p>Added segment sliceview command to make montage images.
     54<li><p>Added resize capability to segmentation image viewer.
     55<li><p>Fixed pick blobs error when everything is clipped.
     56<li><p>Fixed tiling order in orthoslice script, termite gut montages.
     57<li><p>Added fill order option to vop tile command.
     58</ul>
     59
     60<p><b>November 3, 2010</b></p>
     61<ul type=None>
     62<li><p>Made measure contactarea ignore outline boxes.
     63</ul>
     64
     65<p><b>November 2, 2010</b></p>
     66<ul type=None>
     67<li><p>Improved measure contact area patch smoothness.
     68<li><p>Added new color patterns for color by direction.
     69<li><p>Added vop tile operation to make section image montages.
     70</ul>
     71
     72<p><b>November 1, 2010</b></p>
     73<ul type=None>
     74<li><p>Fixed error reporting to include callback info.
     75<li><p>Added segment directioncolor command.
     76</ul>
     77
     78<p><b>October 29, 2010</b></p>
     79<ul type=None>
     80<li><p>Added measure distance command.
     81</ul>
     82
     83<p><b>October 28, 2010</b></p>
     84<ul type=None>
     85<li><p>Fixed segmentation attribute table error for closed segmentation.
     86</ul>
     87
     88<p><b>October 27, 2010</b></p>
     89<ul type=None>
     90<li><p>Implemented zone command.
     91</ul>
     92
     93<p><b>October 26, 2010</b></p>
     94<ul type=None>
     95<li><p>Made segmentation attribute table remove unused columns.
     96</ul>
     97
     98<p><b>October 22, 2010</b></p>
     99<ul type=None>
     100<li><p>Fixed morph map hang.
     101</ul>
     102
     103<p><b>October 19, 2010</b></p>
     104<ul type=None>
     105<li><p>Debugged and fixed ScientificPython netcdf bindings code, 64-bit Windows.
     106</ul>
     107
     108<p><b>October 11, 2010</b></p>
     109<ul type=None>
     110<li><p>Made mouse segmentation avoid showing all watershed regions.
     111</ul>
     112
     113<p><b>October 6, 2010</b></p>
     114<ul type=None>
     115<li><p>Added measure command contact area operation.
     116<li><p>Made contact area account for partial triangles.
     117</ul>
     118
     119<p><b>October 5, 2010</b></p>
     120<ul type=None>
     121<li><p>Improved error message when fetch from emdb fails.
     122<li><p>Fixed tube and ribbon shape ignoring specfied color with follow bonds.
     123</ul>
     124
     125<p><b>October 4, 2010</b></p>
     126<ul type=None>
     127<li><p>Fixed shape tube followbonds option, ribbon band coloring.
     128<li><p>Fixed multiscale colors, made 64-bit same as 32-bit.
     129</ul>
     130
     131<p><b>October 1, 2010</b></p>
     132<ul type=None>
     133<li><p>Added images to region attribute table and segmentation files.
     134<li><p>Added error handling when map size wrong when masking to region.
     135</ul>
     136
     137<p><b>September 30, 2010</b></p>
     138<ul type=None>
     139<li><p>Added exporting region attributes as comma separated values.
     140<li><p>Implemented read and write of segmentation region attributes in hdf5.
     141<li><p>Simplified region attribute filter syntax, no more function calls.
     142</ul>
     143
     144<p><b>September 29, 2010</b></p>
     145<ul type=None>
     146<li><p>Made measure spine region attributes appear in region list.
     147<li><p>Fixed sym command bug, two models for coord sys arg.
     148<li><p>Added filtering to region attribute list.
     149</ul>
     150
     151<p><b>September 28, 2010</b></p>
     152<ul type=None>
     153<li><p>Made segmentation attribute browser using sortable table.
     154</ul>
     155
     156<p><b>September 27, 2010</b></p>
     157<ul type=None>
     158<li><p>Checked in ribbon slice and curvature code.
     159</ul>
     160
     161<p><b>September 24, 2010</b></p>
     162<ul type=None>
     163<li><p>Updated segger in chimera, segment unbin and show all fixes.
     164</ul>
     165
     166<p><b>September 23, 2010</b></p>
     167<ul type=None>
     168<li><p>Fixed headless chimera movie recording.
     169</ul>
     170
     171<p><b>September 22, 2010</b></p>
     172<ul type=None>
     173<li><p>Added curvature measurement to measure spine calculation.
     174<li><p>Implemented shape ribbon command to show bacteria center slices.
     175</ul>
     176
     177<p><b>September 21, 2010</b></p>
     178<ul type=None>
     179<li><p>Added rectangle to shape command.
     180<li><p>Added connection failed error message, fit pdbs from emdb web service.
     181<li><p>Fixed byte order of machst in mrc files written by chimera.
     182<li><p>Made mac use immediate mode surf rendering for small surface pieces.
     183</ul>
     184
     185<p><b>September 17, 2010</b></p>
     186<ul type=None>
     187<li><p>Fixed segment unbin so it shows region surfaces.
     188</ul>
     189
     190<p><b>September 15, 2010</b></p>
     191<ul type=None>
     192<li><p>Fixed natural spline with single point, caused fly error.
     193<li><p>Fixed bug where mask ijk to xyz transform wrong when map closed.
     194<li><p>Fixed fit to segments closed mol, list reg number, transpar bugs.
     195</ul>
     196
     197<p><b>September 14, 2010</b></p>
     198<ul type=None>
     199<li><p>Fixed fit to segments save fits menu entry.
     200</ul>
     201
     202<p><b>September 13, 2010</b></p>
     203<ul type=None>
     204<li><p>Better error message when unable to write marker file.
     205<li><p>Fixed emdb fetch error causing hang.
     206<li><p>Fixed volume dialog session save with 2-d image stack.
     207<li><p>Fixed multiscale bug deleting chains.
     208<li><p>Fixed volume tracer bug opening marker set.
     209</ul>
     210
     211<p><b>August 27, 2010</b></p>
     212<ul type=None>
     213<li><p>Allowed multiscale model creation without multiscale dialog existing,
     214allows nogui or headless Chimera use.
     215<li><p>Added surfaces keyword option to sym command for multiscale surfaces.
     216<li><p>Added biological unit button to model panel.
     217<li><p>Made multiscale use task manager when creating copies of molecules.
     218</ul>
     219
     220<p><b>August 25, 2010</b></p>
     221<ul type=None>
     222<li><p>Fixed eman hdf file reading, python 2.7 / idle error.
     223</ul>
     224
     225<p><b>August 6, 2010</b></p>
     226<ul type=None>
     227<li><p>Added list of fits to fit to segments dialog.
     228<li><p>Made volume dialog show value type in balloon when mouse over "Range"
     229dialog label (below histogram).
     230<li><p>Made gaussian filter use original data value type by default.  Formerly
     231it created a map with 32-bit float.
     232</ul>
     233
     234<p><b>August 4, 2010</b></p>
     235<ul type=None>
     236<li><p>Fixed make transparent / opaque segment map menu entries when nothing selected.
     237</ul>
     238
     239<p><b>August 3, 2010</b></p>
     240<ul type=None>
     241<li><p>Fixed fly command quaternion rotation interpolation.  Sometimes twirled
     242360 degrees for close orientations.
     243<li><p>Made fly command using natural cubic spline instead of Overhauser spline
     244for smoother paths.
     245<li><p>Made command file error halt processing and report error in reply log.
     246Formerly command processing continued even after an error in a script.
     247</ul>
     248
     249<p><b>August 2, 2010</b></p>
     250<ul type=None>
     251<li><p>Fixed saving masked region with segment map dialog, bounds were wrong.
     252<li><p>Fixed render by attribute, numpy 1.4.1 int/long type problem.
     253<li><p>Fixed show adjacent error in segment map when some regions have no contacts.
     254<li><p>Fixed empty segmentation menu in segment map dialog.
     255<li><p>Fixed segment map hide menu entry not working on grouped regions.
     256<li><p>Fixed segger color density map error, numpy int/long problem.
     257</ul>
     258
     259<p><b>July 27, 2010</b></p>
     260<ul type=None>
     261<li><p>Fixed watershed calc error 32-bit only, numpy 1.4 type error int/long.
     262</ul>
     263
     264<p><b>July 22, 2010</b></p>
     265<ul type=None>
     266<li><p>Added movie crossfade command.
     267</ul>
     268
     269<p><b>July 19, 2010</b></p>
     270<ul type=None>
     271<li><p>Fixed python 2.7 msms surface error on Windows.  Method for suppressing
     272console window for mscalc program no longer valid in python 2.7.
     273</ul>
     274
     275<p><b>July 15, 2010</b></p>
     276<ul type=None>
     277<li><p>Made segment mouse mode accept clicks on single-plane volume.
     278<li><p>Fixed bug in solid coloring using mask, array size mismatch.
     279<li><p>Made group/ungroup buttons work when grouped subregions selected.
     280</ul>
     281
     282<p><b>July 13, 2010</b></p>
     283<ul type=None>
     284<li><p>Implemented segment command unbin operation to apply a mask computed
     285on binned volume data to produce mask for the original full size volume data.
     286<li><p>Fixed coordset holdSteady option when jumping to a single frame.
     287</ul>
     288
     289<p><b>July 9, 2010</b></p>
     290<ul type=None>
     291<li><p>Made segmentation not keep grid indices for each region.  This reduces
     292memory use of the segment map tool.
     293</ul>
     294
     295<p><b>July 7, 2010</b></p>
     296<ul type=None>
     297<li><p>Added solid style volume coloring using a segmentation to the segment
     298map dialog (color density menu entry).  Formerly only colored volume surfaces.
     299</ul>
     300
     301<p><b>July 6, 2010</b></p>
     302<ul type=None>
     303<li><p>Optimized measure spine command using small c++ routine, 59x faster.
     304</ul>
     305
     306<p><b>July 2, 2010</b></p>
     307<ul type=None>
     308<li><p>Made spine diameter report orthogonal diameters at mid-point along
     309computed spine.
     310</ul>
     311
     312<p><b>July 1, 2010</b></p>
     313<ul type=None>
     314<li><p>Made measure spine not need segmentation map open.
     315</ul>
     316
     317<p><b>June 29, 2010</b></p>
     318<ul type=None>
     319<li><p>Fixed two bugs in fit to segments, neg corr, molmap replace
     320</ul>
     321
     322<p><b>June 25, 2010</b></p>
     323<ul type=None>
     324<li><p>Improved imod seg file reader error message for non-IMOD files
     325<li><p>Made render-by-attribute dialog handle segmentation regions
     326</ul>
     327
     328<p><b>June 23, 2010</b></p>
     329<ul type=None>
     330<li><p>Fixed solid volume memory leak, Solid.matrix held reference
     331<li><p>Made flatten filter use 64-bit float, needed for large maps
     332<li><p>Added measure spine command to compute bacteria paths and lengths
     333</ul>
     334
     335<p><b>June 22, 2010</b></p>
     336<ul type=None>
     337<li><p>Made masking to regions handle full res maps with binned masks
     338</ul>
     339
     340<p><b>June 21, 2010</b></p>
     341<ul type=None>
     342<li><p>Fixed dbpuppet ac_key_error messages, Laura Morris
     343<li><p>Implemented natural cubic spline, smoother than Overhauser spline
     344<li><p>Added vop unbend operation, straighten bacteria
     345<li><p>Wrote code to trace spine of bacteria automatically
     346</ul>
     347
     348<p><b>June 17, 2010</b></p>
     349<ul type=None>
     350<li><p>Wrote code to unbend volume along path for straightening bacteria
     351</ul>
     352
     353<p><b>June 1, 2010</b></p>
     354<ul type=None>
     355<li><p>Made segment mouse click on background show only ungrouped regions
     356</ul>
     357
     358<p><b>June 14, 2010</b></p>
     359<ul type=None>
     360<li><p>Fixed cocoa open dialog nsscroller mouse click crashes
     361<li><p>Added segger to chimera distribution
     362</ul>
     363
     364<p><b>June 10, 2010</b></p>
     365<ul type=None>
     366<li><p>Added "3d" shortcut to toggle between sequential stereo and mono
     367</ul>
     368
     369<p><b>June 2, 2010</b></p>
     370<ul type=None>
     371<li><p>Fixed region delete bug in segment map
     372<li><p>Added flatten operation to volume filter dialog and vop command
     373<li><p>Improved mouse segmentation grouping to avoid start of drag abrupt group size change
     374</ul>
     375
     376<p><b>June 1, 2010</b></p>
     377<ul type=None>
     378<li><p>Added gui for enabling segment grouping mouse mode
     379<li><p>Added ability to read old segger 1.4 regions files
     380</ul>
     381
     382<p><b>May 28, 2010</b></p>
     383<ul type=None>
     384<li><p>Fixed mac universal build, tcltk docs not installed for debug version
     385<li><p>Added menu entries to show grouped and ungrouped segmentation surfaces
     386<li><p>Improved measure and color blobs to report sizes, boundary lengths
     387</ul>
     388
     389<p><b>May 27, 2010</b></p>
     390<ul type=None>
     391<li><p>Allowed mouse mode grouping of single regions for blocking growth
     392<li><p>Made segment command to group regions using a second segmentation
     393<li><p>Fixed surface model front center, not ignoring hidden surface pieces
     394</ul>
     395
     396<p><b>May 26, 2010</b></p>
     397<ul type=None>
     398<li><p>Made segmentation mouse mode detect clicked mask region, not density
     399<li><p>Made seg mouse mode show contacting regions after changing a region
     400<li><p>Added boundary region selection to find unclipped bacteria
     401</ul>
     402
     403<p><b>May 21, 2010</b></p>
     404<ul type=None>
     405<li><p>Made mac ppc install debugging tcltk to avoid start-up crash
     406</ul>
     407
     408<p><b>May 19, 2010</b></p>
     409<ul type=None>
     410<li><p>Made linux spacenavigator not print "connect error" to shell
     411<li><p>Made connectivity mouse mode make region groups that can be saved
     412</ul>
     413
     414<p><b>May 13, 2010</b></p>
     415<ul type=None>
     416<li><p>Fixed tix combobox menu behind dialog on cocoa
     417<li><p>Fixed error deleting coord sys model during move command
     418</ul>
     419
     420<p><b>May 12, 2010</b></p>
     421<ul type=None>
     422<li><p>Made debug graphics dialog not appear for new chimera version
     423<li><p>Separated segger into separate segmentation and fitting dialogs
     424</ul>
     425
     426<p><b>May 11, 2010</b></p>
     427<ul type=None>
     428<li><p>Fixed cocoa inactive menus not gray, tk_setPalette cocoa tk bug
     429</ul>
     430
     431<p><b>May 10, 2010</b></p>
     432<ul type=None>
     433<li><p>Made all chimera builds use tk 8.6
     434<li><p>Eliminated mac carbon builds
     435</ul>
     436
     437<p><b>May 5, 2010</b></p>
     438<ul type=None>
     439<li><p>Made segger group and ungroup buttons change smoothing levels if nothing selected
     440<li><p>Allowed small region removal after segmenting
     441</ul>
     442
     443<p><b>May 4, 2010</b></p>
     444<ul type=None>
     445<li><p>Added density map surface coloring by segmentation region
     446</ul>
     447
     448<p><b>May 3, 2010</b></p>
     449<ul type=None>
     450<li><p>Worked around ctrl double click atom in graphics not showing menu, Eric
     451</ul>
     452
     453<p><b>April 29, 2010</b></p>
     454<ul type=None>
     455<li><p>Fixed segger minimum region size option
     456<li><p>Made changing segger "max regions to display" have immediate effect
     457</ul>
     458
     459<p><b>April 28, 2010</b></p>
     460<ul type=None>
     461<li><p>Optimized segger segmentation speed, about 5x speed-up
     462<li><p>Changed segger hdf5 file format for faster read and write, smaller file
     463</ul>
     464
     465<p><b>April 27, 2010</b></p>
     466<ul type=None>
     467<li><p>Made watershed segmentation use 26 neighbors for local maxima instead of 6
     468<li><p>Added surface granularity parameter to segger
     469</ul>
     470
     471<p><b>April 23, 2010</b></p>
     472<ul type=None>
     473<li><p>Preserved colors when using skeletons to edit a segmentation
     474</ul>
     475
     476<p><b>April 21, 2010</b></p>
     477<ul type=None>
     478<li><p>Made segger read and write segmentation hdf5 file format
     479<li><p>Fixed eman hdf reader, pixel size
     480</ul>
     481
     482<p><b>April 19, 2010</b></p>
     483<ul type=None>
     484<li><p>Eliminated intel and ppc processor-specific mac daily builds from download page
     485</ul>
     486
     487<p><b>April 16, 2010</b></p>
     488<ul type=None>
     489<li><p>Sped up segger grouping by adding track to maximum routine to _segment module
     490<li><p>Avoided creating segger region surfaces unless needed.
     491</ul>
     492
     493<p><b>April 15, 2010</b></p>
     494<ul type=None>
     495<li><p>Fixed linux space nav support, libspnav.so was not distributed
     496</ul>
     497
     498<p><b>April 14, 2010</b></p>
     499<ul type=None>
     500<li><p>Made segger use new C++ module _segment for watershed calculation eliminating need for temporary file
     501</ul>
     502
     503<p><b>April 13, 2010</b></p>
     504<ul type=None>
     505<li><p>Made transform coordinates dialog work with non-molecules
     506<li><p>Added skeleton routines and menu to segger
     507</ul>
     508
     509<p><b>April 6, 2010</b></p>
     510<ul type=None>
     511<li><p>Fixed bug in volume filter casting int16 -> uint16 bug where all values became 65535
     512<li><p>Fixed wrong normals when contouring unsigned data
     513<li><p>Made segger filtering small regions use connected size
     514</ul>
     515
     516<p><b>March 29, 2010</b></p>
     517<ul type=None>
     518<li><p>Fixed fetch directory preference not saving, was requiring Enter key press
     519</ul>
     520
     521<p><b>March 25, 2010</b></p>
     522<ul type=None>
     523<li><p>Fixed bug where center-of-view rotation not updating
     524</ul>
     525
     526<p><b>March 17, 2010. Version 1.5</b></p>
     527<ul type=None>
     528<li><p>Fixed front-center to not move center during rotation.
     529<li><p>Made opening pdb on command-line look for compressed local files.
     530<li><p>Made opening python scripts not clear globals when finished.
     531<li><p>Made turn keyword center accept "view", "models", "front".
     532<li><p>Disabled silhouette outline drawing for volumetric rendering.
     533</ul>
     534
     535<p><b>March 16, 2010. Version 1.5</b></p>
     536<ul type=None>
     537<li><p>Worked around cocoa bug unicode arrow keys in entry fields.
     538<li><p>Fixed saxs profile calc to work with more than one molecule.
     539</ul>
     540
     541<p><b>March 15, 2010. Version 1.5</b></p>
     542<ul type=None>
     543<li><p>Made saxs gui give better error if local execution fails.
     544</ul>
     545
     546<p><b>March 9, 2010. Version 1.5</b></p>
     547<ul type=None>
     548<li><p>Put max number of regions to display in segger dialog.
     549<li><p>Fixed segger bug, grouped regions remain displayed.
     550</ul>
     551
     552<p><b>March 8, 2010. Version 1.5</b></p>
     553<ul type=None>
     554<li><p>Fixed arrow key menu shortcuts / cursor motion bug, cocoa.
     555</ul>
     556
     557<p><b>March 5, 2010. Version 1.5</b></p>
     558<ul type=None>
     559<li><p>Made segger not accumulate smoothing when done twice.
     560</ul>
     561
     562<p><b>March 3, 2010. Version 1.5</b></p>
     563<ul type=None>
     564<li><p>Remade segger dialog, added progress/cancel, menu reset, options pane...
     565<li><p>Made segger save of region and map files show a file chooser dialog.
     566</ul>
     567
     568<p><b>March 2, 2010. Version 1.5</b></p>
     569<ul type=None>
     570<li><p>Fixed missing cocoa menu check-marks, tk patch.
     571<li><p>Made pdb personal directories try hierarchical layout.
     572</ul>
     573
     574<p><b>March 1, 2010. Version 1.5</b></p>
     575<ul type=None>
     576<li><p>Added tk cocoa patch to fix option-e crash.
     577</ul>
     578
     579<p><b>February 23, 2010. Version 1.5</b></p>
     580<ul type=None>
     581<li><p>Made default movie recording use variable bit rate, q = 8.
     582<li><p>Debugged and fixed new ffmpeg bit rate in bits/sec instead of Kbits/sec.
     583</ul>
     584
     585<p><b>February 21, 2010. Version 1.5</b></p>
     586<ul type=None>
     587<li><p>Worked around cocoa user interface lock-out on cocoa.
     588</ul>
     589
     590<p><b>February 19, 2010. Version 1.5</b></p>
     591<ul type=None>
     592<li><p>Made close command accept multiple models.
     593<li><p>Fixed reset command to work with now unhashable xform objects.
     594</ul>
     595
     596<p><b>February 18, 2010. Version 1.5</b></p>
     597<ul type=None>
     598<li><p>Made write command allow "#" preceding model number.
     599</ul>
     600
     601<p><b>February 17, 2010. Version 1.5</b></p>
     602<ul type=None>
     603<li><p>Made segger calculate sim map automatically for groups of regions.
     604<li><p>Made measure inertia report center of ellipsoid.
     605</ul>
     606
     607<p><b>February 8, 2010. Version 1.5</b></p>
     608<ul type=None>
     609<li><p>Changed segger to show pastel region colors.
     610<li><p>Fixed segger axes alignment and normal direction.
     611</ul>
     612
     613<p><b>February 5, 2010. Version 1.5</b></p>
     614<ul type=None>
     615<li><p>Included 32-bit / 64-bit info in benchmark submissions.
     616<li><p>Made chimera About dialog report 32-bit or 64-bit.
     617</ul>
     618
     619<p><b>February 4, 2010. Version 1.5</b></p>
     620<ul type=None>
     621<li><p>Added ppc mac cocoa and cocoa universal daily build targets.
     622</ul>
     623
     624<p><b>February 3, 2010. Version 1.5</b></p>
     625<ul type=None>
     626<li><p>Fixed tk cocoa open/save double click by having no default button.
     627<li><p>Made 17 small user interface improvments to segger.
     628</ul>
     629
     630<p><b>February 1, 2010. Version 1.5</b></p>
     631<ul type=None>
     632<li><p>Added error checking in movie record command option values.
     633</ul>
     634
     635<p><b>January 29, 2010. Version 1.5</b></p>
     636<ul type=None>
     637<li><p>Started 64-bit mac daily builds using Tk Cocoa and NSOPENGL.
     638</ul>
     639
     640<p><b>January 22, 2010. Version 1.5</b></p>
     641<ul type=None>
     642<li><p>Made gaussian cube file reader handle skewed data axes.
     643</ul>
     644
     645<p><b>January 20, 2010. Version 1.5</b></p>
     646<ul type=None>
     647<li><p>Fixed movie recorder dialog bug, director not initialized.
     648</ul>
     649
     650<p><b>January 19, 2010. Version 1.5</b></p>
     651<ul type=None>
     652<li><p>Debugged cocoa actions/color menu not showing, images freed while in use.
     653<li><p>Fixed cocoa application menu and wrong dock icon.
     654</ul>
     655
     656<p><b>January 15, 2010. Version 1.5</b></p>
     657<ul type=None>
     658<li><p>Debugged cocoa model panel wrapped text, patched tix.
     659</ul>
     660
     661<p><b>January 13, 2010. Version 1.5</b></p>
     662<ul type=None>
     663<li><p>Added color images to cocoa chimera color menu.
     664<li><p>Fixed model panel scroll down-only, reported aqua tk bug, 2931538.
     665<li><p>Allowed raytrace and supersample movie record options to change.
     666</ul>
     667
     668<p><b>January 12, 2010. Version 1.5</b></p>
     669<ul type=None>
     670<li><p>SAX dialog fixes, raise dialog, remember empty executable pref.
     671</ul>
     672
     673<p><b>January 11, 2010. Version 1.5</b></p>
     674<ul type=None>
     675<li><p>Started making cocoa daily builds with Tk 8.6.
     676</ul>
     677
     678<p><b>January 6, 2010. Version 1.5</b></p>
     679<ul type=None>
     680<li><p>Added progress/cancel to gaussian filter using new task manager.
     681</ul>
     682
     683<p><b>January 5, 2010. Version 1.4.1</b></p>
     684<ul type=None>
     685<li><p>Made side view cap clipped surfaces button only show dialog.
     686<li><p>Made model panel focus button enable near/far clipping.
     687</ul>
     688
     689<p><b>December 21, 2009. Version 1.5</b></p>
     690<ul type=None>
     691<li><p>Optimized gaussian filter to use efficient fft sizes.
     692<li><p>Made gaussian filter not-cyclic wrap, 2x speed penalty.
     693<li><p>Made gaussian filter more memory efficient, compute one plane at a time.
     694</ul>
     695
     696<p><b>December 15, 2009. Version 1.4.1</b></p>
     697<ul type=None>
     698<li><p>Fixed movie recorder dialog size parsing error.
     699</ul>
     700
     701<p><b>December 9, 2009. Version 1.5</b></p>
     702<ul type=None>
     703<li><p>Fixed keyboard shortcuts dialog to list all shortcuts.
     704<li><p>Added filter entry to keyboard shortcut dialog.
     705</ul>
     706
     707<p><b>December 8, 2009. Version 1.5</b></p>
     708<ul type=None>
     709<li><p>Made volume session not precede relative paths with './' or '.\'.
     710</ul>
     711
     712<p><b>December 4, 2009. Version 1.5</b></p>
     713<ul type=None>
     714<li><p>Made shape command default coordinate system use surface model.
     715</ul>
     716
     717<p><b>December 3, 2009. Version 1.5</b></p>
     718<ul type=None>
     719<li><p>Added rotation, qrotation, name arguments to shape command.
     720<li><p>Added ellipsoid to shape command.
     721</ul>
     722
     723<p><b>November 25, 2009. Version 1.5</b></p>
     724<ul type=None>
     725<li><p>Removed phantom force feedback tool from distribution.
     726</ul>
     727
     728<p><b>November 24, 2009. Version 1.5</b></p>
     729<ul type=None>
     730<li><p>Made top view mode of side view dialog always show focal plane.
     731<li><p>Fixed focal plane behind eye black-out bug.
     732<li><p>Added movement mouse mode to structure editing menu.
     733</ul>
     734
     735<p><b>November 23, 2009. Version 1.4</b></p>
     736<ul type=None>
     737<li><p>Made dialog auto-placement not override session restore placement.
     738<li><p>Made session restore not place dialogs off-screen.
     739</ul>
     740
     741<p><b>November 20, 2009. Version 1.4</b></p>
     742<ul type=None>
     743<li><p>Fixed aqua menu response by delaying menu post by 1 msec.
     744</ul>
     745
     746<p><b>November 17, 2009. Version 1.4</b></p>
     747<ul type=None>
     748<li><p>Fixed front-center rotation updating too often.
     749<li><p>Fixed morph map on volume subregion.
     750</ul>
     751
     752<p><b>November 8, 2009. Version 1.4 and 1.5</b></p>
     753<ul type=None>
     754<li><p>Added use new plot window option to saxs dialog, default false (Chimera 1.5).
     755<li><p>Added mw molecular weight shortcut (Chimera 1.4).
     756</ul>
     757
     758<p><b>November 6, 2009. Version 1.4</b></p>
     759<ul type=None>
     760<li><p>Fixed uninitialized memory errors, no init of surfnet grid.
     761</ul>
     762
     763<p><b>November 3, 2009. Version 1.4</b></p>
     764<ul type=None>
     765<li><p>Added Linux space navigator support.
     766</ul>
     767
     768<p><b>November 2, 2009. Version 1.4</b></p>
     769<ul type=None>
     770<li><p>Fixed morph map error when volume closed during playback
     771</ul>
     772
     773<p><b>October 30, 2009. Version 1.5</b></p>
     774<ul type=None>
     775<li><p>Added fit in map correlation about zero option, the default.
     776<li><p>Made meshmol command produce model with new id number.
     777</ul>
     778
     779<p><b>October 28, 2009. Version 1.5</b></p>
     780<ul type=None>
     781<li><p>Added msms warning message for wrong number of atom areas.
     782<li><p>Optimized memory use in resampling maps.
     783</ul>
     784
     785<p><b>October 16, 2009. Version 1.4</b></p>
     786<ul type=None>
     787<li><p>Made fit map gray out optimize and whole molecule options when not avail.
     788</ul>
     789
     790<p><b>October 15, 2009. Version 1.4</b></p>
     791<ul type=None>
     792<li><p>Removed SAXS module.
     793<li><p>Removed volume processing standalone programs from distribution.
     794</ul>
     795
     796</p>
     797<p><b>October 8, 2009.  Version 1.4</b></p>
     798<ul type=None>
     799<li><p>Made match command showMatrix argument print motion from current position
     800in addition to motion from original file coordinates.
     801<li><p>Don't print rotation when fitting only selected atoms with
     802Fit in Map dialog.
     803</ul>
     804
     805<p><b>October 7, 2009.  Version 1.4</b></p>
     806<ul type=None>
     807<li><p>Added fit dialog option to optimize correlation about zero instead of correlation about mean.
     808<li><p>Made fit dialog option to move only selected atoms instead of whole
     809molecules.
     810<li><p>Added undo/redo motion buttons to fit dialog.
     811</ul>
     812
     813<p><b>October 6, 2009.  Version 1.4</b></p>
     814<ul type=None>
     815<li><p>Made session merge not savepos session-start if that position already
     816exists.
     817<li><p>Replaced matrixcopy relativeTo keyword with "moving" keyword.
     818<li><p>Made set light_quality command update quality in lighting dialog.
     819<li><p>Added check for matching grid sizes in vop morph command.
     820<li><p>Made vop cover update rendering options of source map -- was setting
     821those options but failed to show them.
     822<li><p>Fixed session merging error handling of old sessions.
     823</ul>
     824
     825<p><b>October 2, 2009.  Version 1.4</b></p>
     826<ul type=None>
     827<li><p>Added hide command-line to bottom of command history menu.
     828<li><p>Made session merge keep old window size and camera/viewer settings.
     829</ul>
     830
     831<p><b>October 1, 2009.  Version 1.4</b></p>
     832<ul type=None>
     833<li><p>Made vrml models not use glossy shader, avoids black vrml objects.
     834</ul>
     835
     836<p><b>September 30, 2009.  Version 1.4</b></p>
     837<ul type=None>
     838<li><p>Fixed glossy lighting fog so alpha is not used.  Needed so that
     839100% transparent surfaces are invisible.
     840<li><p>Added showSlabs option to measure rotation command.
     841<li><p>Improved file fetch error on socket errors which are not IOError.
     842<li><p>Added relativeXform option to matrixcopy to fix misaligned sessions.
     843<li><p>Made session merging align old and new lowest id models.
     844</ul>
     845
     846<p><b>September 29, 2009.  Version 1.4</b></p>
     847<ul type=None>
     848<li><p>Added update keyword to sym command, default false.
     849<li><p>Added toggle outline box shortcut "ob".
     850</ul>
     851
     852<p><b>September 28, 2009.  Version 1.4</b></p>
     853<ul type=None>
     854<li><p>Made selection object model order follow vertex order.  Allows
     855vop add command to get correct model order.
     856<li><p>Fixed surface zone session restore bug with molecular surfaces.
     857<li><p>Added minRMS option to vop subtract for subtracting fit maps.
     858<li><p>Made vop subtract operation use interpolation like vop add.
     859</ul>
     860
     861<p><b>September 25, 2009.  Version 1.4</b></p>
     862<ul type=None>
     863<li><p>Made vop add not extend grid due to round-off if grids are identical.
     864<li><p>Added multipliers arg to vop add.
     865<li><p>Made open viper:1bbt fetch from viperdb instead of pdb.
     866</ul>
     867
     868<p><b>September 18, 2009.  Version 1.4</b></p>
     869<ul type=None>
     870<li><p>Made ~surf command close molecular surfaces with closed molecules.
     871</ul>
     872
     873<p><b>September 17, 2009.  Version 1.4</b></p>
     874<ul type=None>
     875<li><p>Fixed fit in map, with simulated map didn't move atoms.
     876<li><p>Made measure buriedarea report buried areas for both atom sets.
     877</ul>
     878
     879<p><b>September 16, 2009.  Version 1.4</b></p>
     880<ul type=None>
     881<li><p>Made mz shortcut place marker at origin in selected models local coords.
     882<li><p>Added center and axis arguments to sym command.
     883</ul>
     884
     885<p><b>September 15, 2009.  Version 1.4</b></p>
     886<ul type=None>
     887<li><p>Added symmetry group argument to sym command.
     888</ul>
     889
     890<p><b>September 14, 2009.  Version 1.4</b></p>
     891<ul type=None>
     892<li><p>Improved color zone out-of-memory error message.
     893</ul>
     894
     895<p><b>September 11, 2009.  Version 1.4</b></p>
     896<ul type=None>
     897<li><p>Added move molecule mouse mode.
     898</ul>
     899
     900<p><b>September 10, 2009.  Version 1.4</b></p>
     901<ul type=None>
     902<li><p>Implemented vop cover operation for periodic map extension.
     903</ul>
     904
     905<p><b>September 9, 2009.  Version 1.4</b></p>
     906<ul type=None>
     907<li><p>Fixed vanishing surface cap on Windows.
     908</ul>
     909
     910<p><b>September 7, 2009.  Version 1.4</b></p>
     911<ul type=None>
     912<li><p>Fixed pseudobondgroup bounding box calculation, wrong coordinate system.
     913<li><p>Added playDirection, playRange and addMode options to vop morph command.
     914<li><p>Fixed front-center, was using mid-depth even when model intercepted.
     915<li><p>Fixed color parsing error in measure inertia.
     916</ul>
     917
     918<p><b>September 4, 2009.  Version 1.4</b></p>
     919<ul type=None>
     920<li><p>Added vop morph command.
     921<li><p>Added number of cells option to unit cell dialog.
     922<li><p>Made unit cell outline button toggle outline off.
     923</ul>
     924
     925<p><b>September 3, 2009.  Version 1.4</b></p>
     926<ul type=None>
     927<li><p>Added options panel to unit cell dialog.
     928</ul>
     929
     930<p><b>September 2, 2009.  Version 1.4</b></p>
     931<ul type=None>
     932<li><p>Made unit cell dialog handle inverting symmetries.
     933</ul>
     934
     935<p><b>August 31, 2009.  Version 1.4</b></p>
     936<ul type=None>
     937<li><p>Made marker note labels set using actions label menu save in sessions.
     938<li><p>Fixed bug where deleting marker did not delete residue.
     939<li><p>Fixed split map by color bug, numpy array in sessions.
     940</ul>
     941
     942<p><b>August 25, 2009.  Version 1.4</b></p>
     943<ul type=None>
     944<li><p>Added command "set light_quality glossy|normal".
     945</ul>
     946
     947<p><b>August 24, 2009.  Version 1.4</b></p>
     948<ul type=None>
     949<li><p>Made surface color dialog show offset field only for electrostatics.
     950</ul>
     951
     952<p><b>August 21, 2009.  Version 1.4</b></p>
     953<ul type=None>
     954<li><p>Translated mesh subdivision python to c++ for faster calculation.
     955<li><p>Made error dialog not report full traceback, just a few lines.
     956<li><p>Fixed shape command color parsing, was generating an error.
     957<li><p>Made surface zone and color zone save arrays as strings in session files.
     958<li><p>Fixed shape command, was adding to existing surface when none specified.
     959</ul>
     960
     961<p><b>August 20, 2009.  Version 1.4</b></p>
     962<ul type=None>
     963<li><p>Saved surface data as strings in sessions, smaller files and faster
     964save and restore.
     965</ul>
     966
     967<p><b>August 19, 2009.  Version 1.4</b></p>
     968<ul type=None>
     969<li><p>Fixed aqua double menu posting bug.
     970<li><p>Fixed shape command model id parsing error.
     971<li><p>Added sop surface operation command. The finerMesh operation
     972subdivides surface meshes to have uniform edge length.
     973<li>Added offset keyword to scolor command to allow coloring by volume data
     974or volume gradient at a position offset from a surface along the surface
     975normals.  The offset can be a single signed float value, or a range given by
     976two values start, end, and an integer N (e.g. offset 0,8.5,4) specifying that
     977N offsets should be used and the average volume value used.  This is for
     978coloring by projecting a slab of volume data.
     979<li><p>Made mouse rotation center allow z and xy rotation when model
     980rotation center is far off screen.  The xy-rotation region of the window now
     981always includes a circle centered on the window with diameter half the window
     982size (minimum of window width and height).
     983</ul>
     984
     985<p><b>August 18, 2009.  Version 1.4</b></p>
     986<ul type=None>
     987<li><p>Fixed error when overwriting missing volume data file.
     988<li><p>Fixed bug where volume selection outline box used new molecule
     989preferences.
     990</ul>
     991
     992<p><b>August 17, 2009.  Version 1.4</b></p>
     993<ul type=None>
     994<li><p>Added linux space navigator support contributed by Thomas Margraf.
     995</ul>
     996
     997<p><b>August 14, 2009.  Version 1.4</b></p>
     998<ul type=None>
     999<li><p>Made volume data contour calculation catch memory allocation exception
     1000so Chimera does not crash.
     1001</ul>
     1002
     1003<p><b>August 12, 2009.  Version 1.4</b></p>
     1004<ul type=None>
     1005<li><p>Made molmap command allow specifying map subid.
     1006</ul>
     1007
     1008<p><b>August 11, 2009.  Version 1.4</b></p>
     1009<ul type=None>
     1010<li><p>Updated saxs profile calculation user interface, no longer requires
     1011form factor file.
     1012</ul>
     1013
     1014<p><b>August 10, 2009.  Version 1.4</b></p>
     1015<ul type=None>
     1016<li><p>Made initial molecule display style not apply to volume tracer
     1017marker models.
     1018</ul>
     1019
     1020<p><b>August 7, 2009.  Version 1.4</b></p>
     1021<ul type=None>
     1022<li><p>Fixed volume eraser error caused by new volume tracer api.
     1023<li><p>Added surface color dialog offset option for electrostatic coloring.
     1024<li><p>Fixed tile command argument parsing error.
     1025</ul>
     1026
     1027<p><b>August 5, 2009.  Version 1.4</b></p>
     1028<ul type=None>
     1029<li><p>Added tube display to shape command.
     1030</ul>
     1031
     1032<p><b>August 4, 2009.  Version 1.4</b></p>
     1033<ul type=None>
     1034<li><p>Made volume tracer tubes use surface model instead of vrml.
     1035</ul>
     1036
     1037<p><b>August 3, 2009.  Version 1.4</b></p>
     1038<ul type=None>
     1039<li><p>Fixed volume outline box to avoid coloring and capping.
     1040<li><p>Made volume flip normals for thresholds less than 0 default off.
     1041<li><p>Added tile command.
     1042<li><p>Made volume save command handle multifile save with %d index.
     1043</ul>
     1044
     1045<p><b>July 31, 2009.  Version 1.4</b></p>
     1046<ul type=None>
     1047<li><p>Fixed subsampled grid data caching, caused blank histogram display.
     1048<li><p>Added vop boxes operation to extract subregions around markers.
     1049</ul>
     1050
     1051<p><b>July 29, 2009.  Version 1.4</b></p>
     1052<ul type=None>
     1053<li><p>Made volume tracer work without graphical user interface.
     1054<li><p>Added vop median and scale filter operations.
     1055</ul>
     1056
     1057<p><b>July 28, 2009.  Version 1.4</b></p>
     1058<ul type=None>
     1059<li><p>Replaced vop and volume command use_step/use_subregion arguments with step/subregion.
     1060<li><p>Fixed imod reader bug, error reading point size records.
     1061</ul>
     1062
     1063<p><b>July 24, 2009.  Version 1.4</b></p>
     1064<ul type=None>
     1065<li><p>Added measure inertia command for molecules and surfaces.
     1066</ul>
     1067
     1068<p><b>July 22, 2009.  Version 1.4</b></p>
     1069<ul type=None>
     1070<li><p>Made scale filter clamp integer values to data type limits.
     1071<li><p>Changed frame update timers to assure minimum event processing time.  Prevents some lock-outs during continuous rendering on aqua.
     1072<li><p>Fixed broken mask command.
     1073<li><p>Made mask command ignore hidden parts of surface.
     1074</ul>
     1075
     1076<p><b>July 21, 2009.  Version 1.4</b></p>
     1077<ul type=None>
     1078<li><p>Made molmap accept a # character in the modelId argument.
     1079</ul>
     1080
     1081<p><b>July 20, 2009.  Version 1.4</b></p>
     1082<ul type=None>
     1083<li><p>Fixed binning filter step size bug.
     1084</ul>
     1085
     1086<p><b>July 17, 2009.  Version 1.4</b></p>
     1087<ul type=None>
     1088<li><p>Changed vop syntax, operation first arg, rejects invalid keywords.
     1089<li><p>Fixed meshmol bug, error due to obsolete volume tracer call.
     1090</ul>
     1091
     1092<p><b>July 16, 2009.  Version 1.4</b></p>
     1093<ul type=None>
     1094<li><p>Made session saving eliminate indent on long lists, smaller file size.
     1095<li><p>Fixed emdb fetch bug where xml and web service used when not needed.
     1096</ul>
     1097
     1098<p><b>July 15, 2009.  Version 1.4</b></p>
     1099<ul type=None>
     1100<li><p>Fixed bug in vop permute, permutation incorrect.
     1101</ul>
     1102
     1103<p><b>July 14, 2009.  Version 1.4</b></p>
     1104<ul type=None>
     1105<li><p>Added vop add command.
     1106<li><p>Added useGridStep, useGridSubregion, boundingGrid vop resample options.
     1107<li><p>Made volumes with unicode filenames open.
     1108</ul>
     1109
     1110<p><b>July 13, 2009.  Version 1.4</b></p>
     1111<ul type=None>
     1112<li><p>Added set/reset and cumulative transform to molecule transform dialog.
     1113<li><p>Updated to pytables 2.1.1 to allow reading Chimera map format files with unicode file names.
     1114</ul>
     1115
     1116<p><b>July 10, 2009.  Version 1.4</b></p>
     1117<ul type=None>
     1118<li><p>Made fit in map only use displayed subregion when counting points outside contour.
     1119</ul>
     1120
     1121<p><b>June 23, 2009.  Version 1.4</b></p>
     1122<ul type=None>
     1123<li><p>Fixed non-orthogonal rotation errors in reading profec volume maps.
     1124<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.
     1125<li><p>Made mouse rotation virtual sphere center be the model center of rotation.
     1126</ul>
     1127
     1128<p><b>June 22, 2009.  Version 1.4</b></p>
     1129<ul type=None>
     1130<li><p>Fixed incorrect default center for scolor command.
     1131</ul>
     1132
     1133<p><b>June 19, 2009.  Version 1.4</b></p>
     1134<ul type=None>
     1135<li><p>Fixed per-pixel surface color bugs with transparent surfaces.
     1136<li><p>Implemented scolor command for surface color dialog functionality.
     1137</ul>
     1138
     1139<p><b>June 18, 2009.  Version 1.4</b></p>
     1140<ul type=None>
     1141<li><p>Fixed surface transparency color hierarchy problems.
     1142</ul>
     1143
     1144<p><b>June 17, 2009.  Version 1.4</b></p>
     1145<ul type=None>
     1146<li><p>Added frames argument to surftransparency command.
     1147<li><p>Made surftransparency command work on non-msms surfaces.
     1148</ul>
     1149
     1150<p><b>June 12, 2009.  Version 1.4</b></p>
     1151<ul type=None>
     1152<li><p>Fixed session save error with empty marker set.
     1153</ul>
     1154
     1155<p><b>June 10, 2009.  Version 1.4</b></p>
     1156<ul type=None>
     1157<li><p>Added bin operation to vop command.
     1158</ul>
     1159
     1160<p><b>June 9, 2009.  Version 1.4</b></p>
     1161<ul type=None>
     1162<li><p>Implemented volume binning filter.
     1163<li><p>Made per-pixel surface color use colormap end values instead of black.
     1164<li><p>Fixed per-pixel surface color lighting.
     1165</ul>
     1166
     1167<p><b>June 5, 2009.  Version 1.4</b></p>
     1168<ul type=None>
     1169<li><p>Made pick blobs and volume tracer work with per-model clipped surfaces.
     1170</ul>
     1171
     1172<p><b>June 4, 2009.  Version 1.4</b></p>
     1173<ul type=None>
     1174<li><p>Added volume tracer mouse mode for marker placement on surfaces.
     1175<li><p>Put each volume tracer marker in its own residue to allow specifying
     1176numeric ranges in commands.
     1177</ul>
     1178
     1179<p><b>June 3, 2009.  Version 1.4</b></p>
     1180<ul type=None>
     1181<li><p>Added mask command invertMask option.
     1182<li><p>Added caps argument to shape command for cylinder caps.
     1183</ul>
     1184
     1185<p><b>June 2, 2009.  Version 1.4</b></p>
     1186<ul type=None>
     1187<li><p>Made copy/paste work in aqua for bug report dialog "gathered info" field.
     1188<li><p>Fixed morph map movie record bug, backslash t in file interpreted as tab.
     1189</ul>
     1190
     1191<p><b>May 29, 2009.  Version 1.4</b></p>
     1192<ul type=None>
     1193<li><p>Added per pixel coloring to surface color dialog using textures.
     1194<li><p>Made surface textures support luminance and border colors.
     1195<li><p>Updated function names for emdb web service search.
     1196</ul>
     1197
     1198<p><b>May 27, 2009.  Version 1.4</b></p>
     1199<ul type=None>
     1200<li><p>Made transparent texture coloring of surfaces work.
     1201<li><p>Added texture coloring to surface color dialog.
     1202<li><p>Fixed bug where 3d texture not updated when color mode changed.
     1203<li><p>Fixed bug where volume color mode not updated when switching between 2d and 3d solid style.
     1204</ul>
     1205
     1206
     1207<p><b>May 20, 2009.  Version 1.4</b></p>
     1208
     1209<ul type=None>
     1210<li><p>Fixed space navigator lag and poor response on aqua. TG
     1211<li><p>Fixed actions missing some models with no selection when multiscale surfaces present. TG
     1212</ul>
     1213
     1214<p><b>May 19, 2009.  Version 1.4</b></p>
     1215
     1216<ul type=None>
     1217<li><p>Made emdb web search show citation and map release date. TG
     1218<li><p>Made fetch panel show search field only for searchable databases. TG
     1219</ul>
     1220
     1221<p><b>May 18, 2009.  Version 1.4</b></p>
     1222
     1223<ul type=None>
     1224<li><p>Made volume save command handle "~" paths. TG
     1225</ul>
     1226
     1227<p><b>May 11, 2009.  Version 1.4</b></p>
     1228
     1229<ul type=None>
     1230<li><p>Made reply dialog text selectable and copyable on aqua. TG
     1231<li><p>Made ~/Desktop/xxx paths work on windows. TG
     1232</ul>
     1233
     1234<p><b>May 7, 2009.  Version 1.4</b></p>
     1235
     1236<ul type=None>
     1237<li><p>Made movie encoding friendly error if output directory doesn't exist. TG
     1238</ul>
     1239
     1240<p><b>May 1, 2009.  Version 1.4</b></p>
     1241
     1242<ul type=None>
     1243<li><p>Added tilde expansion to movie encoding output path. TG
     1244</ul>
     1245
     1246<p><b>April 30, 2009.  Version 1.4</b></p>
     1247
     1248<ul type=None>
     1249<li><p>Fixed demo auto-play sometimes freezing Chimera.  Aqua Tk menu callback bug. TG
     1250</ul>
     1251
     1252<p><b>April 27, 2009.  Version 1.4</b></p>
     1253
     1254<ul type=None>
     1255<li><p>Added silhouette, depth cue, subdivision "set" command options. TG
     1256<li><p>Added coordset command to play trajectories, for movie scripts. TG
     1257</ul>
     1258
     1259<p><b>April 24, 2009.  Version 1.4</b></p>
     1260
     1261<ul type=None>
     1262<li><p>Made command-` and shift-command-` cycle aqua windows. TG
     1263<li><p>Removed aqua focus follows mouse code and preference setting. TG
     1264<li><p>Made emdb fetch use web service to find fit pdbs, was using xml file. TG
     1265</ul>
     1266
     1267<p><b>April 20, 2009.  Version 1.4</b></p>
     1268
     1269<ul type=None>
     1270<li><p>Made multiscale copy isHet to avoid water chaining. TG
     1271</ul>
     1272
     1273<p><b>April 15, 2009.  Version 1.4</b></p>
     1274
     1275<ul type=None>
     1276<li><p>Made mac aqua tk use click-through. TG
     1277</ul>
     1278
     1279<p><b>April 9, 2009.  Version 1.4</b></p>
     1280
     1281<ul type=None>
     1282<li><p>Fixed fetch dialog to hide when return key pressed in id field. TG
     1283</ul>
     1284
     1285<p><b>April 7, 2009.  Version 1.4</b></p>
     1286
     1287<ul type=None>
     1288<li><p>Fixed export obj bug where wrong material file path written. TG
     1289</ul>
     1290
     1291<p><b>March 30, 2009.  Version 1.4</b></p>
     1292
     1293<ul type=None>
     1294<li><p>Added memory error check in volume filter. TG
     1295</ul>
     1296
     1297<p><b>March 25, 2009.  Version 1.4</b></p>
     1298
     1299<ul type=None>
     1300<li><p>Added emdb search capability to fetch by id dialog. TG
     1301</ul>
     1302
     1303<p><b>March 24, 2009.  Version 1.4</b></p>
     1304
     1305<ul type=None>
     1306<li><p>Fixed bug where last used data matrix for a volume not kept in cache. TG
     1307<li><p>Increased volume data default cache size to 512 Mb, was 32 Mb. TG
     1308</ul>
     1309
     1310<p><b>March 20, 2009.  Version 1.4</b></p>
     1311
     1312<ul type=None>
     1313<li><p>Added slab option to shape command. TG
     1314<li><p>Made mcopy copy bond properties, fixed label copy. TG
     1315</ul>
     1316
     1317<p><b>March 19, 2009.  Version 1.4</b></p>
     1318
     1319<ul type=None>
     1320<li><p>Fixed mcopy bug, coordinate copy did not work. TG
     1321</ul>
     1322
     1323<p><b>March 16, 2009.  Version 1.4</b></p>
     1324
     1325<ul type=None>
     1326<li><p>Fixed bug in dock grid error message. TG
     1327<li><p>Made clip command give user-friendly near>far error message. TG
     1328</ul>
     1329
     1330<p><b>March 13, 2009.  Version 1.4</b></p>
     1331
     1332<ul type=None>
     1333<li><p>Made modbase and castp fetch use downlaod directory. TG
     1334</ul>
     1335
     1336<p><b>March 12, 2009.  Version 1.4</b></p>
     1337
     1338<ul type=None>
     1339<li><p>Made pubchem fetch use download directory. TG
     1340</ul>
     1341
     1342<p><b>March 11, 2009.  Version 1.4</b></p>
     1343
     1344<ul type=None>
     1345<li><p>Fixed fly command bug where an extra frame count was used. TG
     1346<li><p>Made color command handle r,g,b,a numeric color arguments. TG
     1347<li><p>Added fetching emdb maps to fetch-by-id dialog. TG
     1348<li><p>Added button to fetch by id dialog shows download directory preferences. TG
     1349<li><p>Added cancel link in progress messages to cancel fetch operation. TG
     1350<li>Enabled uncompressing fetched data files. TG
     1351<li>Made bondcolor and colordef handle r,g,b,a numeric arguments. TG
     1352</ul>
     1353
     1354<p><b>March 10, 2009.  Version 1.4</b></p>
     1355
     1356<ul type=None>
     1357<li><p>Added mcopy command to copy molecule settings. TG
     1358<li><p>Added fetch-by-id download directory for eds, viperdb, pqs, pdb, cif, scop, ndb. TG
     1359</ul>
     1360
     1361<p><b>March 6, 2009.  Version 1.4</b></p>
     1362
     1363<ul type=None>
     1364<li><p>Made all command color arguments accept tk colors, comma-separated rgba. TG
     1365</ul>
     1366
     1367<p><b>March 5, 2009.  Version 1.4</b></p>
     1368
     1369<ul type=None>
     1370<li><p>Made volume scale filter respond when enter key pressed. TG
     1371</ul>
     1372
     1373<p><b>March 4, 2009.  Version 1.4</b></p>
     1374
     1375<ul type=None>
     1376<li><p>Made measure rotation mention coordinate system in reply log output. TG
     1377<li><p>Made measure and vop keyword abbreviations work and case insensitive. TG
     1378<li><p>Made rotation axis color be model color. TG
     1379<li><p>Allowed markers/links to have no color, uses molecule color. TG
     1380<li><p>Improved per-model clipping shorcuts cc, ca and removed tc. TG
     1381<li><p>Made scale/shift volume filter update when filter settings changed. TG
     1382</ul>
     1383
     1384<p><b>February 26, 2009.  Version 1.4</b></p>
     1385
     1386<ul type=None>
     1387<li><p>Fixed saving markers as xml when atoms/bonds deleted. TG
     1388</ul>
     1389
     1390<p><b>February 25, 2009.  Version 1.4</b></p>
     1391
     1392<ul type=None>
     1393<li><p>Added showAxis option to measure rotation command. TG
     1394</ul>
     1395
     1396<p><b>February 20, 2009.  Version 1.4</b></p>
     1397
     1398<ul type=None>
     1399<li><p>Fixed molmap to work with molecules with different transforms. TG
     1400<li><p>Made stl export for 3-d printing. TG
     1401</ul>
     1402
     1403<p><b>February 17, 2009.  Version 1.4</b></p>
     1404
     1405<ul type=None>
     1406<li><p>Made matrixcopy handle multiple destination models. TG
     1407<li><p>Made shape command hide some mesh edges for icosahedron and cylinder. TG
     1408<li><p>Added lighting attributes, normals, edge mask to surface session save. TG
     1409<li><p>Made color zone with bond zone respect half-bond coloring. TG
     1410</ul>
     1411
     1412<p><b>February 13, 2009.  Version 1.4</b></p>
     1413
     1414<ul type=None>
     1415<li><p>Added silhouette edge drawing for transparent models. TG
     1416<li><p>Added one layer and all layers transparency menu entries. TG
     1417<li><p>Fixed multiscale bug where chain associated with original molecule
     1418deleted, and other surfaces recalculated at new resolution. TG
     1419<li><p>Fixed bug where volume session restore tried to set solid model
     1420orientation when that model did not exist. TG
     1421<li><p>Fixed bug where opening solid model did not set initial camera view. TG
     1422</ul>
     1423
     1424<p><b>February 11, 2009.  Version 1.4</b></p>
     1425
     1426<ul type=None>
     1427<li><p>Made session save include molecular surface attributes: smoothing,
     1428lighting on/off, two-sided lighting, dot and line widths. TG
     1429<li><p>Added one transparent layer surface option.  Added equivalent option
     1430to volume dialog surface and mesh panel. TG
     1431<li><p>Added shortcuts t5 and t0 to make surfaces 50% and 0% transparent. TG
     1432</ul>
     1433
     1434
     1435<p><b>February 10, 2009.  Version 1.4</b></p>
     1436
     1437<ul type=None>
     1438<li><p>Made move/turn/rock/roll move inactive models when "models"
     1439keyword used. TG
     1440<li><p>Made open volumes use absolute paths even if specified with relative
     1441paths so that data can be read later if current working directory changed. TG
     1442</ul>
     1443
     1444<p><b>February 9, 2009.  Version 1.4</b></p>
     1445
     1446<ul type=None>
     1447<li><p>Improved rendering of multiple transparent surface models so model
     1448behind does not appear in front. TG
     1449</ul>
     1450
     1451<p><b>January 28, 2009.  Version 1.4</b></p>
     1452
     1453<ul type=None>
     1454<li><p>Made multiscale contacts not select chain surfaces when atoms of
     1455chain are selected. TG
     1456</ul>
     1457
     1458<p><b>January 21, 2009.  Version 1.4</b></p>
     1459
     1460<ul type=None>
     1461<li><p>Wrote fly command to smoothly interpolate positions/camera. TG
     1462</ul>
     1463<p><b>January 20, 2009.  Version 1.4</b></p>
     1464
     1465<ul type=None>
     1466<li><p>Fixed swapped buried ses/sas area atom attributes. TG
     1467</ul>
     1468
     1469<p><b>January 19, 2009.  Version 1.4</b></p>
     1470
     1471<ul type=None>
     1472<li><p>Fixed reset with frame count error when model closed. TG
     1473<li><p>Made volume surface outline box unlit when using glossy lighting. TG
     1474<li><p>Fixed bug where hide dust turned volume square mesh into triangles. TG
     1475</ul>
     1476
     1477<p><b>January 18, 2009.  Version 1.4</b></p>
     1478
     1479<ul type=None>
     1480<li><p>Made hdf map read use planes along smallest chunk shape axis. TG
     1481<li><p>Added use step/subregion/zone options to volume save command. TG
     1482<li><p>Added scale/shift/cast operation to volume filter dialog. TG
     1483<li><p>Added permuteaxes operation to vop command. TG
     1484</ul>
     1485
     1486<p><b>January 16, 2009.  Version 1.4</b></p>
     1487
     1488<ul type=None>
     1489<li><p>Fixed bug in histogram calculation that caused slightly incorrect
     1490volume threshold. TG
     1491y<li><p>Added buried area to measure command. TG
     1492</ul>
     1493
     1494<p><b>January 15, 2009.  Version 1.4</b></p>
     1495
     1496<ul type=None>
     1497<li><p>Fixed matplotlib on windows, wasn't finding tcl/tk headers. TG
     1498<li><p>Fixed turn/roll/rock bug, inactive models moved when center specified. TG
     1499</ul>
     1500
     1501<p><b>January 14, 2009.  Version 1.4</b></p>
     1502
     1503<ul type=None>
     1504<li><p>Fixed shader code to not throw error on compile/link info messages. TG
     1505<li><p>Fixed esp coloring bug, coloring method not set. TG
     1506<li><p>Fixed bright edges from glossy lighting, had diffuse light on
     1507both sides of surface. TG
     1508<li><p>Made correlation matplotlib plot use tk instead of native Mac window. TG
     1509</ul>
     1510
     1511<p><b>January 13, 2009.  Version 1.4</b></p>
     1512
     1513<ul type=None>
     1514<li><p>Fixed bug move,turn,roll,rock coordinateSystem arg not working. TG
     1515<li><p>Fixed disappearing light arrows in light panel. TG
     1516<li><p>Made turn/roll/rock/move use coord system of center or axis spec. TG
     1517</ul>
     1518
     1519<p><b>January 9, 2009.  Version 1.4</b></p>
     1520
     1521<ul type=None>
     1522<li><p>Added matplotlib 2d plotting library to distribution, used for showing
     1523correlation of map with rotated map. TG
     1524</ul>
     1525
     1526<p><b>January 8, 2009.  Version 1.4</b></p>
     1527
     1528<ul type=None>
     1529<li><p>Added correlation for rotated map positions to measure command. TG
     1530
     1531</ul>
     1532
     1533<p><b>January 7, 2009.  Version 1.4</b></p>
     1534
     1535<ul type=None>
     1536<li><p>Wrote measure command to show rotation axis connecting two models. TG
     1537<li><p>Handle new delphi map format on mac with 64 bit floats. TG
     1538<li><p>Made turn,roll,rock,move accept 2 atom or bond spec for axis. TG
     1539<li><p>Added surface volume and area to measure command. TG
     1540<li><p>Added map correlation to measure command. TG
     1541<li><p>Made glossy lighting not apply to unlit lines, caused dim molecule
     1542wires. TG
     1543y</ul>
     1544
     1545<p><b>January 6, 2009.  Version 1.4</b></p>
     1546
     1547<ul type=None>
     1548<li><p>Added median filtering to filter dialog. TG
     1549<li><p>Added clip volume (cv), clip adjust (ca), glossy lighting (gl)
     1550shortcuts. TG
     1551<li><p>Made clip and cap shortcut act on selected model, not show dialogs. TG
     1552<li><p>Fixed bug where single color volume solid dimmed by factor
     1553of red component. TG
     1554</ul>
     1555
     1556<p><b>January 2, 2009.  Version 1.4</b></p>
     1557
     1558<ul type=None>
     1559<li><p>Fixed bug where surface cap not updated when mask changed. TG
     1560<li><p>Added options panel to gaussian filter dialog, including
     1561immediate update option. TG
     1562<li><p>Made filter dialog adjust thresholds for constant volume
     1563use the enclosed volume for the gaussian filtered volume rather than
     1564the original volume. TG
     1565<li><p>Made Filter button just update existing volume
     1566if active volume is a gaussian filtered volume. TG
     1567</ul>
     1568
     1569<p><b>December 30, 2008.  Version 1.4</b></p>
     1570
     1571<ul type=None>
     1572<li><p>Moved per-pixel lighting option from effects panel to lighting panel. TG
     1573<li><p>Fixed mac x11 start error when glossy lighting preference not supported. TG
     1574<li><p>Fixed bug where glossy mode sometimes had no effect because
     1575graphics context was not current when setting shader. TG
     1576</ul>
     1577
     1578<p><b>December 29, 2008.  Version 1.4</b></p>
     1579
     1580<ul type=None>
     1581<li><p>Allowed depth cue start >= 1 for back lighting effect. TG
     1582<li><p>Made surface cap use only visible parts of surfaces, helps castp. TG
     1583</ul>
     1584
     1585<p><b>December 19, 2008.  Version 1.4</b></p>
     1586
     1587<ul type=None>
     1588<li><p>Added "glossy" lighting mode using an opengl shader providing
     1589per-pixel lighting and angle-dependent transparency. TG
     1590</ul>
     1591
     1592<p><b>December 18, 2008.  Version 1.4</b></p>
     1593
     1594<ul type=None>
     1595<li><p>Replace depth cue yon intensity parameter with end depth. TG
     1596</ul>
     1597
     1598<p><b>December 16, 2008.  Version 1.4</b></p>
     1599
     1600<ul type=None>
     1601<li><p>Added slider to control width of gaussian filter. TG
     1602</ul>
     1603
     1604<p><b>December 10, 2008.  Version 1.4</b></p>
     1605
     1606<ul type=None>
     1607<li><p>Added hide dust tool that hides small connected surface blobs. TG
     1608<li><p>Increased surface cap default offset 0.001 to 0.01 to avoid disappearing
     1609caps. TG
     1610<li><p>Made sum of gaussians routine (used by molmap) able to take
     1611different standard deviations along 3 axes for PALM/STORM microscopy data. TG
     1612</ul>
     1613
     1614<p><b>December 9, 2008.  Version 1.4</b></p>
     1615
     1616<ul type=None>
     1617<li><p>Disabled used of Chimera user interface while volume data load is loaded,
     1618allowing only cancel of data load. TG
     1619<li><p>Moved volume auto display subregion option from data display panel to
     1620subregion selection panel. TG
     1621<li><p>Allowed volume auto-cropping (resampling) with rotated subregion box.
     1622With solid style rendering this does a good job of showing slices that are not
     1623parallel to the volume box faces. TG
     1624</ul>
     1625
     1626<p><b>December 8, 2008.  Version 1.4</b></p>
     1627
     1628<ul type=None>
     1629<li><p>Fixed subregion resampling box when source map has local rotation. TG
     1630<li><p>Debugged blank volume histogram when session restored,
     1631cache size not set before volume dialog created. TG
     1632</ul>
     1633
     1634<p><b>December 5, 2008.  Version 1.4</b></p>
     1635
     1636<ul type=None>
     1637<li><p>Added session saving for icosahedron tool. TG
     1638</ul>
     1639
     1640<p><b>December 3, 2008.  Version 1.4</b></p>
     1641
     1642<ul type=None>
     1643<li><p>Provide user-friendly error message when molecular surface calculation
     1644produces truncated output. TG
     1645<li><p>Suppress Mac 10.5 crash report dialog when molecular surface calculation
     1646fails. TG
     1647</ul>
     1648
     1649<p><b>November 25, 2008.  Version 1.4</b></p>
     1650
     1651<ul type=None>
     1652<li><p>Made move selection mouse mode able to move surface pieces. TG
     1653</ul>
     1654
     1655<p><b>November 21, 2008.  Version 1.2577.</b></p>
     1656
     1657<ul type=None>
     1658<li><p>Made initial volume viewer thresholds symmetric about 0 for
     1659electrostatic potential data and other polar data. TG
     1660<li><p>Added gaussian and laplacian filters to vop command. TG
     1661</ul>
     1662
     1663<p><b>November 20, 2008.  Version 1.2576.</b></p>
     1664
     1665<ul type=None>
     1666<li><p>Made per-model clipping work with solid volume rendering where
     1667projection mode is perpendicular to view (uses 3d textures).
     1668</ul>
     1669
     1670<p><b>November 19, 2008.  Version 1.2576.</b></p>
     1671
     1672<ul type=None>
     1673<li><p>Fixed error reading mrc file > 2 Gbytes. TG
     1674</ul>
     1675
     1676<p><b>November 18, 2008.  Version 1.2575.</b></p>
     1677
     1678<ul type=None>
     1679<li><p>Fixed hkcage command error when invoked second time with surface
     1680capping enabled. TG
     1681<li><p>Added planes keyword to volume command to show sequence of planes. TG
     1682<li><p>Made turn, move, ... not raise error if model deleted during motion. TG
     1683<li><p>Added volume outline box linewidth setting. TG
     1684<li><p>Fixed reset command to preserve relative orientations. TG
     1685</ul>
     1686
     1687<p><b>November 17, 2008.  Version 1.2575.</b></p>
     1688
     1689<ul type=None>
     1690<li><p>Fixed bug that caused extra frames during movie capture scripts
     1691that read volume data, caused by progress messages. TG
     1692<li><p>Made movie encode command print status messages on main status line. TG
     1693</ul>
     1694
     1695<p><b>November 14, 2008.  Version 1.2575.</b></p>
     1696
     1697<ul type=None>
     1698<li><p>Fixed incorrect center of rotation when a model is closed where another
     1699model has the same id. TG
     1700<li><p>Made actions / focus with nothing selected turn of near/far clipping. TG
     1701</ul>
     1702
     1703<p><b>November 13, 2008.  Version 1.2574.</b></p>
     1704
     1705<ul type=None>
     1706<li><p>Suppress Mac 10.5 crash report dialog when molecular surface
     1707calculation mscalc program crashes. TG
     1708<li><p>Fixed volume command bug setting color of solid rendering. TG
     1709</ul>
     1710
     1711<p><b>November 12, 2008.  Version 1.2574.</b></p>
     1712
     1713<ul type=None>
     1714<li><p>Fixed bugs writing image stacks as single hdf (*.cmap) files. TG
     1715</ul>
     1716
     1717<p><b>November 11, 2008.  Version 1.2574.</b></p>
     1718
     1719<ul type=None>
     1720<li><p>Made molecule bounds include atom radii to avoid clipping atom spheres
     1721when near/far clipping is turned off. TG
     1722
     1723<li><p>Fixed error closing volumes when new session opened. TG
     1724<li><p>Fixed bug where distant opaque solid volume models appeared in front of
     1725closer opaque soild volume models. TG
     1726<li><p>Fixed bug where restored traced surface not saved in subsequent sessions.
     1727TG
     1728</ul>
     1729
     1730<p><b>November 10, 2008.  Version 1.2574.</b></p>
     1731
     1732<ul type=None>
     1733<li><p>Added warning when restoring a session file written by a newer chimera
     1734version. TG
     1735<li><p>Fixed bug restoring volume / surface coloring from session files written
     1736by Chimera version more than 1 year old. TG
     1737</ul>
     1738
     1739<p><b>November 6, 2008.  Version 1.2573.</b></p>
     1740
     1741<ul type=None>
     1742
     1743<li><p>Fixed volume eraser bug introduce Sept 30. TG
     1744</ul>
     1745
     1746<p><b>November 4, 2008.  Version 1.2573.</b></p>
     1747
     1748<ul type=None>
     1749<li><p>Made surface capping on by default. TG
     1750<li><p>Made space navigator preserve front-center rotation point during
     1751rotation. TG
     1752</ul>
     1753
     1754<p><b>November 3, 2008.  Version 1.2573.</b></p>
     1755
     1756<ul type=None>
     1757<li><p>Made near/far clip planes off by default. TG
     1758</ul>
     1759
     1760<p><b>October 31, 2008.  Version 1.2572.</b></p>
     1761
     1762<ul type=None>
     1763<li><p>Made surface bounds calculation use bounding sphere instead of box
     1764resulting in tighter bounds for sphere-like surfaces. Effects amount of camera
     1765zoom when the first model show is a surface. TG
     1766</ul>
     1767
     1768<p><b>October 29, 2008.  Version 1.2572.</b></p>
     1769
     1770<ul type=None>
     1771<li><p>Changed default surface transparency blend model to dim (alpha,1-alpha).
     1772TG
     1773<li><p>Added center of rotation mode name options "fixed", "front", "models",
     1774and "independent" to cofr command. TG
     1775<li><p>Made coordinateSystem arguments to movement commands work without '#'. TG
     1776</ul>
     1777
     1778<p><b>October 28, 2008.  Version 1.2571.</b></p>
     1779
     1780<ul type=None>
     1781<li><p>Fixed failure to hide clicked triangle using pick blobs tool. TG
     1782<li><p>Cleared surface visibility/color atom attributes when surface closed. TG
     1783</ul>
     1784
     1785<p><b>October 27, 2008.  Version 1.2571.</b></p>
     1786
     1787<ul type=None>
     1788<li><p>Fixed bug where hiding a molecular surface piece made subsequent surface
     1789show not work. TG
     1790</ul>
     1791
     1792<p><b>October 24, 2008.  Version 1.2571.</b></p>
     1793
     1794<ul type=None>
     1795<li><p>Changed the default center of rotation mode to front-center. TG
     1796<li><p>Fixed multiscale session save error that happened after chain deleted. TG
     1797</ul>
     1798
     1799<p><b>October 22, 2008.  Version 1.2569.</b></p>
     1800
     1801<ul type=None>
     1802<li><p>Added front-center center of rotation mode. TG
     1803<li><p>Added coordinate system, center, models arguments to turn, roll, rock,
     1804         and move commands. TG
     1805<li><p>Made benchmark dialog show warning if models are open. TG
     1806<li><p>Allowed move command to move along all 3 axes at once. TG
     1807<li><p>Made cofr command accept point coordinates and coord sys arguments. TG
     1808<li><p>Added center, coord system, model id args to shape command. TG
     1809</ul>
     1810
     1811<p><b>October 20, 2008.  Version 1.2567.</b></p>
     1812
     1813<ul type=None>
     1814<li><p>Made options panel for morph map and added roundtrip option. TG
     1815</ul>
     1816
     1817<p><b>October 15, 2008.  Version 1.2566.</b></p>
     1818
     1819<ul type=None>
     1820<li><p>Fixed actions menu entries focus, set pivot, surface
     1821hide/show/repr/tranparency and color when a molecular surface is selected
     1822but not its atoms. TG
     1823</ul>
     1824
     1825<p><b>October 14, 2008.  Version 1.2566.</b></p>
     1826
     1827<ul type=None>
     1828<li><p>Made focus command and action use center-of-models when nothing selected.
     1829TG
     1830<li><p>Fixed session saving error after closing traced surface model. TG
     1831</ul>
     1832
     1833<p><b>October 10, 2008.  Version 1.2566.</b></p>
     1834
     1835<ul type=None>
     1836<li><p>Fixed model panel configure dialog bug, pmw tabs not raising in
     1837Mac Aqua Chimera. TG
     1838</ul>
     1839
     1840<p><b>October 1, 2008.  Version 1.2561.</b></p>
     1841
     1842<ul type=None>
     1843
     1844<li><p>Made molecular surface show "all components" false in selection
     1845inspector if all-component calculation failed and instead used single-component.
     1846TG
     1847<li><p>Fixed volume show/hide icon update error on model close. TG
     1848</ul>
     1849
     1850<p><b>September 29, 2008.  Version 1.2561.</b></p>
     1851
     1852<ul type=None>
     1853<li><p>Added memory checking to c++ python array allocation used in volume
     1854and surface calculations. TG
     1855</ul>
     1856
     1857<p><b>September 25, 2008.  Version 1.2561.</b></p>
     1858
     1859<ul type=None>
     1860<li><p>Added ls keyboard shortcut to open last session file. TG
     1861</ul>
     1862
     1863<p><b>September 23, 2008.  Version 1.2560.</b></p>
     1864
     1865<ul type=None>
     1866<li><p>Fixed volume solid color mode and projection mode bugs. TG
     1867</ul>
     1868
     1869<p><b>September 19, 2008.  Version 1.2559.</b></p>
     1870
     1871<ul type=None>
     1872<li><p>Added out-of-memory test for large surfaces. TG
     1873<li><p>Turn off mesh lighting for single plane volume display. TG
     1874<li><p>Made volume planes switch to solid style only when "one" button pressed.
     1875TG
     1876<li><p>Made single plane volume contour surface without capping render with
     1877mesh to show 2d contours. TG
     1878</ul>
     1879
     1880<p><b>September 12, 2008.  Version 1.2558.</b></p>
     1881
     1882<ul type=None>
     1883<li><p>Added fourier transform to vop command, removed fourier transform
     1884menu entry. TG
     1885</ul>
     1886
     1887<p><b>September 11, 2008.  Version 1.2558.</b></p>
     1888
     1889<ul type=None>
     1890<li><p>Made volume square mesh option show box cap diagonals.
     1891The square mesh code that excluded box cap diagonals also excluded all
     1892contours for single data planes. TG
     1893<li><p>Added volume planes cycle option with plane count and speed control.
     1894Replaces "play" button. TG
     1895<li><p>Added button to volume planes panel to preload data. Allows faster
     1896moving through planes. TG
     1897</ul>
     1898
     1899<p><b>September 10, 2008.  Version 1.2558.</b></p>
     1900
     1901<ul type=None>
     1902<li><p>Fixed volume tracer bug where first marker on empty space mispositioned
     1903if no models are opened. TG
     1904</ul>
     1905
     1906<p><b>September 9, 2008.  Version 1.2558.</b></p>
     1907
     1908<ul type=None>
     1909<li><p>Changed volume dialog origin field to show index of xyz origin instead
     1910of xyz coordinates of index 0,0,0. Allows changing voxel size without altering
     1911xyz origin position within array. TG
     1912<li><p>Added originIndex keyword to volume command for specifying the xyz origin
     1913in grid index units.  Changing voxelSize with volume command now preserves
     1914index of xyz 0,0,0 rather than xyz of index 0,0,0. TG
     1915<li><p>Added single volume plane surface and mesh display.  Allows drawing
     19162d contour lines.  Formerly surface and mesh style volume display showed
     1917nothing for single planes. TG
     1918</ul>
     1919
     1920<p><b>September 8, 2008.  Version 1.2557.</b></p>
     1921
     1922<ul type=None>
     1923<li><p>Made solid volume rendering status messages about color appear
     1924only once per frame. Were showing for every data plane. TG
     1925<li><p>Fixed erratic incorrect use of x or y projection axes in solid
     1926rendering. TG
     1927<li><p>Fixed netcdf out of memory error message. TG
     1928<li><p>Fixed bugs where volume dialog did not update display style and
     1929hide/show icon when solid style hidden (and hence solid model closed). TG
     1930</ul>
     1931
     1932<p><b>September 5, 2008.  Version 1.2557.</b></p>
     1933
     1934<ul type=None>
     1935<li><p>Added luminance color for volume rendering so single color modes need
     1936not display white. TG
     1937<li><p>Added auto projection mode that chooses 2d z planes rendering volume
     1938slabs with aspect 4:1 or greater, otherwise xyz planes (using more memory). TG
     1939</ul>
     1940
     1941<p><b>September 3, 2008.  Version 1.2554.</b></p>
     1942
     1943<ul type=None>
     1944<li><p>Removed colormap mode from solid style volume rendering. TG
     1945</ul>
     1946
     1947<p><b>September 2, 2008.  Version 1.2554.</b></p>
     1948
     1949<ul type=None>
     1950<li><p>Changed electrostatic surface coloring to be opaque red/white/blue. TG
     1951</ul>
     1952
     1953<p><b>August 29, 2008.  Version 1.2554.</b></p>
     1954
     1955<ul type=None>
     1956<li><p>Added volume projection mode option for tomogram viewing using solid
     1957style.  Allows only showing z planes.  3x less memory use versus xyz mode
     1958where planes most parallel to screen used. More memory efficient. TG
     1959
     1960<li><p>Change volume solid style rendering to not make full 3-d temporary color
     1961array. Instead computes only 2-d color planes at a time.  Reduces memory use. TG
     1962</ul>
     1963
     1964<p><b>August 28, 2008.  Version 1.2554.</b></p>
     1965
     1966<ul type=None>
     1967<li><p>Added support for volume color pixel formats (opengl texture
     1968format): RGB, luminance/alpha, luminance, 4,8,12 or 16-bit.  Formerly
     1969only RGBA 8-bit used.  More memory efficient, faster transfer to
     1970graphics card, allows display of larger maps.
     1971</ul>
     1972
     1973<p><b>August 27, 2008.  Version 1.2554.</b></p>
     1974
     1975<ul type=None>
     1976<li><p>Fixed color zone session restore bug on msms surfaces. TG
     1977</ul>
     1978
     1979<p><b>August 26, 2008.  Version 1.2553.</b></p>
     1980
     1981<ul type=None>
     1982<li><p>Updated surface model programmer's guide documentation. TG
     1983<li><p>Made morph map not report error on reset/cancel movie recording. TG
     1984</ul>
     1985
     1986<p><b>August 25, 2008.  Version 1.2552.</b></p>
     1987
     1988<ul type=None>
     1989<li><p>Sped up volume plane display solid rendering 2x by reusing color array. TG
     1990</ul>
     1991
     1992<p><b>August 22, 2008.  Version 1.2552.</b></p>
     1993
     1994<ul type=None>
     1995<li><p>Delayed volume dialog histogram and range updates to speed up
     1996cycling through volume planes. TG
     1997<li>Optimized speed of volume plane display. TG
     1998</ul>
     1999
     2000<p><b>August 21, 2008.  Version 1.2552.</b></p>
     2001
     2002<ul type=None>
     2003<li><p>Added Chimera video documentation to web site. AL
     2004<li><p>Changed implementation of solid style volume rendering with
     2005colormaps to not use opengl pixel transfer. Avoids graphics driver
     2006bug on GeForce 7300 Mac graphics. TG
     2007<li><p>Made solid volume colormap use 8-bit color values instead of float,
     2008more memory efficient. TG
     2009</ul>
     2010
     2011<p><b>August 20, 2008.  Version 1.2552.</b></p>
     2012
     2013<ul type=None>
     2014<li><p>Made imod file reader to correctly handle open vs closed contours. TG
     2015<li><p>Added support uint8 rgba color values in solid rendering, more
     2016memory efficient. TG
     2017</ul>
     2018
     2019<p><b>August 19, 2008.  Version 1.2552.</b></p>
     2020
     2021<ul type=None>
     2022<li><p>Removed broken spotlight help/search menu entry on aqua mac 10.5. TG
     2023<li><p>Fixed color_by_volume() routine used in scripts. TG
     2024</ul>
     2025
     2026<p><b>August 15, 2008.  Version 1.2550.</b></p>
     2027
     2028<ul type=None>
     2029<li><p>Added 8-bit color indices for solid volume rendering, more
     2030memory efficient.  Formerly only 16-bit indices used. TG
     2031</ul>
     2032
     2033<p><b>August 14, 2008.  Version 1.2550.</b></p>
     2034
     2035<ul type=None>
     2036<li><p>Made surface color tool ignore volume outline boxes. TG
     2037</ul>
     2038
     2039<p><b>August 13, 2008.  Version 1.2550.</b></p>
     2040
     2041<ul type=None>
     2042<li><p>Making imod file reader properly skip unused records. TG
     2043<li><p>Updated tomoplane extension to new surface model api. TG
     2044
     2045</ul>
     2046
     2047<p><b>August 12, 2008.  Version 1.2549.</b></p>
     2048
     2049<ul type=None>
     2050<li><p>Fixed bug where closing volume series removed wrong entry from menu. TG
     2051</ul>
     2052
     2053<p><b>August 1, 2008.  Version 1.2549.</b></p>
     2054
     2055<ul type=None>
     2056<li><p>Fixed black covering status line on aqua when graphics window
     2057resized smaller. TG
     2058</ul>
     2059
     2060<p><b>July 31, 2008.  Version 1.2548.</b></p>
     2061
     2062<ul type=None>
     2063<li><p>Added focus follows mouse preference, only shown and used on aqua. TG
     2064</ul>
     2065
     2066<p><b>July 30, 2008.  Version 1.2547.</b></p>
     2067
     2068<ul type=None>
     2069<li><p>Fixed pif map bug where integer file values scaled by floating point
     2070scale factor remained as an integer map.  Caused sparse histograms. TG
     2071<li><p>Made volume cap facing initially off for PIF maps since they are
     2072most often inverted. TG
     2073<li><p>Made marker resize mouse mode use caps lock instead of alt key. TG
     2074<li><p>Added option to hide in-window menus on aqua. TG
     2075</ul>
     2076
     2077
     2078<p><b>July 29, 2008.  Version 1.2546.</b></p>
     2079
     2080<ul type=None>
     2081<li><p>Moved create color key button to options panel. TG
     2082</ul>
     2083
     2084
     2085<p><b>July 28, 2008.  Version 1.2546.</b></p>
     2086
     2087<ul type=None>
     2088<li><p>Put new movie making tutorial on chimera tutorials and
     2089animations web pages. TG
     2090</ul>
     2091
     2092<p><b>July 23, 2008.  Version 1.2544.</b></p>
     2093
     2094<ul type=None>
     2095
     2096<li><p>Made volume series update histograms for all series.  Was only updating
     2097one when multiple series played simultaneosly. TG
     2098<li><p>
     2099</ul>
     2100
     2101<p><b>July 22, 2008.  Version 1.2544.</b></p>
     2102
     2103<ul type=None>
     2104<li><p>Made volume series tool handle multiwavelength priism data. TG
     2105<li><p>Made volume series tool allow playing all series at once. TG
     2106<li><p>Fixed memory leak when volumes created and closed. Data array
     2107was deallocated but not surface model and volume python object. TG
     2108<li><p>Added showDialog option to molmap command to suppress display of
     2109volume dialog (useful in MD trajectory per-frame scripts). TG
     2110<li><p>Made fetch eds able to set model id on command-line. TG
     2111</ul>
     2112
     2113<p><b>July 21, 2008.  Version 1.2544.</b></p>
     2114
     2115<ul type=None>
     2116<li><p>Fixed bug when volume data read canceled on opening,
     2117session save failed. TG
     2118</ul>
     2119
     2120<p><b>July 18, 2008.  Version 1.2544.</b></p>
     2121
     2122<ul type=None>
     2123<li><p>Made volume series tool copy changes in voxel size and volume origin. TG
     2124<li><p>Fixed bug saving volume over original file on a different file system
     2125than /tmp (file move didn't work). TG
     2126<li><p>Fixed bug where msms calculation says it succeeded but actually returns
     2127an incorrect empty surface. TG
     2128<li><p>Fixed movie recorder ffmpeg encoding on aqua, trouble reporting status
     2129from non-gui thread.  Disabled status reporting on aqua. TG
     2130<li><p>Made movie recorder not raise main window when doing image capture. TG
     2131</ul>
     2132
     2133<p><b>July 15, 2008.  Version 1.2542.</b></p>
     2134
     2135<ul type=None>
     2136<li><p>Fixed bug, surface color wrong if volume moved while data is being
     2137read. TG
     2138<li><p>Fixed space navigator lag on aqua. TG
     2139</ul>
     2140
     2141<p><b>July 9, 2008.  Version 1.2540.</b></p>
     2142
     2143<ul type=None>
     2144<li><p>Production release Chimera 1.2540.
     2145</ul>
     2146
     2147<p><b>July 8, 2008.  Version 1.2540.</b></p>
     2148
     2149<ul type=None>
     2150
     2151<li><p>Fixed bug where NaN volume normals caused raytracing failure. TG
     2152</ul>
     2153
     2154<p><b>July 7, 2008.  Version 1.2540.</b></p>
     2155
     2156<ul type=None>
     2157<li><p>Made vop resample command undisplay original instead of
     2158grid volume. TG
     2159<li><p>Fixed volume dialog shown/hidden indicator updating for new volumes. TG
     2160<li><p>Made crash report dialog on mac not appear for
     2161mscalc crashes (msms surface calculation). TG
     2162</ul>
     2163
     2164<p><b>July 2, 2008.  Version 1.2540.</b></p>
     2165
     2166<ul type=None>
     2167<li><p>Fixed aqua bug: patched pmw to make open dialog history popup menus
     2168appear on top. TG
     2169
     2170</ul>
     2171
     2172<p><b>July 1, 2008.  Version 1.2537.</b></p>
     2173
     2174<ul type=None>
     2175<li><p>Made volume solid style coloring properly color min/max data values. In
     2176some cases the data values corresponding to the end nodes on the volume
     2177histogram were not colored. TG
     2178<li><p>Fixed molecule copies behavior of crystal contacts tool
     2179and added command version. TG
     2180</ul>
     2181
     2182<p><b>June 30, 2008.  Version 1.2537.</b></p>
     2183
     2184<ul type=None>
     2185<li><p>Optimized morph map, 8x faster linear combination on 256^3 array. TG
     2186<li><p>Made vop resample command use better name for new volume. TG
     2187<li><p>Fixed aqua bug: patched pmw notebook bubble buttons and borders for
     2188aqua tk 8.5.2. TG
     2189
     2190</ul>
     2191
     2192<p><b>June 27, 2008.  Version 1.2537.</b></p>
     2193
     2194<ul type=None>
     2195<li><p>Fixed aqua bug: clipped volume plane button text and feature buttons. TG
     2196<li><p>Fixed volume show/hide icon in volume dialog in solid mode. Sometimes
     2197showed incorrect display state. TG
     2198</ul>
     2199
     2200<p><b>June 26, 2008.  Version 1.2537.</b></p>
     2201
     2202<ul type=None>
     2203<li><p>Added mS shortcut to place markers on selected atoms. TG
     2204</ul>
     2205
     2206<p><b>June 25, 2008.  Version 1.2537.</b></p>
     2207
     2208<ul type=None>
     2209<li><p>Added aqua in-window menubars for all dialogs: castp,
     2210selection workbench, modbase, rotamers, render by attr, viewdock, demo, movie,
     2211multalign. TG
     2212</ul>
     2213
     2214<p><b>June 24, 2008.  Version 1.2535.</b></p>
     2215
     2216<ul type=None>
     2217<li><p>Fixed aqua bug: disappearing bonds (stick style) and vrml cylinders
     2218when zooming. TG
     2219<li><p>Fixed aqua bug: playing morph map gave volume dialog focus
     2220prevented stopping morph playback. TG
     2221<li><p>Fixed aqua bug: mouse scroll wheel zooming very insensitive. TG
     2222</ul>
     2223
     2224<p><b>June 19, 2008.  Version 1.2534.</b></p>
     2225
     2226<ul type=None>
     2227<li><p>Fixed volume dialog surface brightness and transparency sliders.
     2228They were producing color component values > 1 causing error messages. TG
     2229<li><p>Made command-q and the main window close button show the quit
     2230confirmation dialog on aqua. TG
     2231</ul>
     2232
     2233<p><b>June 18, 2008.  Version 1.2532.</b></p>
     2234
     2235<ul type=None>
     2236<li><p>Added in-window menu bars to volume and tracer dialog windows in aqua. TG
     2237<li><p>Added vop subtract operation for making difference maps. TG
     2238<li><p>Fixed volume histogram flickering on aqua. TG
     2239</ul>
     2240
     2241<p><b>June 17, 2008.  Version 1.2531.</b></p>
     2242
     2243<ul type=None>
     2244<li><p>Fixed divide by zero warning message appearing in shell when
     2245using volume solid style rendering with opacity = 1. TG
     2246</ul>
     2247
     2248<p><b>June 16, 2008.  Version 1.2531.</b></p>
     2249
     2250<ul type=None>
     2251<li><p>Fixed error when deleting volumes caused by trying to update
     2252volume shown indicator (dash icon) after deletion. TG
     2253<li><p>Added option/command key 3-button mouse emulation in aqua. TG
     2254</ul>
     2255
     2256<p><b>June 13, 2008.  Version 1.2531.</b></p>
     2257
     2258<ul type=None>
     2259
     2260<li><p>Added MacMolPlt/Gamess quantum orbitals volume file reader. TG
     2261</ul>
     2262
     2263<p><b>June 12, 2008.  Version 1.2531.</b></p>
     2264
     2265<ul type=None>
     2266<li><p>Made volume viewer and volume tracer show menu bar at top of screen
     2267on aqua. TG
     2268</ul>
     2269
     2270<p><b>June 11, 2008.  Version 1.2529.</b></p>
     2271
     2272<ul type=None>
     2273<li><p>Fixed display of headings in preferences tools pane on aqua. TG
     2274<li><p>Added focus follow mouse mode for aqua. TG
     2275</ul>
     2276
     2277<p><b>June 10, 2008.  Version 1.2527.</b></p>
     2278
     2279<ul type=None>
     2280<li><p>Made opening electrostatic potential file formats (delphi, apbs, uhbd)
     2281and molecular orbital file formats (gaussian, gopenmol) turn of box face
     2282surface capping so that negative threshold levels do not result in box surface.
     2283TG
     2284<li><p>Fixed actions menu surface transparency on molecular surfaces colored
     2285by molecule. TG
     2286<li><p>Made in-memory writable volumes created by volume eraser have names
     2287ending in "copy" to distinguish them from original volumes. TG
     2288<li><p>Made opening volume file not use data from already opened writable
     2289volume since that data may be modified later. TG
     2290<li>Fixed aqua 60% cpu usage when showing model panel, but in tix
     2291scrolledhlist with headers. TG
     2292</ul>
     2293
     2294<p><b>June 9, 2008.  Version 1.2527.</b></p>
     2295
     2296<ul type=None>
     2297<li><p>Made model menus use multiple columns on x11 if they have more than
     229835 entries to avoid inaccessible entries off bottom of screen. TG
     2299
     2300<li><p>Made saving volume data update the volume name in volume dialog
     2301and menus. TG
     2302</ul>
     2303
     2304<p><b>June 6, 2008.  Version 1.2525.</b></p>
     2305
     2306<ul type=None>
     2307<li><p>Made surface display use opengl vertex buffer objects instead of display
     2308lists, leading to 2x faster rendering on two tested graphics cards. TG
     2309</ul>
     2310
     2311<p><b>June 5, 2008.  Version 1.2525.</b></p>
     2312
     2313<ul type=None>
     2314<li><p>Made priism volume file reader set correct voxel size. TG
     2315<li><p>Made molecular surface display for a set of atoms not override
     2316partial surface display done with surface zone tool. TG
     2317<li><p>Made active volume name highlighting on aqua use blue color. Was using
     2318white which was identical to inactive background. TG
     2319
     2320<li><p>Made main window have focus at startup on aqua. TG
     2321</ul>
     2322
     2323<p><b>June 3, 2008.  Version 1.2525.</b></p>
     2324
     2325<ul type=None>
     2326<li><p>Fixed hang on aqua caused by benchmark dialog horizontal scrollbar
     2327display/undisplay. TG
     2328<li><p>Fixed aqua bug where movie recorder could not be stopped because
     2329graphics window was given focus at each frame preventing pressing the Stop
     2330button. TG
     2331<li><p>Fixed aqua bug where movie recorder could not find ffmpeg executable. TG
     2332</ul>
     2333
     2334<p><b>June 2, 2008.  Version 1.2525.</b></p>
     2335
     2336<ul type=None>
     2337<li><p>Made priism volume file reader handle xywzt and xyzwt data orders
     2338(w = wavelength, t = time). TG
     2339
     2340</ul>
     2341
     2342<p><b>May 30, 2008.  Version 1.2524.</b></p>
     2343
     2344<ul type=None>
     2345<li><p>Fixed molecular surface bug where closing surface model and then
     2346reshowing surface for subset of atoms showed entire surface. TG
     2347<li><p>Made toolbar and model panel balloons not take focus in aqua. TG
     2348</ul>
     2349
     2350<p><b>May 28, 2008.  Version 1.2523.</b></p>
     2351
     2352<ul type=None>
     2353<li><p>Padded selection button in lower right corner of main window so that
     2354text is not clipped on aqua. TG
     2355<li><p>Made atom spec balloons on aqua not have window frame, and not take
     2356focus. TG
     2357<li><p>Added apple application menu entries for About Chimera... and
     2358Preferences... on aqua. TG
     2359
     2360<li><p>Made model panel Select button work on molecular surfaces. TG
     2361</ul>
     2362
     2363<p><b>May 27, 2008.  Version 1.2522.</b></p>
     2364
     2365<ul type=None>
     2366<li><p>Fixed volume image stack session saving bug. TG
     2367<li><p>Fixed recently introduced bug where color byatom with a surface shown
     2368generated an error. TG
     2369<li><p>Fixed aqua chimera crash when any dialog shown by disabling apple event
     2370handling code. TG
     2371</ul>
     2372
     2373<p><b>May 26, 2008.  Version 1.2522.</b></p>
     2374
     2375<ul type=None>
     2376<li><p>Made actions atom/ribbon/surface menus work with multiscale models. TG
     2377
     2378</ul>
     2379
     2380<p><b>May 22, 2008.  Version 1.2517.</b></p>
     2381
     2382<ul type=None>
     2383<li><p>Made space navigator work with independent center of rotation mode. TG
     2384<li><p>Made select command on surfaces select all the surface pieces. TG
     2385</ul>
     2386
     2387<p><b>May 21, 2008.  Version 1.2517.</b></p>
     2388
     2389<ul type=None>
     2390<li><p>Fixed recently introduced bug where cofr command did not work on
     2391undisplayed selected surfaces. TG
     2392</ul>
     2393
     2394<p><b>May 20, 2008.  Version 1.2514.</b></p>
     2395
     2396<ul type=None>
     2397<li><p>Made selecting molecular surface select atoms and bonds. TG
     2398<li><p>Made action menu set pivot work on selected surfaces. TG
     2399<li><p>Made volume viewer detect surface color/style changes made from Actions menu or by other means. TG
     2400</ul>
     2401
     2402<p><b>May 19, 2008.  Version 1.2511.</b></p>
     2403
     2404<ul type=None>
     2405<li><p>Fixed fit map error when no atoms selected and simulated map enabled. TG
     2406</ul>
     2407
     2408<p><b>May 15, 2008.  Version 1.2511.</b></p>
     2409
     2410<ul type=None>
     2411<li><p>Made Actions / Focus menu entry work for selected surfaces. TG
     2412<li><p>Fixed volume series error when playing series when active volume
     2413in not in series. TG
     2414<li><p>Fixed volume series bug undisplaying surfaces when caching off. TG
     2415</ul>
     2416
     2417<p><b>May 13, 2008.  Version 1.2510.</b></p>
     2418
     2419<ul type=None>
     2420<li><p>Made Actions menu entries work when molecular surfaces are selected.
     2421Formerly they only worked when atoms were selected. TG
     2422<li><p>Made selecting a surface in mesh or dot style require clicking on
     2423a mesh line or dot.  Formerly any area of the surface could be clicked.
     2424The new behavior allows selecting molecules within surfaces. TG
     2425<li><p>Made volume surfaces selectable. TG
     2426<li><p>Made Actions / Surface and Actions / Color menu entries work on
     2427non-molecular surfaces. TG
     2428<li><p>Removed Actions / Target menu. TG
     2429</ul>
     2430
     2431<p><b>May 12, 2008.  Version 1.2510.</b></p>
     2432
     2433<ul type=None>
     2434<li><p>Fixed crash at startup on mac when remote displaying caused by
     2435space navigator tool. Same problem when --nogui mode used and the user
     2436is not logged in to the mac console. TG
     2437</ul>
     2438
     2439<p><b>May 9, 2008.  Version 1.2510.</b></p>
     2440
     2441<ul type=None>
     2442<li><p>Made molecular surface calculation report the number of surface
     2443components and the solvent excluded and solvent accessible surface areas. TG
     2444<li><p>Fixed error in surface color tool when surface is colored by volume
     2445value and the volume is closed and then the surface is changed. TG
     2446</ul>
     2447
     2448<p><b>May 8, 2008.  Version 1.2510.</b></p>
     2449
     2450<ul type=None>
     2451<li><p>Removed accelerators on/off menu entries from Tools / General Controls
     2452menu and renamed Accelerators List entry to Keyboard Shortcuts.  Keyboard
     2453shortcuts are now enabled with a switch on the dialog and that setting is now
     2454saved in preferences automatically. TG
     2455</ul>
     2456
     2457<p><b>May 7, 2008.  Version 1.2510.</b></p>
     2458
     2459<ul type=None>
     2460<li><p>Made Fetch Structure by ID report download progress in status line. TG
     2461</ul>
     2462
     2463<p><b>May 6, 2008.  Version 1.2510.</b></p>
     2464
     2465<ul type=None>
     2466<li><p>Fixed recently introduced bug in model panel Tile button where models
     2467were placed in random order on screen.  Fixed ordering is by model id number. TG
     2468
     2469</ul>
     2470
     2471<p><b>May 5, 2008.  Version 1.2510.</b></p>
     2472
     2473<ul type=None>
     2474<li><p>Put least used controls of surface color dialog in options panel. TG
     2475<li><p>Made surface color dialog use a separate volume menu that is displayed
     2476when color method is by volume data value. Formerly every volume appeared as
     2477an entry in the coloring method menu. TG
     2478<li><p>Added electrostatic coloring method to surface color dialog. This is
     2479the same as coloring by volume data value, only with dialog text specialized
     2480to save "electrostatic potential" to reduce confusion. TG
     2481<li><p> Fixed session saving bug with custom colored molecular surface models.
     2482Bug introduced in past month.  TG
     2483</ul>
     2484
     2485<p><b>May 2, 2008.  Version 1.2510.</b></p>
     2486
     2487<ul type=None>
     2488
     2489<li><p>Made benchmark tool draw models on screen to avoid inflated frame rates.
     2490Formerly drawing was done in an internal buffer and not shown and newer drivers
     2491shortcut the rendering leading to frame rates sometimes 2x higher than in
     2492actual use.  TG
     2493<li><p>Added "report scores" button to benchmark tool to send scores to
     2494RBVI for posting on web. TG
     2495<li><p>Simplified benchmark dialog to show only the commonly used controls,
     2496with others hidden in an options panel. TG
     2497<li><p>Fixed bug in benchmark tool with solid rendering where volume was not
     2498in field of view so some graphics drivers rendered nothing leading to very
     2499large test cases which caused memory errors. TG
     2500</ul>
     2501
     2502<p><b>April 30, 2008.  Version 1.2508.</b></p>
     2503
     2504<ul type=None>
     2505<li><p>Fixed bug in crystal contacts tool where contacts between a crystal
     2506asymmetric unit and copies translated by unit cell translations were not
     2507detected. TG
     2508<li><p>Added option to crystal contacts tool to create moleucule models for
     2509contacting copies. TG
     2510</ul>
     2511
     2512<p><b>April 28, 2008.  Version 1.2506.</b></p>
     2513
     2514<ul type=None>
     2515<li><p>Made volume eraser radius slider resize when the dialog is resized. TG
     2516</ul>
     2517
     2518<p><b>April 25, 2008.  Version 1.2506.</b></p>
     2519
     2520<ul type=None>
     2521<li><p>Made model panel Tile button highlight when non-molecule models selected. TG
     2522</ul>
     2523
     2524<p><b>April 24, 2008.  Version 1.2506.</b></p>
     2525
     2526<ul type=None>
     2527<li><p>Made model panel Tile button work with all models, not just molecules. TG
     2528</ul>
     2529
     2530<p><b>April 18, 2008.  Version 1.2505.</b></p>
     2531
     2532<ul type=None>
     2533<li><p>Made phantom force feedback tool volume aligned cross-hair display
     2534correctly when local volume coordinates are rotated. TG
     2535</ul>
     2536
     2537<p><b>April 17, 2008.  Version 1.2504.</b></p>
     2538
     2539<ul type=None>
     2540<li><p>Added color palette option menu and a button to reverse color order
     2541to surface color tool. TG
     2542</ul>
     2543
     2544<p><b>April 16, 2008.  Version 1.2503.</b></p>
     2545
     2546<ul type=None>
     2547<li><p>Made multiscale tool with surface resolution = 0 (solvent excluded
     2548surface) use probe radius, vertex density and disjoint component preference
     2549settings.  Formerly it used values that could not be changed. TG
     2550<li><p>Made relative orientation schematic shortcut "ai" not give an error
     2551when rotation angle is zero. TG
     2552</ul>
     2553
     2554<p><b>April 15, 2008.  Version 1.2503.</b></p>
     2555
     2556<ul type=None>
     2557<li><p>Made phantom force feedback tool handle volume step change, and
     2558made move marker warn if no marker is under cursor. TG
     2559</ul>
     2560
     2561<p><b>April 11, 2008.  Version 1.2503.</b></p>
     2562
     2563<ul type=None>
     2564
     2565<li><p>Simplified Phantom Force Feedback dialog.  Made key commands work from
     2566main Chimera window.  Changed move models, zoom, contour level, move marker
     2567keyboard commands to press once to activate, again to deactivate.  Formerly key
     2568had to be held down. TG
     2569<li><p>Included Phantom force feedback OpenHaptics event handling in Windows
     2570Chimera distribution. User is required to install OpenHaptics driver. TG
     2571</ul>
     2572
     2573<p><b>April 10, 2008.  Version 1.2503.</b></p>
     2574
     2575<ul type=None>
     2576<li><p>Fixed bug where molecular surface calculation for zero atoms failed. TG
     2577</ul>
     2578
     2579<p><b>April 8, 2008.  Version 1.2503.</b></p>
     2580
     2581<ul type=None>
     2582<li><p>Made "ac" command accept arguments which are keyboard shortcuts to run.
     2583Without arguments it still enables typing keyboard shortcuts to main window. TG
     2584</ul>
     2585
     2586<p><b>April 7, 2008.  Version 1.2503.</b></p>
     2587
     2588<ul type=None>
     2589<li><p>Added support for Space Navigator six degree-of-freedom input device
     2590to Windows Chimera versions. TG
     2591</ul>
     2592
     2593<p><b>April 4, 2008.  Version 1.2503.</b></p>
     2594
     2595<ul type=None>
     2596<li><p>Made molecular surface calculation not show a console window on Windows.
     2597TG
     2598</ul>
     2599
     2600<p><b>April 3, 2008.  Version 1.2503.</b></p>
     2601
     2602<ul type=None>
     2603<li><p>Fixed molecular surface calculation on Windows. Was interpreting ctrl-z
     2604as end of input. Also mscalc program was not started correctly. TG
     2605</ul>
     2606
     2607<p><b>April 2, 2008.  Version 1.2502.</b></p>
     2608
     2609<ul type=None>
     2610<li><p>Added support for Space Navigator six degree-of-freedom input device
     2611to Mac Chimera versions. TG
     2612</ul>
     2613
     2614<p><b>April 1, 2008.  Version 1.2502.</b></p>
     2615
     2616<ul type=None>
     2617<li><p>Fixed bug where enabling surface capping and surface coloring caused
     2618continuous recalculation of cap and colors. TG
     2619
     2620<li><p>Made surface cap color not flicker to solid color when moving cap. TG
     2621</ul>
     2622
     2623<p><b>March 27, 2008.  Version 1.2502.</b></p>
     2624
     2625<ul type=None>
     2626<li><p>Made multiscale dialog use stand-alone program molecular surface
     2627calculation when resolution set to zero for solvent excluded surface. TG
     2628</ul>
     2629
     2630<p><b>March 26, 2008.  Version 1.2501.</b></p>
     2631
     2632<ul type=None>
     2633<li><p>Optimized surface distance calculation (keyboard shortcut "sd") by
     2634translating Python code to C++.  Several hundred times faster.  TG
     2635</ul>
     2636
     2637<p><b>March 25, 2008.  Version 1.2501.</b></p>
     2638
     2639<ul type=None>
     2640<li><p>Changed solvent excluded/accessible surface area calculation to use
     2641analytical values instead of approximate values calculated from the triangulated
     2642surface (which depended on vertex density). TG
     2643<li><p>Added per-residue solvent excluded/accessible surface area (areaSES,
     2644areaSAS) attributes viewable with Render by Attribute tool. TG
     2645<li><p>Added solvent excluded/accessible surface area in Reply Log
     2646output when molecular surface is calculated.
     2647<li><p>Made up and down arrow keys work with selected surface pieces. TG
     2648<li><p>Fixed bug in IMOD mesh file reader where normal vectors appeared in
     2649the surface vertex array resulting in wrong inertia calculation. TG
     2650<li><p>Added "ra" keyboard shortcut for showing render-by-attribute dialog. TG
     2651<li><p>Added "se" keyboard shortcut for toggling silhouette edge display. TG
     2652<li><p>Fixed bug in surface distance calculation where distance to an
     2653edge was used when the closest distance was actually to a vertex. TG
     2654</ul>
     2655
     2656<p><b>March 20, 2008.  Version 1.2501.</b></p>
     2657
     2658<ul type=None>
     2659<li><p>Fixed meshmol command on molecular surfaces, "truth value ambiguous"
     2660error. TG
     2661<li><p>Fixed error in Measure and Color Blobs, "array cannot be safely
     2662cast to required type" on 64-bit Chimera versions. TG
     2663<li><p>Made Color Zone, Surface Zone and Surface Color work on MSMS surface
     2664caps. TG
     2665</ul>
     2666
     2667<p><b>March 18, 2008.  Version 1.2500.</b></p>
     2668
     2669<ul type=None>
     2670<li><p>Made Chimera calculate solvent excluded molecular surfaces using a
     2671standalone application so crashes do not crash Chimera.  TG
     2672<li><p>Made molecular surface calculation assign per-atom solvent excluded
     2673surface area (areaSES) and solvent accessible surface area (areaSAS) values
     2674that can be used with Render by Attribute dialog or the "select" command. TG
     2675<li><p>Molecular surfaces now are implemented using SurfaceModel.  Some
     2676new attributes of this type of model are visible in the selection and model
     2677attribute inspector dialogs. TG
     2678<li><p>Eliminated warning messages that appeared in the Chimera reply log
     2679on Mac OS 10.5 about an unhandled apple event.  TG
     2680<li><p>Changed Benchmark molecule tests to only time one molecule instead of
     2681six.
     2682<li><p>Fixed ribbon benchmark timing, previous scores invalid.  TG
     2683</ul>
     2684
     2685<p><b>March 17, 2008.  Version 1.2500.</b></p>
     2686
     2687<ul type=None>
     2688<li><p>Fixed a triangle template allocation bug in MSMS molecular surface
     2689calculation reducing number of crash cases in half.  Also changed to allow
     2690surface calculation when one atom is entirely inside of another.  TG
     2691<li><p>Made Movie Recorder respect preference for saving POVray files. TG
     2692<li><p>Fixed InterSurf to use new SurfaceModel Python names. TG
     2693</ul>
     2694
     2695<p><b>March 11, 2008.  Version 1.2500.</b></p>
     2696
     2697<ul type=None>
     2698<li><p>Renamed Surface_Model to SurfaceModel and changed Python method
     2699names and attributes to eliminated underscore characters.  TG
     2700</ul>
     2701
     2702<p><b>March 5, 2008.  Version 1.2499.</b></p>
     2703
     2704<ul type=None>
     2705<li><p>Added dot surface display and dot size setting to surface models,
     2706settable with selection inspector. TG
     2707</ul>
     2708
     2709<p><b>March 4, 2008.  Version 1.2498.</b></p>
     2710
     2711<ul type=None>
     2712<li><p>Reduced memory use of volume solid style rendering in color map
     2713mode.  Was unnecessarily making floating point copy of map. TG
     2714</ul>
     2715
     2716<p><b>February 29, 2008.  Version 1.2497.</b></p>
     2717
     2718<ul type=None>
     2719<li><p>Removed setting to flip surface lighting normals visible in
     2720selection inspector dialog. TG
     2721</ul>
     2722
     2723<p><b>February 28, 2008.  Version 1.2496.</b></p>
     2724
     2725<ul type=None>
     2726<li><p>Added consistency checking (valid record size) in delphi map
     2727file reader. TG
     2728</ul>
     2729
     2730<p><b>February 27, 2008.  Version 1.2495.</b></p>
     2731
     2732<ul type=None>
     2733<li><p>Added checkbuttons to volume tracer mouse mode panel that match
     2734those in the Mouse menu. TG
     2735<li><p>Fixed volume tracer session restore bug where a second traced surfaces
     2736model was created after restoring a session containing traced surfaces. TG
     2737
     2738<li><p>Made volume tracer delete surface panel only delete selected
     2739traced surfaces.  Was deleting any selected surface. TG
     2740<li><p>Made volume tracer continuous marker placement while dragging
     2741work with "on spot", "on plane", or "outside data" mouse mode.  Was ignoring
     2742those settings and always dropping markers on plane. TG
     2743</ul>
     2744
     2745<p><b>February 26, 2008.  Version 1.2495.</b></p>
     2746
     2747<ul type=None>
     2748<li><p>Fixed volume tracer bug where traceback given if "marker color
     2749matches volume color" enabled and marker is placed. TG
     2750<li><p>Made crash dump detection for bug reporting work on Mac OS 10.5.
     2751Mac OS 10.5 uses separate file for each crash, while 10.4 used one file
     2752for all crashes of the same application. TG
     2753</ul>
     2754
     2755<p><b>February 22, 2008.  Version 1.2495.</b></p>
     2756
     2757<ul type=None>
     2758<li><p>Modified per-model clipping command to not modify existing clip
     2759plane axis or origin unless explicit options are given. TG
     2760
     2761</ul>
     2762
     2763<p><b>February 21, 2008.  Version 1.2495.</b></p>
     2764
     2765<ul type=None>
     2766<li><p>Added option to create simulated map (uses molmap command)
     2767to the fit map dialog. TG
     2768</ul>
     2769
     2770<p><b>February 20, 2008.  Version 1.2495.</b></p>
     2771
     2772<ul type=None>
     2773<li><p>Added per-model clipping command mclip. TG
     2774<li><p>Fixed volume eraser bug that gave traceback when erasing done
     2775with eraser sphere entirely outside of volume. TG
     2776<li><p>Fixed bug on movement mouse mode where no translation was possible
     2777if near clip plane was at or in front of eye position.  Changed behavior
     2778so amount of translation is based on dragging center of rotation of object.
     2779TG
     2780</ul>
     2781
     2782<p><b>February 19, 2008.  Version 1.2494.</b></p>
     2783
     2784<ul type=None>
     2785<li><p>Added zflip option to vop (volume operation) command to change
     2786the hand of a map by reversing the order of the z planes. TG
     2787</ul>
     2788
     2789<p><b>February 15, 2008.  Version 1.2493.</b></p>
     2790
     2791<ul type=None>
     2792<li><p>Added IMOD map file reader, file suffix ".rec". These are MRC maps
     2793but signed 8-bit mode is interpreted as unsigned. TG
     2794<li><p>Changed volume solid style transparency modulation from
     2795t -&gt; t ** (1.0/planes) to t -&gt; t ** (1.0/(planes*t)). Here planes
     2796= minimum number of planes along each axis times the transparency factor
     2797and the initial transparency t is the height of the transfer function on
     2798the histogram (0-1 range). For transparent voxels the change is minor.
     2799For opaque voxels it makes the effective thickness smaller and avoids
     2800a large brightness jump between opacity 0.99 and 1.0. TG
     2801
     2802</ul>
     2803
     2804<p><b>February 13, 2008.  Version 1.2493.</b></p>
     2805
     2806<ul type=None>
     2807<li><p>Fixed bug where deleting volume tracer links by means other than
     2808the "delete links" menu entry would later cause session saving to fail.  TG
     2809<li><p>Made session saving for volume opens put paths in the session file
     2810that are relative to the session file directory if the volume data lies
     2811within or below that directory. This allows restoring the session file after
     2812moving a directory containing session files and volume data. TG
     2813<li><p>Added linewidth option to shape command for meshes. TG
     2814<li><p>Made shape command show mesh by default only for icosahedron
     2815(not sphere) with lattice option specified. TG
     2816<li><p>Changed shape command default color to "gray". TG
     2817</ul>
     2818
     2819<p><b>February 12, 2008.  Version 1.2493.</b></p>
     2820
     2821<ul type=None>
     2822
     2823<li><p>Added displayThreshold option to molmap command to set the initial
     2824contour level of the new map so that the specified fraction of total mass
     2825is contained within the contour.  Default value 0.95.  TG
     2826<li><p>Changed effect of volume solid style transparency slider so that
     2827it modulates transparency even when factor times depth in planes is less
     2828than 1.  This allows making completely opaque single planes. TG
     2829</ul>
     2830
     2831<p><b>February 8, 2008.  Version 1.2493.</b></p>
     2832
     2833<ul type=None>
     2834<li><p>Reduced memory use when saving a volume zone. For maps larger than
     283516 Mvoxels the map mask is computed plane by plane.  Smaller maps use 12
     2836bytes per voxel overhead.  TG
     2837</ul>
     2838
     2839<p><b>February 7, 2008.  Version 1.2493.</b></p>
     2840
     2841<ul type=None>
     2842<li><p>Fixed split map button in color zone dialog. TG
     2843</ul>
     2844
     2845<p><b>January 31, 2008.  Version 1.2492.</b></p>
     2846
     2847<ul type=None>
     2848<li><p>Combined "fit model in map" and "fit map in map" dialogs into a single
     2849dialog, and combined menu entries into one entry.  Dialog has new layout but
     2850same functionality as original two dialogs. TG
     2851<li><p>Added option for real-time updating of correlation and average map
     2852value to fit map dialog. TG
     2853</ul>
     2854
     2855<p><b>January 30, 2008.  Version 1.2486.</b></p>
     2856
     2857<ul type=None>
     2858<li><p>Added ability to create surfaces from stacks of loops and curves
     2859with the volume path tracer tool.  Uses the new Surface panel of the volume
     2860path tracer dialog. TG
     2861<li><p>Renamed "volume path tracer" to "volume tracer".  TG
     2862<li><p>Reordered volume tools menu to put more frequently useful tools near
     2863the top and group them by functionality. TG
     2864<li><p>Added split map button to color zone dialog and eliminated separate
     2865volume tools menu entry for split map. TG
     2866
     2867<li><p>Changed molmap ratio of resolution to Gaussian standard deviation
     2868to be 1/(pi*sqrt(2)) (~0.225) from former value of 1/(2*sqrt(pi)) (~0.282). TG
     2869<li>Made split map by color zone give proper alignment when map coordinates
     2870involve a rotation.
     2871</ul>
     2872
     2873<p><b>January 29, 2008.  Version 1.2485.</b></p>
     2874
     2875<ul type=None>
     2876<li><p>Added keyboard shortcut "or" to toggle orthographic projection. TG
     2877</ul>
     2878
     2879<p><b>January 25, 2008.  Version 1.2485.</b></p>
     2880
     2881<ul type=None>
     2882<li><p>Added ability to export surfaces in Wavefront OBJ format using
     2883File / Export Scene.  TG
     2884<li><p>Optimized "split map by color zone" to use less memory.  Operates
     2885plane by plane for maps larger than 16 Mvoxels.  TG
     2886
     2887<li><p>Added mouse mode to resize a selected surface by dragging.  Enabled
     2888for one drag use by keyboard shortcut sz.  TG
     2889<li><p>Added keyboard shortcut "ao" to activate only selected surfaces. TG
     2890<li><p>Added keyboard shortcut "oc" to allow typing one command and then
     2891automatically return to entering keyboard shortcuts. TG
     2892<li><p>Allowed resizing volume path tracer markers by dragging the mouse
     2893while holding the Alt key down if the move/resize mode is enabled. TG
     2894</ul>
     2895
     2896<p><b>January 24, 2008.  Version 1.2485.</b></p>
     2897
     2898<ul type=None>
     2899<li><p>Added "resample" operation to vop command to resample one volume
     2900data set on the grid of a second volume data set.  TG
     2901</ul>
     2902
     2903<p><b>January 23, 2008.  Version 1.2485.</b></p>
     2904
     2905<ul type=None>
     2906
     2907<li><p>Fixed incorrect rainbow colormap direction for volumes with
     2908rotated local coordinates. TG
     2909<li><p>Made "measure and color blobs" dialog and mask command ignore
     2910outline boxes around volume data. TG
     2911<li><p>Added "shape" command that makes surfaces having standard geometric
     2912shapes.  Handles cylinder, sphere, and icosahedron.  Includes icosahedral
     2913mesh capabilities of hkcage command.  Includes interpolating icosahedron
     2914with sphere and alternate coordinates systems as in the Icosahedron surface
     2915dialog. TG
     2916<li><p>Changed vm keyboard shortcut to mask active volume using selected
     2917surfaces.  Formerly it masked volume using volume contour surface.  TG
     2918</ul>
     2919
     2920<p><b>January 22, 2008.  Version 1.2485.</b></p>
     2921
     2922<ul type=None>
     2923<li><p>Made volume contour surfaces have correct lighting when the voxel
     2924size along an axis is made negative to flip the hand of the map.  Formerly
     2925two sided lighting gave dark surface in this case. TG
     2926<li><p>Made image stack volume reader handle multi-page tiff images. TG
     2927<li><p>Fixed surface capping bug when new surface created while capping is
     2928enabled.  TG
     2929</ul>
     2930
     2931<p><b>January 18, 2008.  Version 1.2485.</b></p>
     2932
     2933<ul type=None>
     2934<li><p>Added molmap command to make volume from a molecule by summing
     2935Gaussians at each atom position. TG
     2936</ul>
     2937
     2938<p><b>January 16, 2008.  Version 1.2483.</b></p>
     2939
     2940<ul type=None>
     2941<li><p>Made opening tiff image stacks work by selecting all images in the
     2942open dialog.  Formerly only one image was selected and others that had the
     2943same prefix and different numeric suffix were inferred. TG
     2944<li><p>Made image stack reader handle image types other than TIFF.  Can
     2945handle any image format understood by the Python image library (e.g. png,
     2946jpeg). TG
     2947</ul>
     2948
     2949<p><b>January 15, 2008.  Version 1.2483.</b></p>
     2950
     2951<ul type=None>
     2952
     2953<li><p>Fixed chimera "--send" startup option on mac.  Was always starting
     2954a new instance of chimera. TG
     2955</ul>
     2956
     2957<p><b>January 11, 2008.  Version 1.2483.</b></p>
     2958
     2959<ul type=None>
     2960<li><p>Removed marker set models closed with the file menu entry in
     2961the volume path tracer dialog.  Formerly the models were just emptied
     2962of markers. TG
     2963<li><p>Changed mask command sandwich option default value to true. TG
     2964<li><p>Changed mask command fullmap option to require a true/false value.
     2965Formerly the option took no value. TG
     2966</ul>
     2967
     2968<p><b>January 10, 2008.  Version 1.2483.</b></p>
     2969
     2970<ul type=None>
     2971<li><p>Made default projection axis for mask command y instead of z. TG
     2972
     2973<li><p>Renamed "pick surface pieces" dialog and menu entry to the more
     2974descriptive "measure and color blobs". TG
     2975<li><p>Added slab option to mask command to mask using a slab of specified
     2976thickness created by thickening a surface. TG
     2977</ul>
     2978
     2979<p><b>January 9, 2008.  Version 1.2483.</b></p>
     2980
     2981<ul type=None>
     2982<li><p>Added selection inspector attributes for surface pieces:
     2983surface piece count, line thickness, line smoothing, lighting, two
     2984sided lighting, lighting normal direction, transparency brightness. TG
     2985<li><p>Made selection inspector attributes for surface models and pieces
     2986update when changed using other dialogs or commands. TG
     2987</ul>
     2988
     2989<p><b>January 8, 2008.  Version 1.2481.</b></p>
     2990
     2991<ul type=None>
     2992<li><p>Added attributes to selection inspector dialog for surfaces and
     2993surface pieces.  Attributes: color, display style (mesh/solid), displayed,
     2994triangle count, active, selectable with mouse.  TG
     2995
     2996<li><p>Made selected surfaces show green outline even when "selectable with
     2997mouse" is turned off.  TG
     2998<li><p>Made keyboard shortcuts work on surfaces selected with select command.
     2999The select command selects the surface model but not the surface components.
     3000TG
     3001</ul>
     3002
     3003<p><b>January 7, 2008.  Version 1.2481.</b></p>
     3004
     3005<ul type=None>
     3006<li><p>Made surfnet tool create a surface model instead of a vrml model.
     3007Allows measuring enclosed volume, coloring, splitting disjoint components,
     3008....  TG
     3009<li><p>Eliminated _cubes contour calculation module.  TG
     3010</ul>
     3011
     3012<p><b>January 2, 2008.  Version 1.2481.</b></p>
     3013
     3014<ul type=None>
     3015<li><p>Added fill value option to vop command.  Large negative fill values
     3016can produce flat cut faces when erasing an octant.  TG
     3017
     3018</ul>
     3019
     3020<p><b>December 21, 2007.  Version 1.2480.</b></p>
     3021
     3022<ul type=None>
     3023<li><p>Made help command show documentation for commands volume, topo, sym,
     3024bondzone, split, msc, meshmol, mask, hkcage, crystalcontacts.  TG
     3025<li><p>Added vop (volume operation command) to erase an octant.  Plan to
     3026support many other volume modifying operations (gaussian filter, erase
     3027outside sphere, interpolate, ...) as options to this command in the future.
     3028TG
     3029<li><p>Changed volume suffixes from <N> format (e.g. "map.mrc <1>")
     3030to instead append model id number.  Previous suffix number was not the
     3031model id number.  TG
     3032</ul>
     3033
     3034<p><b>December 20, 2007.  Version 1.2480.</b></p>
     3035
     3036<ul type=None>
     3037<li><p>Made meshmol command work when surface has the same model id number
     3038as an existing molecule.  TG
     3039<li><p>Fixed bug in multiscale tool where molecule copies were not closed
     3040when multiscale model deleted.  TG
     3041</ul>
     3042
     3043<p><b>December 18, 2007.  Version 1.2479.</b></p>
     3044
     3045<ul type=None>
     3046<li><p>Made changing volume step size with step menu not turn off automatic
     3047step size adjustment.  Now the voxel limit for automatic step adjustment is
     3048instead changed to the number of voxels shown with the chosen step.  TG
     3049<li><p>Changed default volume solid threshold brightness at 99% rank data
     3050value from 1.0 to 0.99 to avoid completely opaque voxels.  TG
     3051<li><p>Reduced memory allocation used to zero volume solid 3-d texture from
     30524*(number of voxels) bytes to 4*(number of voxels in one xy plane).  TG
     3053<li><p>Optimized pick surface piece tool.  About 10x faster in typical case.
     3054TG
     3055<li><p>Added Tools / Volume Data menu entry that adds Volume menu to main
     3056window menu bar, and remembers this setting for future sessions.  TG
     3057</ul>
     3058
     3059<p><b>December 14, 2007.  Version 1.2476.</b></p>
     3060
     3061<ul type=None>
     3062<li><p>Fixed toggle surface selectability keyboard shortcut ts.  TG
     3063</ul>
     3064
     3065<p><b>December 12, 2007.  Version 1.2476.</b></p>
     3066
     3067<ul type=None>
     3068<li><p>Made topography command work with yz and xz planes.  Formerly only
     3069handled xy planes.  TG
     3070<li><p>Added topography command "replace" option to replace the existing
     3071topography surface rather than create a new one.  TG
     3072<li><p>Made volume planes show the correct depth after All planes button is
     3073pressed when step size is greater than 1.  TG
     3074<li><p>Fixed volume command writing brix, mrc and netcdf formats.
     3075Was giving an error message and not writing file. TG
     3076</ul>
     3077
     3078<p><b>December 11, 2007.  Version 1.2476.</b></p>
     3079
     3080<ul type=None>
     3081<li><p>Made volume solid rendering model have same id number as volume
     3082surface model.  Wasn't doing that when solid was shown first.  TG
     3083</ul>
     3084
     3085<p><b>December 7, 2007.  Version 1.2476.</b></p>
     3086
     3087<ul type=None>
     3088<li>Fixed bug where volume data set menu and list box contained deleted
     3089volumes. TG
     3090<li><p>Fixed error in session restore where multiscale models of volume
     3091path tracer marker sets were present.  TG
     3092</ul>
     3093
     3094<p><b>December 5, 2007.  Version 1.2476.</b></p>
     3095
     3096<ul type=None>
     3097
     3098<li><p>Removed checkbutton volume planes panel of volume dialog and added
     3099"one", "all" buttons to control display of single plane or all planes.
     3100New interface makes it clearer that plane display is not a mode, and makes
     3101display of all planes more reliable. TG
     3102<li><p>Made sessions include derived maps (e.g. Gaussian filter) that have
     3103been saved to a separate volume file. TG
     3104</ul>
     3105
     3106<p><b>December 4, 2007.  Version 1.2476.</b></p>
     3107
     3108<ul type=None>
     3109<li><p>Fixed bug that caused volume histogram to be off by a few percent
     3110in number of voxels counts per value bin.  TG
     3111<li><p>Added threshold normalization to morph map dialog.  Adjusts volume
     3112threshold to keep a fixed number of grid points within the contour surface
     3113for all interpolated maps.  TG
     3114</ul>
     3115
     3116<p><b>November 30, 2007.  Version 1.2475.</b></p>
     3117
     3118<ul type=None>
     3119<li><p>Added key shortcuts to create a new volume using the zone display of
     3120the active volume (zv), and the region outside the zone (ez, erase zone). TG
     3121
     3122</ul>
     3123
     3124<p><b>November 29, 2007.  Version 1.2475.</b></p>
     3125
     3126<ul type=None>
     3127<li><p>Added topography command which creates a surface corresponding to
     3128a volume data plane.  The surface height above the volume plane is
     3129proportional to the volume data value.  TG
     3130</ul>
     3131
     3132<p><b>November 27, 2007.  Version 1.2473.</b></p>
     3133
     3134<ul type=None>
     3135<li><p>Made Chimera compatible with 2 year old Chimera 1.2154 preferences files.
     3136Showing volume with new Chimera and old preferences file caused error.  TG
     3137<li><p>Made restoring a session that uses the Surface Color tool not display
     3138the Surface Color dialog unless it was displayed when the session was saved.
     3139TG
     3140<li><p>Added TIFF volume file reader support for 16-bit unsigned integer,
     314132 bit floating point, and 32 bit integer pixel values.  TG
     3142<li><p>Added volume file writing in BRIX  format (used by crystallography
     3143program O). TG
     3144
     3145</ul>
     3146
     3147<p><b>November 15, 2007.  Version 1.2470.</b></p>
     3148
     3149<ul type=None>
     3150<li><p>Chimera production release 1.2470.
     3151</ul>
     3152
     3153<p><b>November 13, 2007.  Version 1.2469.</b></p>
     3154
     3155<ul type=None>
     3156<li><p>Made Gaussian filter copy the local coordinate rotation of original
     3157map. TG
     3158<li><p>Made volume subregion resampling pad by half a voxel between the
     3159displayed outline box and the resampling grid.  This allows resampling on
     3160the exact grid of a second map by clicking outside that map to outline it
     3161(which includes a half voxel padding).  TG
     3162<li><p>Added display full volume keyboard shortcut fv.  Useful after
     3163showing a subregion for returning to full map display.  TG
     3164</ul>
     3165
     3166<p><b>November 8, 2007.  Version 1.2468.</b></p>
     3167
     3168<ul type=None>
     3169<li><p>Fixed priism volume file reader byte order detection code.  Did
     3170not work correctly with 8-bit data values.  TG
     3171</ul>
     3172
     3173<p><b>November 7, 2007.  Version 1.2468.</b></p>
     3174
     3175<ul type=None>
     3176<li><p>Added options to the Gaussian filter dialog to use only the displayed
     3177subsampling, and to use only the displayed subregion. TG
     3178<li><p>Fixed volume caching bug that sometimes caused single plane volume
     3179data display to be blank.  TG
     3180<li><p>Fixed bug in morph map where the first map was modified instead of
     3181creating a new interpolated map when the first map was writable. TG
     3182</ul>
     3183
     3184<p><b>November 6, 2007.  Version 1.2468.</b></p>
     3185
     3186<ul type=None>
     3187<li><p>Made Chimera start correctly on Mac OS 10.5 (Leopard) by preventing
     3188Chimera from trying to automatically start the X server, since that is now
     3189done by the operating system.  TG
     3190<li><p>Fixed bug in error message displayed when reading truncated XPLOR
     3191volume files.  TG
     3192</ul>
     3193
     3194<p><b>November 5, 2007.  Version 1.2468.</b></p>
     3195
     3196<ul type=None>
     3197<li><p>Made BRIX/DSN6 (O map) volume file reader apply scale and shift from
     3198file header to 8-bit values to produce floating point values.  TG
     3199</ul>
     3200
     3201<p><b>October 31, 2007.  Version 1.2467.</b></p>
     3202
     3203<ul type=None>
     3204<li><p>Made mask command handle degenerate cases where projected grid lines
     3205exactly intersect surface vertices or edges.  TG
     3206</ul>
     3207
     3208<p><b>October 29, 2007.  Version 1.2466.</b></p>
     3209
     3210<ul type=None>
     3211<li><p>Added "sandwich" option to mask command for extracting the volume
     3212between two surfaces along a projection axis.  Without this option regions
     3213between one surface and the volume box boundary are also included.  TG
     3214</ul>
     3215
     3216<p><b>October 26, 2007.  Version 1.2466.</b></p>
     3217
     3218<ul type=None>
     3219<li><p>Changed hkcage command which makes icosahedral cages use keyword
     3220options instead of requiring options to be in fixed order.  Added "replace"
     3221keyword option to replace the existing cage instead of creating a new model.
     3222TG
     3223
     3224</ul>
     3225
     3226<p><b>October 24, 2007.  Version 1.2465.</b></p>
     3227
     3228<ul type=None>
     3229<li><p>Made MRC volume files written by Chimera contain the Chimera version
     3230and date. TG
     3231<li><p>Made split command which places chains of an atomic model in separate
     3232models do nothing when applied to a single chain. TG
     3233</ul>
     3234
     3235<p><b>October 23, 2007.  Version 1.2465.</b></p>
     3236
     3237<ul type=None>
     3238<li><p>Added mask command which creates a volume data set containing
     3239only the values within a surface. TG
     3240<li><p>Fixed bug in close points calculation used by Find Clashes,
     3241Color Zone and Surface Zone tools which in rare cases may have led to
     3242incorrect neighbor calculation or hanging. TG
     3243</ul>
     3244
     3245<p><b>October 22, 2007.  Version 1.2465.</b></p>
     3246
     3247<ul type=None>
     3248<li><p>Fixed bug where meshmol command would create a model aligned
     3249with the model with lowest id number instead of the original mesh model. TG
     3250<li><p>Fixed bug where resampled volume had no name in volume dialog and
     3251model panel. TG
     3252<li><p>Made volume display tolerate externally deleted contour surface groups,
     3253for example with Ds keyboard shortcut. TG
     3254</ul>
     3255
     3256<p><b>October 18, 2007.  Version 1.2463.</b></p>
     3257
     3258<ul type=None>
     3259<li><p>Fixed volume series bug opening priism format data. TG
     3260</ul>
     3261
     3262<p><b>October 17, 2007.  Version 1.2463.</b></p>
     3263
     3264<ul type=None>
     3265<li><p>Made morph map volume browse button display the opened data. TG
     3266</ul>
     3267
     3268<p><b>October 11, 2007.  Version 1.2458.</b></p>
     3269
     3270<ul type=None>
     3271<li><p>Made calculation of volume enclosed in a surface handle surface holes
     3272but placing a point at the center of each boundary curve and making a triangle
     3273fan to cover the hole. TG
     3274<li><p>Add split map and fourier transform menu entries (Tools / Volume Data).
     3275TG
     3276</ul>
     3277
     3278<p><b>October 10, 2007.  Version 1.2456.</b></p>
     3279
     3280<ul type=None>
     3281<li><p>Added several tools from experimental features web page to the
     3282distribution: morph map, transform molecule coordinates, mesh to molecule,
     3283icosahedral cage (hkcage command), surface distance, crystal contacts, volume
     3284series, movement mouse mode, flatten icosahedron, split molecule, multiscale
     3285color command, pick surface pieces, symmetry copies command (sym).  TG
     3286<li><p>Added Tools menu to volume dialog. TG
     3287<li><p>Optimized speed of Find Clashes tool. TG
     3288<li><p>Added version number to Chimera HDF map file format. TG
     3289</ul>
     3290
     3291<p><b>October 9, 2007.  Version 1.2455.</b></p>
     3292
     3293<ul type=None>
     3294<li><p>Added "cap high values at box faces" volume surface rendering option. TG
     3295<li><p>Made popup balloons for IMOD object surfaces give object name.
     3296Mousing over other selectable surfaces will also show names.  TG
     3297<li>Add keyboard shortcut Ds to delete selected surfaces and Sc to split
     3298selected surfaces into one surface for each connected component. TG
     3299</ul>
     3300
     3301<p><b>October 6, 2007.  Version 1.2454.</b></p>
     3302
     3303<ul type=None>
     3304<li><p>Made volume contour surfaces use lighting normals parallel to data
     3305gradient instead of averaged surface triangle normals.  Gives less faceted
     3306apperance.  TG
     3307<li><p>Made multiscale model tool use surface lighting normals based on
     3308gradient of atom density rather than average normal of surface triangles.
     3309Small improvement in surface smoothness.  TG
     3310</ul>
     3311
     3312<p><b>October 5, 2007.  Version 1.2454.</b></p>
     3313
     3314<ul type=None>
     3315<li><p>Added IMOD mesh file reader. TG
     3316<li><p>Added Gaussian filter tool to smooth volume data by convolving with
     3317a gaussian. TG
     3318<li><p>Added Fourier transform keyboard shortcut FT to display 3-dimensional
     3319Fourier transform of volume data. TG
     3320<li><p>Added keyboard shortcut sm to split a volume data set into multiple
     3321data sets, one for each color of the original volume, as colored by the
     3322color zone tool. TG
     3323<li><p>Made multiscale model tool not change the display style of the original
     3324molecule used in building multimeric assembly.  Only displays new copies as
     3325surfaces.  TG
     3326
     3327</ul>
     3328
     3329<p><b>October 4, 2007.  Version 1.2454.</b></p>
     3330
     3331<ul type=None>
     3332<li><p>Made surface capping not show a cap for a clipped unit cell outline box.
     3333(Bug 4605). TG
     3334<li><p>Made unit cell tool pack asymmetric unit in single unit cell even when
     3335molecule atoms/ribbon is undisplayed (as when using Multiscale).  Now uses
     3336center of all atoms rather than center of displayed atoms for packing.
     3337(Bug 4606). TG
     3338</ul>
     3339
     3340<p><b>October 3, 2007.  Version 1.2454.</b></p>
     3341
     3342<ul type=None>
     3343<li><p>Added tool to print mean, standard deviation and RMS for volume data
     3344(Tools / Volume Data / Volume Mean, SD, RMS). TG
     3345<li><p>Made color zone slider range equal to diagonal size of surface bounding
     3346box.  Formerly maximum slider value was always 30.  TG
     3347<li><p>Made surface capping not create a cap for clipped volume outline box. TG
     3348
     3349</ul>
     3350
     3351<p><b>October 2, 2007.  Version 1.2451.</b></p>
     3352
     3353<ul type=None>
     3354<li><p>Made volume contour surfaces cover volume box faces where high
     3355density is exposed.  TG
     3356</ul>
     3357
     3358<p><b>September 26, 2007.  Version 1.2450.</b></p>
     3359
     3360<ul type=None>
     3361<li><p>Made volume contour calculation work on volumes up to size 4 Gvoxels.
     3362Formerly the limit was 4/3 Gvoxels.  TG
     3363</ul>
     3364
     3365<p><b>September 20, 2007.  Version 1.2448.</b></p>
     3366
     3367<ul type=None>
     3368<li><p>Added series of 10 initial volume colors to volume data display
     3369options panel.  Opened data sets are shown in different colors.  TG
     3370</ul>
     3371
     3372<p><b>September 19, 2007.  Version 1.2448.</b></p>
     3373
     3374<ul type=None>
     3375<li><p>Made volume data saving use a temporary file if map is written back
     3376over itself.  Formerly this would cause an error if the map was not entirely
     3377cached in memory because the source file would be erased before all the
     3378needed data was obtained.  TG
     3379</ul>
     3380
     3381<p><b>September 18, 2007.  Version 1.2448.</b></p>
     3382
     3383<ul type=None>
     3384<li><p>Added "compress" option to volume command to compress data when
     3385saving in Chimera map format.  Useful for mask files.  TG
     3386
     3387<li><p>Made volume command region option accept "all" or "full" value
     3388to set region display to show the full data set.  TG
     3389<li><p>Fixed bug where volume command did not accept upper case boolean values
     3390True, TRUE, False, .... TG
     3391<li><p>Fixed volume command so that model id numbers of "solid" models can
     3392be used.  Formerly the model id of the volume surface model was required.  TG
     3393<li><p>Made default solid volume rendering thresholds use only 2 nodes for
     3394mask data sets having just two values 0/1.  TG
     3395<li><p>Made Chimera map file include original file names with suffix stripped
     3396off when multiple maps are written to one file.  TG
     3397</ul>
     3398
     3399<p><b>September 17, 2007.  Version 1.2448.</b></p>
     3400
     3401<ul type=None>
     3402<li><p>Added "symmetry" option to volume command that assigns symmetry
     3403matrices to a volume data set.  It takes an argument "icos,XXX" where XXX
     3404is one of 222, 2n5, n25, 2n3, 222r, 2n5r, n25r, 2n3r to specify icosahedral
     3405symmetry in one of the standard coordinate frames as in the icosahedron
     3406tool.  Future additions will support space and point group and screw symmetries
     3407and BIOMT PDB matrices.  TG
     3408</ul>
     3409
     3410<p><b>September 15, 2007.  Version 1.2448.</b></p>
     3411
     3412<ul type=None>
     3413<li><p>Made experimental "sym" command use symmetries associated with volume
     3414data set.  If there are none it uses BIOMT matrices from PDB model as
     3415previously.  Not yet on web. TG
     3416<li><p>Added "contact" and "range" options to "sym" command to make molecule
     3417copies only when it is near the original copy.  Both parameters take a
     3418distance.  Contact requires a pair of atoms within the threshold distance
     3419while range requires the center of the molecule bounding boxes to be within
     3420the specified range.  Not yet on web. TG
     3421<li>Added keyboard shortcut "ic" to assign icosahedral 222 symmetry to the
     3422active volume data set. TG
     3423</ul>
     3424
     3425<p><b>September 12, 2007.  Version 1.2446.</b></p>
     3426
     3427<ul type=None>
     3428<li><p>Added volume command chunkShape option for writing map files that
     3429allow fast access to yz planes.  TG
     3430</ul>
     3431
     3432<p><b>September 11, 2007.  Version 1.2445.</b></p>
     3433
     3434<ul type=None>
     3435
     3436<li><p>Made CCP4 and MRC separate file formats in File / Open dialog.
     3437Formerly they were treated as one format.  CCP4 reader now will not
     3438incorrectly interpret xorigin, yorigin, zorigin parameters found only
     3439in MRC2000 files.  TG
     3440<li><p>Changed CCP4 and MRC file readers heuristic for deciding whether
     3441origin header values (ncstart, nrstart, nsstart) are valid.  Now requires
     3442that they have magnitude no larger than 10 times the maximum data size along
     3443the 3 axes.  Formerly use limit of 1 times original axis data size for each
     3444axis.  Fixes bug 4473. TG
     3445<li><p>Replaced HDF file reader with two file readers that use HDF: 1) EMAN HDF
     3446and 2) Chimera map format.  TG
     3447<li><p>Added Chimera map file writer.
     3448<li><p>Made movie recorder encode from jpeg images.  Fixes bug 4284.  TG
     3449<li><p>Made surface color properly handle volume data set that is closed
     3450while it is being used for automatic color updates.  TG
     3451</ul>
     3452
     3453<p><b>September 10, 2007.  Version 1.2445.</b></p>
     3454
     3455<ul type=None>
     3456<li><p>Clamped colormap size for solid rendering of volumes to maximum
     3457reported by OpenGL.  Fixed bug 4324. TG
     3458<li><p>Fixed volume path tracer bug where adding third marker set sometimes
     3459caused dialog to go into infinite resizing loop adding and removing a
     3460scrollbar.  Fixes bug 3305. TG
     3461</ul>
     3462
     3463<p><b>September 7, 2007.  Version 1.2445.</b></p>
     3464
     3465<ul type=None>
     3466<li><p>Made opening volume data set with a Chimera command or on the Chimera
     3467command-line give a explanatory error message instead of a Python traceback.
     3468Fixes bug 4450. TG
     3469</ul>
     3470
     3471<p><b>September 5, 2007.  Version 1.2445.</b></p>
     3472
     3473<ul type=None>
     3474<li><p>Made volume command keywords not have underscores, and not be
     3475case sensitive, and allow unique prefix abbreviations. TG
     3476<li><p>Made volume command color
     3477options accept values "colorpanel", "fromeditor", or "editor" in which
     3478case color is taken from color dialog.  Also can now use color names
     3479defined with Chimera colordef command. TG
     3480<li><p>Made volume command save path option accept
     3481"browse" or "browser" in which case a modal save file dialog is opened
     3482to choose the file. TG
     3483<li><p>Fixed bug saving sessions when volume dialog shown but no volumes
     3484are opened. TG
     3485<li><p>Made volume crop button use a circumscribing data axis aligned box
     3486when selection box has been rotated.  TG
     3487</ul>
     3488
     3489<p><b>September 4, 2007.  Version 1.2443.</b></p>
     3490
     3491<ul type=None>
     3492<li><p>Added subregion selection panel controls to copy subregions that
     3493are not aligned with the data axes.  New controls are "rotate selection box"
     3494switch, "resample voxel size" entry, and "resample" button. TG
     3495<li><p>Made mrc, netcdf and hdf file reader and writer code save and
     3496restore data rotation. TG
     3497<li><p>Made solid style volume rendering correctly display skewed data,
     3498common with crystallographic density maps. TG
     3499<li><p>Eliminated "double" and "half" button on subregion selection panel
     3500to reduce crowding.  Rarely used. TG
     3501<li><p>Allow unicode volume files names. Fixes bug 4433. TG
     3502</ul>
     3503
     3504<p><b>August 24, 2007.  Version 1.2442.</b></p>
     3505
     3506<ul type=None>
     3507<li><p>Added "volume" command to change all rendering settings of volume
     3508data, that can be changed with the volume dialog. TG
     3509<li><p>Made volume object a subclass of surface model.  This allows
     3510extension code to more easily obtain the volume object from the list
     3511of open models with chimera.openModels.list(). TG
     3512</ul>
     3513
     3514<p><b>August 23, 2007.  Version 1.2441.</b></p>
     3515
     3516<ul type=None>
     3517<li><p>Changed volume code so that Chimera "open" command can assign model
     3518id numbers when opening volume data. TG
     3519<li><p>Simplified volume data python interface so extensions do not need
     3520to use volume viewer dialog. TG
     3521</ul>
     3522
     3523<p><b>August 10, 2007.  Version 1.2437.</b></p>
     3524
     3525<ul type=None>
     3526<li><p>Made volume dialog display histograms for multiple data sets.
     3527A single line above each histogram shows the data name, size, step menu,
     3528visibility (eye icon) and close map button (dash icon).  Up to 3 histograms
     3529are shown, and this limit can be changed with a new display options setting.
     3530The "active" data set has a white background behind its name.  The level
     3531entry field and color button and rendering options shown in the dialog
     3532effect only the active data set.  There is no provision for changing the
     3533settings for multiple data sets at the same time. TG
     3534<li><p>Removed Show and Unshow buttons from bottom of dialog.  Replaced
     3535by "eye" icon button above each data histogram to show/unshow data.
     3536Eye icon has white background when data is shown. TG
     3537<li><p>Eliminated data menu panel which also showed data size and step.  Added a
     3538Data menu to the dialog menu bar.  The size and step is now shown above each
     3539histogram. TG
     3540<li><p>Moved display style panel (surface/mesh/solid) below histograms.  Formerly
     3541it was above histograms.  Better to put the most useful data sets info at
     3542the top.  Display style is now closer to color and threshold settings. TG
     3543
     3544<li><p>Changed display stye heading from "Show: *surface  *mesh  *solid" to
     3545"Style: *surface  *mesh  *solid".
     3546<li><p>Fixed newly introduced bug in UHBD volume file reader.  TG
     3547</ul>
     3548
     3549<p><b>August 9, 2007.  Version 1.2436.</b></p>
     3550
     3551<ul type=None>
     3552<li><p>Made volume data size show as a single number with superscript 3
     3553if size is the same along all three axes. TG
     3554<li><p>Made moving volume plane slider or changing plane axis not automatically
     3555activate plane display.  Avoids unintended switch into plane mode. TG
     3556<li><p>Made sample grid points always have indices that are multiples of
     3557step size.  Formerly if a volume subregion had an origin that was not a
     3558multiple of the step size then the sample point included that origin.
     3559This change makes precomputed subsamples behave the same way as
     3560subsamples extracted from full resolution arrays. TG
     3561</ul>
     3562
     3563<p><b>August 8, 2007.  Version 1.2436.</b></p>
     3564
     3565<ul type=None>
     3566
     3567<li><p>Made volume plane display checkbutton update when volume region
     3568changed using other interfaces such as subregion selection "Full"
     3569button. TG
     3570<li><p>Made volume dialog File / Open map dialog close as soon as file
     3571is chosen.  Formerly it waited to see if the open succeeded.  TG
     3572</ul>
     3573
     3574<p><b>August 6, 2007.  Version 1.2434.</b></p>
     3575
     3576<ul type=None>
     3577<li><p>Made volume plane display to respect auto step size adjustment to
     3578achieve the user-requested voxel limit.  Formerly plane display did not adjust
     3579the step size. TG
     3580<li><p>Fixed newly introduce volume data caching bug seen when requested
     3581data and cache data have different origins and step sizes. TG
     3582</ul>
     3583
     3584<p><b>August 3, 2007.  Version 1.2434.</b></p>
     3585
     3586<ul type=None>
     3587<li><p>Added volume file reader for HDF5 format used by EMAN and SPARX. TG
     3588
     3589<li><p>Added third party HDF5 library and PyTables 2.0 python module
     3590(interface to hdf5) to the Chimera distribution. TG
     3591</ul>
     3592
     3593<p><b>August 2, 2007.  Version 1.2434.</b></p>
     3594
     3595<ul type=None>
     3596<li><p>Changed volume solid rendering transparency so that voxel brightness
     3597is now multiplied by opacity.  This makes more transparent voxels dimmer.
     3598This mode is now the default.  The former mode can be enabled by turning off
     3599the new "Dim transparent voxels" setting under "Solid rendering options". TG
     3600<li><p>Changed the effect of the transparency slider for solid volume
     3601rendering.  It now is a fraction of displayed data thickness while formerly
     3602it was a thickness value.  The fraction times the number of planes (minimum
     3603for 3 axes) gives a depth in planes that is used as an exponent to modulate
     3604transparency.  Transfer function (1-alpha) is mapped to (1-alpha)**(1/planes).
     3605If the planes values is 2 this means that the new transparency will require
     36062 planes to block as much light as the same amount of light as one plane
     3607using the unmodified transfer function. TG
     3608<li>Changed default solid rendering transfer function ramp.  Now
     3609starts at rank 10% data value ramping up to full brightness at rank
     361099% and continuing to the maximum data value at full brightness.
     3611With new default transparency mode this provides reasonable
     3612brightness views of single planes or full maps. TG
     3613<li><p>Renamed volume viewer "Transparency Factor" (surface rendering) and
     3614"Transparency Depth" (solid rendering) slider headings to "Transparency". TG
     3615</ul>
     3616
     3617<p><b>July 31, 2007.  Version 1.2430.</b></p>
     3618
     3619<ul type=None>
     3620
     3621<li><p>Made reading volume data with step size greater than 1 only allocate
     3622space for the subsampled data.  Formerly the full size data set would be
     3623read into memory.  The new behavior permits display of data sets larger than
     3624will fit in memory. TG
     3625<li><p>Made reading binary volume files report progress every 0.2 seconds
     3626or every data z plane read, which ever is longer.  Previously used a less
     3627reliable estimate for frequency of messages based on bytes of data read.  TG
     3628<li><p>Fixed bug where scale bar value-changed callback occurs when scale
     3629limits are updated if the old scale value does not lie within the limits.
     3630Observed for volume z plane slider when switching between data sets. TG
     3631</ul>
     3632
     3633<p><b>July 27, 2007.  Version 1.2430.</b></p>
     3634
     3635<ul type=None>
     3636<li><p>Made movie recorder turn off raytrace preview overriding the
     3637user preference. TG
     3638<li><p>Made "movie encode" command implicitly do a "movie stop" before
     3639encoding.  Formerly, frame capture continued while encoding was done.  TG
     3640</ul>
     3641
     3642<p><b>July 26, 2007.  Version 1.2430.</b></p>
     3643
     3644<ul type=None>
     3645
     3646<li><p>Added z plane panel to volume viewer.  Allows quick switching between
     3647individual data z planes shown using solid rendering by moving a slider. TG
     3648<li><p>Added volume viewer option to initially display a single z plane when
     3649opening data sets larger than 256 Mvoxels. TG
     3650</ul>
     3651
     3652<p><b>July 25, 2007.  Version 1.2430.</b></p>
     3653
     3654<ul type=None>
     3655<li><p>Made volume dialog not transiently resize when displayed for the first
     3656time. TG
     3657<li><p>Made volume "show data when opened if smaller than X Mvoxels" use
     3658size of subsampled data if a precomputed subsample file is being read. TG
     3659</ul>
     3660
     3661<p><b>July 24, 2007.  Version 1.2430.</b></p>
     3662
     3663<ul type=None>
     3664<li><p>Made volume step size menu add entries for new step sizes that are
     3665entered using the region bounds panel. TG
     3666
     3667<li><p>Made volume region bounds panel not deactivate auto-step adjustment
     3668when new bounds are entered by step values are left the same.  TG
     3669<li><p>Added user-friendly error message when allocating an array for
     3670reading a volume data set fails.  TG
     3671</ul>
     3672
     3673<p><b>July 23, 2007.  Version 1.2430.</b></p>
     3674
     3675<ul type=None>
     3676<li><p>Made each volume have its own auto-adjust step size setting.  Formerly
     3677all volumes used the dialog setting. TG
     3678<li><p>Made newly opened volumes use the default rendering options instead
     3679of the options currently set in the volume dialog. Definitely want this
     3680behavior for auto-adjust step, but no so clear for smoothing, outline box,
     3681others. TG
     3682<li><p>Fixed bug where canceling volume file read disabled updates of volume
     3683display when threshold or step size changed. TG
     3684</ul>
     3685
     3686<p><b>July 21, 2007.  Version 1.2430.</b></p>
     3687
     3688<ul type=None>
     3689
     3690<li><p>Added volume file reader for stacks of TIFF images. TG
     3691<li><p>Added progress report status-line messages when reading volume files.
     3692<li><p>Added cancel link (in blue) in volume progress status messages. TG
     3693<li><p>Added support for multi-color status-line messages and detecting
     3694mouse clicks on parts of status-line messages. TG
     3695<li><p>Made writing MRC or NetCDF volume file read and write one z-plane
     3696at a time to allow writing files larger than can fit in memory. TG
     3697<li><p>Changed volume viewer dialog "step" menu entries to be just a single
     3698number instead of 3 numbers if steps along all 3 axes are the same
     3699(e.g. 2 instead of 2 2 2). TG
     3700<li><p>Eliminated parentheses around volume size shown in volume dialog. TG
     3701<li><p>Eliminated "ctrl-click on histogram to add or delete thresholds" message
     3702from volume dialog.  Not worth the dialog space.  TG
     3703<li><p>Multi-component volume data files are now appear as separate data sets
     3704for each component.  This effects multi-wavelength optical microscopy files
     3705in Priism format.  One histogram is displayed in the volume dialog instead
     3706of multiple histograms. TG
     3707</ul>
     3708
     3709<p><b>July 17, 2007.  Version 1.2430.</b></p>
     3710
     3711<ul type=None>
     3712<li><p>Fixed movie recorder bug when using raytracing and encoding with
     3713"play forward and backward".  GNAT 4208. TG
     3714</ul>
     3715
     3716<p><b>July 7, 2007.  Version 1.2425.</b></p>
     3717
     3718<ul type=None>
     3719<li><p>Made single plane volume data sets display using "solid" rendering
     3720style even if dialog is set to surface or mesh.  Helpful for looking at EM
     3721micrographs. TG
     3722</ul>
     3723
     3724<p><b>July 2, 2007.  Version 1.2425.</b></p>
     3725
     3726<ul type=None>
     3727<li><p>Made volume and multiscale surface models allow variable thickness
     3728silhouette edges. TG
     3729</ul>
     3730
     3731<p><b>June 1, 2007.  Version 1.2417.</b></p>
     3732
     3733<ul type=None>
     3734<li><p>Fixed volume path tracer marker placement when per-model clipping
     3735and solid rendering used.  Was ignoring per-model clip plane. TG
     3736<li><p>Made volume path tracer marker placement with solid rendering use
     3737threshold level given by the lowest node in the solid transfer function
     3738with brightness > 0.  Formerly was using surface threshold. TG
     3739<li><p>Made volume gOpenMol file reader provide a user-friendly error
     3740message when reading an empty file.  GNAT 3952.  TG
     3741</ul>
     3742
     3743<p><b>May 24, 2007.  Version 1.2416.</b></p>
     3744
     3745<ul type=None>
     3746<li><p>Fixed volume path tracer test suite test.  Use of deprecated Python
     3747os.tmpnam() on Windows Vista gave unwritable file.  TG
     3748</ul>
     3749
     3750<p><b>May 17, 2007.  Version 1.2412.</b></p>
     3751
     3752<ul type=None>
     3753<li><p>Fixed mesh benchmark divide by zero that occured with defective
     3754graphics driver that could not render mesh. TG
     3755</ul>
     3756
     3757<p><b>May 15, 2007.  Version 1.2411.</b></p>
     3758
     3759<ul type=None>
     3760<li><p>Fixed 64-bit Linux dependency on system lapack / blas libraries. TG
     3761</ul>
     3762
     3763<p><b>May 14, 2007.  Version 1.2410.</b></p>
     3764
     3765<ul type=None>
     3766<li><p>Fixed movie command bug where (unnecessary) movie reset command
     3767issued after movie encode command which was still working in background.
     3768GNAT 3873.  TG
     3769</ul>
     3770
     3771<p><b>May 9, 2007.  Experimental feature.</b></p>
     3772
     3773<ul type=None>
     3774<li><p>Enhanced IMOD segmentation file reader to read contours and points,
     3775creating a volume path tracer model. TG
     3776</ul>
     3777
     3778<p><b>May 8, 2007.  Version 1.2399.</b></p>
     3779
     3780<ul type=None>
     3781<li><p>Made closing volume path tracer dialog turn off the marker placement
     3782mouse mode.  Reshowing the dialog turns the mouse mode back on. TG
     3783<li><p>Renamed button on movie recorder output path browse dialog
     3784from Save to Set Movie Path.  Bug #2270. TG
     3785<li><p>Fixed bug #3833 where volume menu it fit map in map tool did not update
     3786after a volume was closed.  Made volume menus in fit map, values at atom
     3787positions, and morph map dialog automatically update as soon as a volume data
     3788set is opened or closed. TG
     3789</ul>
     3790
     3791<p><b>May 1, 2007.  Version 1.2392.</b></p>
     3792
     3793<ul type=None>
     3794<li><p>Fixed bug in bondzone command where "if array:" construct used to
     3795test if array is non-empty.  Bug introduced with switch from Numeric to
     3796Numpy library.  TG
     3797</ul>
     3798
     3799<p><b>April 30, 2007.  Version 1.2388.</b></p>
     3800
     3801<ul type=None>
     3802<li><p>Fixed bug opening biological unit model from PQS database using
     3803id on command-line (e.g. "open pqsID:104l") TG
     3804</ul>
     3805
     3806<p><b>April 27, 2007.  Version 1.2388.</b></p>
     3807
     3808<ul type=None>
     3809<li><p>Added code to check the Mac Python crash log to see if the last
     3810invocation of Chimera ended in a crash.  If so, a dialog appears the next
     3811time they run Chimera allowing them to report the crash including the
     3812crash log. TG
     3813<li><p>Added xray fo-fc difference maps from the Uppsala Electron
     3814Density Server to File / Fetch by Id. TG
     3815<li><p>Added biological unit PDB files from the Probably Quaternary Structure
     3816(PQS) server to File / Fetch by Id. TG
     3817</ul>
     3818
     3819<p><b>April 26, 2007.  Version 1.2388.</b></p>
     3820
     3821<ul type=None>
     3822<li><p>Fixed bug #3808 where movie recorder "play forward then backward"
     3823option caused error on Windows. TG
     3824<li><p>Fixed bug #3812 where default movie recorder output movie file location
     3825is unwritable on Windows Vista. TG
     3826</ul>
     3827
     3828<p><b>April 25, 2007.  Version 1.2384.</b></p>
     3829
     3830<ul type=None>
     3831<li><p>Made opening APBS, DelPhi, or UBHD electrostatic potential files
     3832show surface color dialog instead of volume viewer. TG
     3833</ul>
     3834
     3835<p><b>April 11, 2007.  Version 1.2375.</b></p>
     3836
     3837<ul type=None>
     3838<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
     3839<li><p>Bug fix.  Nucleic acid blobs reschains.py error when scale bar shown. TG
     3840<li><p>Bug #3775 fixed.  Fit model in map when map not shown. TG
     3841</ul>
     3842
     3843<p><b>April 9, 2007.  Version 1.2373.</b></p>
     3844
     3845<ul type=None>
     3846
     3847<li><p>Added button to movie recorder to show raytracing preferences. TG
     3848<li><p>Suppressed image saving status messages when capturing with movie recorder. TG
     3849<li><p>Change movie command "loop" keyword to "roundtrip". TG
     3850</ul>
     3851
     3852<p><b>April 6, 2007.  Version 1.2372.</b></p>
     3853
     3854<ul type=None>
     3855<li><p>Included C++ header files in Chimera distributions. TG
     3856<li><p>Restricted movie recorder to PNG image format when raytracing. TG
     3857</ul>
     3858
     3859<p><b>April 5, 2007.  Version 1.2370.</b></p>
     3860
     3861<ul type=None>
     3862
     3863<li><p>Added movie recorder option to play frames forward then backward when encoding. Also added movie command "loop" option to permit this. TG
     3864<li><p>Added raytracing option to movie recorder. TG
     3865</ul>
     3866
     3867<p><b>April 3, 2007.  Version 1.2369.</b></p>
     3868
     3869<ul type=None>
     3870<li><p>Added supersampling option to movie recorder. TG
     3871</ul>
     3872
     3873<p><b>March 28, 2007.  Version 1.2366.</b></p>
     3874
     3875<ul type=None>
     3876<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
     3877<li><p>Made scale bar, path tracer, and multiscale preserve model numbers when
     3878session is restored. TG
     3879
     3880</ul>
     3881
     3882<p><b>March 27, 2007.  Version 1.2365.</b></p>
     3883
     3884<ul type=None>
     3885<li><p>Made measure volume/area tool automatically update as surface changes. TG
     3886</ul>
     3887
     3888<p><b>March 9, 2007.  Version 1.2354.</b></p>
     3889
     3890<ul type=None>
     3891<li><p>Made session restore of volume data sets use original model numbers. TG
     3892</ul>
     3893
     3894}}}