Chimera Change Log

This page lists changes to Chimera that are visible to users, including the date and Chimera version when the change was checked in, and who made the change (TG = Tom Goddard, AL = Andrew Ling).

Ideally this log would record all changes, but we are currently seeing how difficult it is to keep it up to date.

March 30, 2009. Version 1.4

• Added memory error check in volume filter. TG

March 25, 2009. Version 1.4

• Added emdb search capability to fetch by id dialog. TG

March 24, 2009. Version 1.4

• Fixed bug where last used data matrix for a volume not kept in cache. TG

• Increased volume data default cache size to 512 Mb, was 32 Mb. TG

March 20, 2009. Version 1.4

• Added slab option to shape command. TG

• Made mcopy copy bond properties, fixed label copy. TG

March 19, 2009. Version 1.4

• Fixed mcopy bug, coordinate copy did not work. TG

March 16, 2009. Version 1.4

• Fixed bug in dock grid error message. TG

• Made clip command give user-friendly near>far error message. TG

March 13, 2009. Version 1.4

• Made modbase and castp fetch use downlaod directory. TG

March 12, 2009. Version 1.4

• Made pubchem fetch use download directory. TG

March 11, 2009. Version 1.4

• Fixed fly command bug where an extra frame count was used. TG

• Made color command handle r,g,b,a numeric color arguments. TG

• Added fetching emdb maps to fetch-by-id dialog. TG

• Added button to fetch by id dialog shows download directory preferences. TG

• Added cancel link in progress messages to cancel fetch operation. TG

• Enabled uncompressing fetched data files. TG
• Made bondcolor and colordef handle r,g,b,a numeric arguments. TG

March 10, 2009. Version 1.4

• Added mcopy command to copy molecule settings. TG

• Added fetch-by-id download directory for eds, viperdb, pqs, pdb, cif, scop, ndb. TG

March 6, 2009. Version 1.4

• Made all command color arguments accept tk colors, comma-separated rgba. TG

March 5, 2009. Version 1.4

• Made volume scale filter respond when enter key pressed. TG

March 4, 2009. Version 1.4

• Made measure rotation mention coordinate system in reply log output. TG

• Made measure and vop keyword abbreviations work and case insensitive. TG

• Made rotation axis color be model color. TG

• Allowed markers/links to have no color, uses molecule color. TG

• Improved per-model clipping shorcuts cc, ca and removed tc. TG

• Made scale/shift volume filter update when filter settings changed. TG

February 26, 2009. Version 1.4

• Fixed saving markers as xml when atoms/bonds deleted. TG

February 25, 2009. Version 1.4

• Added showAxis option to measure rotation command. TG

February 20, 2009. Version 1.4

• Fixed molmap to work with molecules with different transforms. TG

• Made stl export for 3-d printing. TG

February 17, 2009. Version 1.4

• Made matrixcopy handle multiple destination models. TG

• Made shape command hide some mesh edges for icosahedron and cylinder. TG

• Added lighting attributes, normals, edge mask to surface session save. TG

• Made color zone with bond zone respect half-bond coloring. TG

February 13, 2009. Version 1.4

• Added silhouette edge drawing for transparent models. TG

• Added one layer and all layers transparency menu entries. TG

• Fixed multiscale bug where chain associated with original molecule deleted, and other surfaces recalculated at new resolution. TG

• Fixed bug where volume session restore tried to set solid model orientation when that model did not exist. TG

• Fixed bug where opening solid model did not set initial camera view. TG

February 11, 2009. Version 1.4

• Made session save include molecular surface attributes: smoothing, lighting on/off, two-sided lighting, dot and line widths. TG

• Added one transparent layer surface option. Added equivalent option to volume dialog surface and mesh panel. TG

• Added shortcuts t5 and t0 to make surfaces 50% and 0% transparent. TG

February 10, 2009. Version 1.4

• Made move/turn/rock/roll move inactive models when "models" keyword used. TG

• Made open volumes use absolute paths even if specified with relative paths so that data can be read later if current working directory changed. TG

February 9, 2009. Version 1.4

• Improved rendering of multiple transparent surface models so model behind does not appear in front. TG

January 28, 2009. Version 1.4

• Made multiscale contacts not select chain surfaces when atoms of chain are selected. TG

January 21, 2009. Version 1.4

• Wrote fly command to smoothly interpolate positions/camera. TG

January 20, 2009. Version 1.4

• Fixed swapped buried ses/sas area atom attributes. TG

January 19, 2009. Version 1.4

• Fixed reset with frame count error when model closed. TG

• Made volume surface outline box unlit when using glossy lighting. TG

• Fixed bug where hide dust turned volume square mesh into triangles. TG

January 18, 2009. Version 1.4

• Made hdf map read use planes along smallest chunk shape axis. TG

• Added use step/subregion/zone options to volume save command. TG

• Added scale/shift/cast operation to volume filter dialog. TG

• Added permuteaxes operation to vop command. TG

January 16, 2009. Version 1.4

• Fixed bug in histogram calculation that caused slightly incorrect volume threshold. TG y

• Added buried area to measure command. TG

January 15, 2009. Version 1.4

• Fixed matplotlib on windows, wasn't finding tcl/tk headers. TG

• Fixed turn/roll/rock bug, inactive models moved when center specified. TG

January 14, 2009. Version 1.4

• Fixed shader code to not throw error on compile/link info messages. TG

• Fixed esp coloring bug, coloring method not set. TG

• Fixed bright edges from glossy lighting, had diffuse light on both sides of surface. TG

• Made correlation matplotlib plot use tk instead of native Mac window. TG

January 13, 2009. Version 1.4

• Fixed bug move,turn,roll,rock coordinateSystem arg not working. TG

• Fixed disappearing light arrows in light panel. TG

• Made turn/roll/rock/move use coord system of center or axis spec. TG

January 9, 2009. Version 1.4

• Added matplotlib 2d plotting library to distribution, used for showing correlation of map with rotated map. TG

January 8, 2009. Version 1.4

• Added correlation for rotated map positions to measure command. TG

January 7, 2009. Version 1.4

• Wrote measure command to show rotation axis connecting two models. TG

• Handle new delphi map format on mac with 64 bit floats. TG

• Made turn,roll,rock,move accept 2 atom or bond spec for axis. TG

• Added surface volume and area to measure command. TG

• Added map correlation to measure command. TG

• Made glossy lighting not apply to unlit lines, caused dim molecule wires. TG y

January 6, 2009. Version 1.4

• Added median filtering to filter dialog. TG

• Added clip volume (cv), clip adjust (ca), glossy lighting (gl) shortcuts. TG

• Made clip and cap shortcut act on selected model, not show dialogs. TG

• Fixed bug where single color volume solid dimmed by factor of red component. TG

January 2, 2009. Version 1.4

• Fixed bug where surface cap not updated when mask changed. TG

• Added options panel to gaussian filter dialog, including immediate update option. TG

• Made filter dialog adjust thresholds for constant volume use the enclosed volume for the gaussian filtered volume rather than the original volume. TG

• Made Filter button just update existing volume if active volume is a gaussian filtered volume. TG

December 30, 2008. Version 1.4

• Moved per-pixel lighting option from effects panel to lighting panel. TG

• Fixed mac x11 start error when glossy lighting preference not supported. TG

• Fixed bug where glossy mode sometimes had no effect because graphics context was not current when setting shader. TG

December 29, 2008. Version 1.4

• Allowed depth cue start >= 1 for back lighting effect. TG

• Made surface cap use only visible parts of surfaces, helps castp. TG

December 19, 2008. Version 1.4

• Added "glossy" lighting mode using an opengl shader providing per-pixel lighting and angle-dependent transparency. TG

December 18, 2008. Version 1.4

• Replace depth cue yon intensity parameter with end depth. TG

December 16, 2008. Version 1.4

• Added slider to control width of gaussian filter. TG

December 10, 2008. Version 1.4

• Added hide dust tool that hides small connected surface blobs. TG

• Increased surface cap default offset 0.001 to 0.01 to avoid disappearing caps. TG

• Made sum of gaussians routine (used by molmap) able to take different standard deviations along 3 axes for PALM/STORM microscopy data. TG

December 9, 2008. Version 1.4

• Disabled used of Chimera user interface while volume data load is loaded, allowing only cancel of data load. TG

• Moved volume auto display subregion option from data display panel to subregion selection panel. TG

• Allowed volume auto-cropping (resampling) with rotated subregion box. With solid style rendering this does a good job of showing slices that are not parallel to the volume box faces. TG

December 8, 2008. Version 1.4

• Fixed subregion resampling box when source map has local rotation. TG

• Debugged blank volume histogram when session restored, cache size not set before volume dialog created. TG

December 5, 2008. Version 1.4

• Added session saving for icosahedron tool. TG

December 3, 2008. Version 1.4

• Provide user-friendly error message when molecular surface calculation produces truncated output. TG

• Suppress Mac 10.5 crash report dialog when molecular surface calculation fails. TG

November 25, 2008. Version 1.4

• Made move selection mouse mode able to move surface pieces. TG

November 21, 2008. Version 1.2577.

• Made initial volume viewer thresholds symmetric about 0 for electrostatic potential data and other polar data. TG

• Added gaussian and laplacian filters to vop command. TG

November 20, 2008. Version 1.2576.

• Made per-model clipping work with solid volume rendering where projection mode is perpendicular to view (uses 3d textures).

November 19, 2008. Version 1.2576.

• Fixed error reading mrc file > 2 Gbytes. TG

November 18, 2008. Version 1.2575.

• Fixed hkcage command error when invoked second time with surface capping enabled. TG

• Added planes keyword to volume command to show sequence of planes. TG

• Made turn, move, ... not raise error if model deleted during motion. TG

• Added volume outline box linewidth setting. TG

• Fixed reset command to preserve relative orientations. TG

November 17, 2008. Version 1.2575.

• Fixed bug that caused extra frames during movie capture scripts that read volume data, caused by progress messages. TG

• Made movie encode command print status messages on main status line. TG

November 14, 2008. Version 1.2575.

• Fixed incorrect center of rotation when a model is closed where another model has the same id. TG

• Made actions / focus with nothing selected turn of near/far clipping. TG

November 13, 2008. Version 1.2574.

• Suppress Mac 10.5 crash report dialog when molecular surface calculation mscalc program crashes. TG

• Fixed volume command bug setting color of solid rendering. TG

November 12, 2008. Version 1.2574.

• Fixed bugs writing image stacks as single hdf (*.cmap) files. TG

November 11, 2008. Version 1.2574.

• Made molecule bounds include atom radii to avoid clipping atom spheres when near/far clipping is turned off. TG

• Fixed error closing volumes when new session opened. TG

• Fixed bug where distant opaque solid volume models appeared in front of closer opaque soild volume models. TG

• Fixed bug where restored traced surface not saved in subsequent sessions. TG

November 10, 2008. Version 1.2574.

• Added warning when restoring a session file written by a newer chimera version. TG

• Fixed bug restoring volume / surface coloring from session files written by Chimera version more than 1 year old. TG

November 6, 2008. Version 1.2573.

• Fixed volume eraser bug introduce Sept 30. TG

November 4, 2008. Version 1.2573.

• Made surface capping on by default. TG

• Made space navigator preserve front-center rotation point during rotation. TG

November 3, 2008. Version 1.2573.

• Made near/far clip planes off by default. TG

October 31, 2008. Version 1.2572.

• Made surface bounds calculation use bounding sphere instead of box resulting in tighter bounds for sphere-like surfaces. Effects amount of camera zoom when the first model show is a surface. TG

October 29, 2008. Version 1.2572.

• Changed default surface transparency blend model to dim (alpha,1-alpha). TG

• Added center of rotation mode name options "fixed", "front", "models", and "independent" to cofr command. TG

• Made coordinateSystem arguments to movement commands work without '#'. TG

October 28, 2008. Version 1.2571.

• Fixed failure to hide clicked triangle using pick blobs tool. TG

• Cleared surface visibility/color atom attributes when surface closed. TG

October 27, 2008. Version 1.2571.

• Fixed bug where hiding a molecular surface piece made subsequent surface show not work. TG

October 24, 2008. Version 1.2571.

• Changed the default center of rotation mode to front-center. TG

• Fixed multiscale session save error that happened after chain deleted. TG

October 22, 2008. Version 1.2569.

• Added front-center center of rotation mode. TG

• Added coordinate system, center, models arguments to turn, roll, rock, and move commands. TG

• Made benchmark dialog show warning if models are open. TG

• Allowed move command to move along all 3 axes at once. TG

• Made cofr command accept point coordinates and coord sys arguments. TG

• Added center, coord system, model id args to shape command. TG

October 20, 2008. Version 1.2567.

• Made options panel for morph map and added roundtrip option. TG

October 15, 2008. Version 1.2566.

• Fixed actions menu entries focus, set pivot, surface hide/show/repr/tranparency and color when a molecular surface is selected but not its atoms. TG

October 14, 2008. Version 1.2566.

• Made focus command and action use center-of-models when nothing selected. TG

• Fixed session saving error after closing traced surface model. TG

October 10, 2008. Version 1.2566.

• Fixed model panel configure dialog bug, pmw tabs not raising in Mac Aqua Chimera. TG

October 1, 2008. Version 1.2561.

• Made molecular surface show "all components" false in selection inspector if all-component calculation failed and instead used single-component. TG

• Fixed volume show/hide icon update error on model close. TG

September 29, 2008. Version 1.2561.

• Added memory checking to c++ python array allocation used in volume and surface calculations. TG

September 25, 2008. Version 1.2561.

• Added ls keyboard shortcut to open last session file. TG

September 23, 2008. Version 1.2560.

• Fixed volume solid color mode and projection mode bugs. TG

September 19, 2008. Version 1.2559.

• Added out-of-memory test for large surfaces. TG

• Turn off mesh lighting for single plane volume display. TG

• Made volume planes switch to solid style only when "one" button pressed. TG

• Made single plane volume contour surface without capping render with mesh to show 2d contours. TG

September 12, 2008. Version 1.2558.

• Added fourier transform to vop command, removed fourier transform menu entry. TG

September 11, 2008. Version 1.2558.

• Made volume square mesh option show box cap diagonals. The square mesh code that excluded box cap diagonals also excluded all contours for single data planes. TG

• Added volume planes cycle option with plane count and speed control. Replaces "play" button. TG

• Added button to volume planes panel to preload data. Allows faster moving through planes. TG

September 10, 2008. Version 1.2558.

• Fixed volume tracer bug where first marker on empty space mispositioned if no models are opened. TG

September 9, 2008. Version 1.2558.

• Changed volume dialog origin field to show index of xyz origin instead of xyz coordinates of index 0,0,0. Allows changing voxel size without altering xyz origin position within array. TG

• Added originIndex keyword to volume command for specifying the xyz origin in grid index units. Changing voxelSize with volume command now preserves index of xyz 0,0,0 rather than xyz of index 0,0,0. TG

• Added single volume plane surface and mesh display. Allows drawing 2d contour lines. Formerly surface and mesh style volume display showed nothing for single planes. TG

September 8, 2008. Version 1.2557.

• Made solid volume rendering status messages about color appear only once per frame. Were showing for every data plane. TG

• Fixed erratic incorrect use of x or y projection axes in solid rendering. TG

• Fixed netcdf out of memory error message. TG

• Fixed bugs where volume dialog did not update display style and hide/show icon when solid style hidden (and hence solid model closed). TG

September 5, 2008. Version 1.2557.

• Added luminance color for volume rendering so single color modes need not display white. TG

• Added auto projection mode that chooses 2d z planes rendering volume slabs with aspect 4:1 or greater, otherwise xyz planes (using more memory). TG

September 3, 2008. Version 1.2554.

• Removed colormap mode from solid style volume rendering. TG

September 2, 2008. Version 1.2554.

• Changed electrostatic surface coloring to be opaque red/white/blue. TG

August 29, 2008. Version 1.2554.

• Added volume projection mode option for tomogram viewing using solid style. Allows only showing z planes. 3x less memory use versus xyz mode where planes most parallel to screen used. More memory efficient. TG

• Change volume solid style rendering to not make full 3-d temporary color array. Instead computes only 2-d color planes at a time. Reduces memory use. TG

August 28, 2008. Version 1.2554.

• Added support for volume color pixel formats (opengl texture format): RGB, luminance/alpha, luminance, 4,8,12 or 16-bit. Formerly only RGBA 8-bit used. More memory efficient, faster transfer to graphics card, allows display of larger maps.

August 27, 2008. Version 1.2554.

• Fixed color zone session restore bug on msms surfaces. TG

August 26, 2008. Version 1.2553.

• Updated surface model programmer's guide documentation. TG

• Made morph map not report error on reset/cancel movie recording. TG

August 25, 2008. Version 1.2552.

• Sped up volume plane display solid rendering 2x by reusing color array. TG

August 22, 2008. Version 1.2552.

• Delayed volume dialog histogram and range updates to speed up cycling through volume planes. TG

• Optimized speed of volume plane display. TG

August 21, 2008. Version 1.2552.

• Added Chimera video documentation to web site. AL

• Changed implementation of solid style volume rendering with colormaps to not use opengl pixel transfer. Avoids graphics driver bug on GeForce 7300 Mac graphics. TG

• Made solid volume colormap use 8-bit color values instead of float, more memory efficient. TG

August 20, 2008. Version 1.2552.

• Made imod file reader to correctly handle open vs closed contours. TG

• Added support uint8 rgba color values in solid rendering, more memory efficient. TG

August 19, 2008. Version 1.2552.

• Removed broken spotlight help/search menu entry on aqua mac 10.5. TG

• Fixed color_by_volume() routine used in scripts. TG

August 15, 2008. Version 1.2550.

• Added 8-bit color indices for solid volume rendering, more memory efficient. Formerly only 16-bit indices used. TG

August 14, 2008. Version 1.2550.

• Made surface color tool ignore volume outline boxes. TG

August 13, 2008. Version 1.2550.

• Making imod file reader properly skip unused records. TG

• Updated tomoplane extension to new surface model api. TG

August 12, 2008. Version 1.2549.

• Fixed bug where closing volume series removed wrong entry from menu. TG

August 1, 2008. Version 1.2549.

• Fixed black covering status line on aqua when graphics window resized smaller. TG

July 31, 2008. Version 1.2548.

• Added focus follows mouse preference, only shown and used on aqua. TG

July 30, 2008. Version 1.2547.

• Fixed pif map bug where integer file values scaled by floating point scale factor remained as an integer map. Caused sparse histograms. TG

• Made volume cap facing initially off for PIF maps since they are most often inverted. TG

• Made marker resize mouse mode use caps lock instead of alt key. TG

• Added option to hide in-window menus on aqua. TG

July 29, 2008. Version 1.2546.

• Moved create color key button to options panel. TG

July 28, 2008. Version 1.2546.

• Put new movie making tutorial on chimera tutorials and animations web pages. TG

July 23, 2008. Version 1.2544.

• Made volume series update histograms for all series. Was only updating one when multiple series played simultaneosly. TG

July 22, 2008. Version 1.2544.

• Made volume series tool handle multiwavelength priism data. TG

• Made volume series tool allow playing all series at once. TG

• Fixed memory leak when volumes created and closed. Data array was deallocated but not surface model and volume python object. TG

• Added showDialog option to molmap command to suppress display of volume dialog (useful in MD trajectory per-frame scripts). TG

• Made fetch eds able to set model id on command-line. TG

July 21, 2008. Version 1.2544.

• Fixed bug when volume data read canceled on opening, session save failed. TG

July 18, 2008. Version 1.2544.

• Made volume series tool copy changes in voxel size and volume origin. TG

• Fixed bug saving volume over original file on a different file system than /tmp (file move didn't work). TG

• Fixed bug where msms calculation says it succeeded but actually returns an incorrect empty surface. TG

• Fixed movie recorder ffmpeg encoding on aqua, trouble reporting status from non-gui thread. Disabled status reporting on aqua. TG

• Made movie recorder not raise main window when doing image capture. TG

July 15, 2008. Version 1.2542.

• Fixed bug, surface color wrong if volume moved while data is being read. TG

• Fixed space navigator lag on aqua. TG

July 9, 2008. Version 1.2540.

• Production release Chimera 1.2540.

July 8, 2008. Version 1.2540.

• Fixed bug where NaN volume normals caused raytracing failure. TG

July 7, 2008. Version 1.2540.

• Made vop resample command undisplay original instead of grid volume. TG

• Fixed volume dialog shown/hidden indicator updating for new volumes. TG

• Made crash report dialog on mac not appear for mscalc crashes (msms surface calculation). TG

July 2, 2008. Version 1.2540.

• Fixed aqua bug: patched pmw to make open dialog history popup menus appear on top. TG

July 1, 2008. Version 1.2537.

• Made volume solid style coloring properly color min/max data values. In some cases the data values corresponding to the end nodes on the volume histogram were not colored. TG

• Fixed molecule copies behavior of crystal contacts tool and added command version. TG

June 30, 2008. Version 1.2537.

• Optimized morph map, 8x faster linear combination on 256^3 array. TG

• Made vop resample command use better name for new volume. TG

• Fixed aqua bug: patched pmw notebook bubble buttons and borders for aqua tk 8.5.2. TG

June 27, 2008. Version 1.2537.

• Fixed aqua bug: clipped volume plane button text and feature buttons. TG

• Fixed volume show/hide icon in volume dialog in solid mode. Sometimes showed incorrect display state. TG

June 26, 2008. Version 1.2537.

• Added mS shortcut to place markers on selected atoms. TG

June 25, 2008. Version 1.2537.

• Added aqua in-window menubars for all dialogs: castp, selection workbench, modbase, rotamers, render by attr, viewdock, demo, movie, multalign. TG

June 24, 2008. Version 1.2535.

• Fixed aqua bug: disappearing bonds (stick style) and vrml cylinders when zooming. TG

• Fixed aqua bug: playing morph map gave volume dialog focus prevented stopping morph playback. TG

• Fixed aqua bug: mouse scroll wheel zooming very insensitive. TG

June 19, 2008. Version 1.2534.

• Fixed volume dialog surface brightness and transparency sliders. They were producing color component values > 1 causing error messages. TG

• Made command-q and the main window close button show the quit confirmation dialog on aqua. TG

June 18, 2008. Version 1.2532.

• Added in-window menu bars to volume and tracer dialog windows in aqua. TG

• Added vop subtract operation for making difference maps. TG

• Fixed volume histogram flickering on aqua. TG

June 17, 2008. Version 1.2531.

• Fixed divide by zero warning message appearing in shell when using volume solid style rendering with opacity = 1. TG

June 16, 2008. Version 1.2531.

• Fixed error when deleting volumes caused by trying to update volume shown indicator (dash icon) after deletion. TG

• Added option/command key 3-button mouse emulation in aqua. TG

June 13, 2008. Version 1.2531.

• Added MacMolPlt/Gamess quantum orbitals volume file reader. TG

June 12, 2008. Version 1.2531.

• Made volume viewer and volume tracer show menu bar at top of screen on aqua. TG

June 11, 2008. Version 1.2529.

• Fixed display of headings in preferences tools pane on aqua. TG

• Added focus follow mouse mode for aqua. TG

June 10, 2008. Version 1.2527.

• Made opening electrostatic potential file formats (delphi, apbs, uhbd) and molecular orbital file formats (gaussian, gopenmol) turn of box face surface capping so that negative threshold levels do not result in box surface. TG

• Fixed actions menu surface transparency on molecular surfaces colored by molecule. TG

• Made in-memory writable volumes created by volume eraser have names ending in "copy" to distinguish them from original volumes. TG

• Made opening volume file not use data from already opened writable volume since that data may be modified later. TG

• Fixed aqua 60% cpu usage when showing model panel, but in tix scrolledhlist with headers. TG

June 9, 2008. Version 1.2527.

• Made model menus use multiple columns on x11 if they have more than 35 entries to avoid inaccessible entries off bottom of screen. TG

• Made saving volume data update the volume name in volume dialog and menus. TG

June 6, 2008. Version 1.2525.

• Made surface display use opengl vertex buffer objects instead of display lists, leading to 2x faster rendering on two tested graphics cards. TG

June 5, 2008. Version 1.2525.

• Made priism volume file reader set correct voxel size. TG

• Made molecular surface display for a set of atoms not override partial surface display done with surface zone tool. TG

• Made active volume name highlighting on aqua use blue color. Was using white which was identical to inactive background. TG

• Made main window have focus at startup on aqua. TG

June 3, 2008. Version 1.2525.

• Fixed hang on aqua caused by benchmark dialog horizontal scrollbar display/undisplay. TG

• Fixed aqua bug where movie recorder could not be stopped because graphics window was given focus at each frame preventing pressing the Stop button. TG

• Fixed aqua bug where movie recorder could not find ffmpeg executable. TG

June 2, 2008. Version 1.2525.

• Made priism volume file reader handle xywzt and xyzwt data orders (w = wavelength, t = time). TG

May 30, 2008. Version 1.2524.

• Fixed molecular surface bug where closing surface model and then reshowing surface for subset of atoms showed entire surface. TG

• Made toolbar and model panel balloons not take focus in aqua. TG

May 28, 2008. Version 1.2523.

• Padded selection button in lower right corner of main window so that text is not clipped on aqua. TG

• Made atom spec balloons on aqua not have window frame, and not take focus. TG

• Added apple application menu entries for About Chimera... and Preferences... on aqua. TG

• Made model panel Select button work on molecular surfaces. TG

May 27, 2008. Version 1.2522.

• Fixed volume image stack session saving bug. TG

• Fixed recently introduced bug where color byatom with a surface shown generated an error. TG

• Fixed aqua chimera crash when any dialog shown by disabling apple event handling code. TG

May 26, 2008. Version 1.2522.

• Made actions atom/ribbon/surface menus work with multiscale models. TG

May 22, 2008. Version 1.2517.

• Made space navigator work with independent center of rotation mode. TG

• Made select command on surfaces select all the surface pieces. TG

May 21, 2008. Version 1.2517.

• Fixed recently introduced bug where cofr command did not work on undisplayed selected surfaces. TG

May 20, 2008. Version 1.2514.

• Made selecting molecular surface select atoms and bonds. TG

• Made action menu set pivot work on selected surfaces. TG

• Made volume viewer detect surface color/style changes made from Actions menu or by other means. TG

May 19, 2008. Version 1.2511.

• Fixed fit map error when no atoms selected and simulated map enabled. TG

May 15, 2008. Version 1.2511.

• Made Actions / Focus menu entry work for selected surfaces. TG

• Fixed volume series error when playing series when active volume in not in series. TG

• Fixed volume series bug undisplaying surfaces when caching off. TG

May 13, 2008. Version 1.2510.

• Made Actions menu entries work when molecular surfaces are selected. Formerly they only worked when atoms were selected. TG

• Made selecting a surface in mesh or dot style require clicking on a mesh line or dot. Formerly any area of the surface could be clicked. The new behavior allows selecting molecules within surfaces. TG

• Made volume surfaces selectable. TG

• Made Actions / Surface and Actions / Color menu entries work on non-molecular surfaces. TG

• Removed Actions / Target menu. TG

May 12, 2008. Version 1.2510.

• Fixed crash at startup on mac when remote displaying caused by space navigator tool. Same problem when --nogui mode used and the user is not logged in to the mac console. TG

May 9, 2008. Version 1.2510.

• Made molecular surface calculation report the number of surface components and the solvent excluded and solvent accessible surface areas. TG

• Fixed error in surface color tool when surface is colored by volume value and the volume is closed and then the surface is changed. TG

May 8, 2008. Version 1.2510.

• Removed accelerators on/off menu entries from Tools / General Controls menu and renamed Accelerators List entry to Keyboard Shortcuts. Keyboard shortcuts are now enabled with a switch on the dialog and that setting is now saved in preferences automatically. TG

May 7, 2008. Version 1.2510.

• Made Fetch Structure by ID report download progress in status line. TG

May 6, 2008. Version 1.2510.

• Fixed recently introduced bug in model panel Tile button where models were placed in random order on screen. Fixed ordering is by model id number. TG

May 5, 2008. Version 1.2510.

• Put least used controls of surface color dialog in options panel. TG

• Made surface color dialog use a separate volume menu that is displayed when color method is by volume data value. Formerly every volume appeared as an entry in the coloring method menu. TG

• Added electrostatic coloring method to surface color dialog. This is the same as coloring by volume data value, only with dialog text specialized to save "electrostatic potential" to reduce confusion. TG

• Fixed session saving bug with custom colored molecular surface models. Bug introduced in past month. TG

May 2, 2008. Version 1.2510.

• Made benchmark tool draw models on screen to avoid inflated frame rates. Formerly drawing was done in an internal buffer and not shown and newer drivers shortcut the rendering leading to frame rates sometimes 2x higher than in actual use. TG

• Added "report scores" button to benchmark tool to send scores to RBVI for posting on web. TG

• Simplified benchmark dialog to show only the commonly used controls, with others hidden in an options panel. TG

• Fixed bug in benchmark tool with solid rendering where volume was not in field of view so some graphics drivers rendered nothing leading to very large test cases which caused memory errors. TG

April 30, 2008. Version 1.2508.

• Fixed bug in crystal contacts tool where contacts between a crystal asymmetric unit and copies translated by unit cell translations were not detected. TG

• Added option to crystal contacts tool to create moleucule models for contacting copies. TG

April 28, 2008. Version 1.2506.

• Made volume eraser radius slider resize when the dialog is resized. TG

April 25, 2008. Version 1.2506.

• Made model panel Tile button highlight when non-molecule models selected. TG

April 24, 2008. Version 1.2506.

• Made model panel Tile button work with all models, not just molecules. TG

April 18, 2008. Version 1.2505.

• Made phantom force feedback tool volume aligned cross-hair display correctly when local volume coordinates are rotated. TG

April 17, 2008. Version 1.2504.

• Added color palette option menu and a button to reverse color order to surface color tool. TG

April 16, 2008. Version 1.2503.

• Made multiscale tool with surface resolution = 0 (solvent excluded surface) use probe radius, vertex density and disjoint component preference settings. Formerly it used values that could not be changed. TG

• Made relative orientation schematic shortcut "ai" not give an error when rotation angle is zero. TG

April 15, 2008. Version 1.2503.

• Made phantom force feedback tool handle volume step change, and made move marker warn if no marker is under cursor. TG

April 11, 2008. Version 1.2503.

• Simplified Phantom Force Feedback dialog. Made key commands work from main Chimera window. Changed move models, zoom, contour level, move marker keyboard commands to press once to activate, again to deactivate. Formerly key had to be held down. TG

• Included Phantom force feedback OpenHaptics event handling in Windows Chimera distribution. User is required to install OpenHaptics driver. TG

April 10, 2008. Version 1.2503.

• Fixed bug where molecular surface calculation for zero atoms failed. TG

April 8, 2008. Version 1.2503.

• Made "ac" command accept arguments which are keyboard shortcuts to run. Without arguments it still enables typing keyboard shortcuts to main window. TG

April 7, 2008. Version 1.2503.

• Added support for Space Navigator six degree-of-freedom input device to Windows Chimera versions. TG

April 4, 2008. Version 1.2503.

• Made molecular surface calculation not show a console window on Windows. TG

April 3, 2008. Version 1.2503.

• Fixed molecular surface calculation on Windows. Was interpreting ctrl-z as end of input. Also mscalc program was not started correctly. TG

April 2, 2008. Version 1.2502.

• Added support for Space Navigator six degree-of-freedom input device to Mac Chimera versions. TG

April 1, 2008. Version 1.2502.

• Fixed bug where enabling surface capping and surface coloring caused continuous recalculation of cap and colors. TG

• Made surface cap color not flicker to solid color when moving cap. TG

March 27, 2008. Version 1.2502.

• Made multiscale dialog use stand-alone program molecular surface calculation when resolution set to zero for solvent excluded surface. TG

March 26, 2008. Version 1.2501.

• Optimized surface distance calculation (keyboard shortcut "sd") by translating Python code to C++. Several hundred times faster. TG

March 25, 2008. Version 1.2501.

• Changed solvent excluded/accessible surface area calculation to use analytical values instead of approximate values calculated from the triangulated surface (which depended on vertex density). TG

• Added per-residue solvent excluded/accessible surface area (areaSES, areaSAS) attributes viewable with Render by Attribute tool. TG

• Added solvent excluded/accessible surface area in Reply Log output when molecular surface is calculated.

• Made up and down arrow keys work with selected surface pieces. TG

• Fixed bug in IMOD mesh file reader where normal vectors appeared in the surface vertex array resulting in wrong inertia calculation. TG

• Added "ra" keyboard shortcut for showing render-by-attribute dialog. TG

• Added "se" keyboard shortcut for toggling silhouette edge display. TG

• Fixed bug in surface distance calculation where distance to an edge was used when the closest distance was actually to a vertex. TG

March 20, 2008. Version 1.2501.

• Fixed meshmol command on molecular surfaces, "truth value ambiguous" error. TG

• Fixed error in Measure and Color Blobs, "array cannot be safely cast to required type" on 64-bit Chimera versions. TG

• Made Color Zone, Surface Zone and Surface Color work on MSMS surface caps. TG

March 18, 2008. Version 1.2500.

• Made Chimera calculate solvent excluded molecular surfaces using a standalone application so crashes do not crash Chimera. TG

• Made molecular surface calculation assign per-atom solvent excluded surface area (areaSES) and solvent accessible surface area (areaSAS) values that can be used with Render by Attribute dialog or the "select" command. TG

• Molecular surfaces now are implemented using SurfaceModel. Some new attributes of this type of model are visible in the selection and model attribute inspector dialogs. TG

• Eliminated warning messages that appeared in the Chimera reply log on Mac OS 10.5 about an unhandled apple event. TG

• Changed Benchmark molecule tests to only time one molecule instead of six.

• Fixed ribbon benchmark timing, previous scores invalid. TG

March 17, 2008. Version 1.2500.

• Fixed a triangle template allocation bug in MSMS molecular surface calculation reducing number of crash cases in half. Also changed to allow surface calculation when one atom is entirely inside of another. TG

• Made Movie Recorder respect preference for saving POVray files. TG

• Fixed InterSurf to use new SurfaceModel Python names. TG

March 11, 2008. Version 1.2500.

• Renamed Surface_Model to SurfaceModel and changed Python method names and attributes to eliminated underscore characters. TG

March 5, 2008. Version 1.2499.

• Added dot surface display and dot size setting to surface models, settable with selection inspector. TG

March 4, 2008. Version 1.2498.

• Reduced memory use of volume solid style rendering in color map mode. Was unnecessarily making floating point copy of map. TG

February 29, 2008. Version 1.2497.

• Removed setting to flip surface lighting normals visible in selection inspector dialog. TG

February 28, 2008. Version 1.2496.

• Added consistency checking (valid record size) in delphi map file reader. TG

February 27, 2008. Version 1.2495.

• Added checkbuttons to volume tracer mouse mode panel that match those in the Mouse menu. TG

• Fixed volume tracer session restore bug where a second traced surfaces model was created after restoring a session containing traced surfaces. TG

• Made volume tracer delete surface panel only delete selected traced surfaces. Was deleting any selected surface. TG

• Made volume tracer continuous marker placement while dragging work with "on spot", "on plane", or "outside data" mouse mode. Was ignoring those settings and always dropping markers on plane. TG

February 26, 2008. Version 1.2495.

• Fixed volume tracer bug where traceback given if "marker color matches volume color" enabled and marker is placed. TG

• Made crash dump detection for bug reporting work on Mac OS 10.5. Mac OS 10.5 uses separate file for each crash, while 10.4 used one file for all crashes of the same application. TG

February 22, 2008. Version 1.2495.

• Modified per-model clipping command to not modify existing clip plane axis or origin unless explicit options are given. TG

February 21, 2008. Version 1.2495.

• Added option to create simulated map (uses molmap command) to the fit map dialog. TG

February 20, 2008. Version 1.2495.

• Added per-model clipping command mclip. TG

• Fixed volume eraser bug that gave traceback when erasing done with eraser sphere entirely outside of volume. TG

• Fixed bug on movement mouse mode where no translation was possible if near clip plane was at or in front of eye position. Changed behavior so amount of translation is based on dragging center of rotation of object. TG

February 19, 2008. Version 1.2494.

• Added zflip option to vop (volume operation) command to change the hand of a map by reversing the order of the z planes. TG

February 15, 2008. Version 1.2493.

• Added IMOD map file reader, file suffix ".rec". These are MRC maps but signed 8-bit mode is interpreted as unsigned. TG

• Changed volume solid style transparency modulation from t -> t ** (1.0/planes) to t -> t ** (1.0/(planes*t)). Here planes = minimum number of planes along each axis times the transparency factor and the initial transparency t is the height of the transfer function on the histogram (0-1 range). For transparent voxels the change is minor. For opaque voxels it makes the effective thickness smaller and avoids a large brightness jump between opacity 0.99 and 1.0. TG

February 13, 2008. Version 1.2493.

• Fixed bug where deleting volume tracer links by means other than the "delete links" menu entry would later cause session saving to fail. TG

• Made session saving for volume opens put paths in the session file that are relative to the session file directory if the volume data lies within or below that directory. This allows restoring the session file after moving a directory containing session files and volume data. TG

• Added linewidth option to shape command for meshes. TG

• Made shape command show mesh by default only for icosahedron (not sphere) with lattice option specified. TG

• Changed shape command default color to "gray". TG

February 12, 2008. Version 1.2493.

• Added displayThreshold option to molmap command to set the initial contour level of the new map so that the specified fraction of total mass is contained within the contour. Default value 0.95. TG

• Changed effect of volume solid style transparency slider so that it modulates transparency even when factor times depth in planes is less than 1. This allows making completely opaque single planes. TG

February 8, 2008. Version 1.2493.

• Reduced memory use when saving a volume zone. For maps larger than 16 Mvoxels the map mask is computed plane by plane. Smaller maps use 12 bytes per voxel overhead. TG

February 7, 2008. Version 1.2493.

• Fixed split map button in color zone dialog. TG

January 31, 2008. Version 1.2492.

• Combined "fit model in map" and "fit map in map" dialogs into a single dialog, and combined menu entries into one entry. Dialog has new layout but same functionality as original two dialogs. TG

• Added option for real-time updating of correlation and average map value to fit map dialog. TG

January 30, 2008. Version 1.2486.

• Added ability to create surfaces from stacks of loops and curves with the volume path tracer tool. Uses the new Surface panel of the volume path tracer dialog. TG

• Renamed "volume path tracer" to "volume tracer". TG

• Reordered volume tools menu to put more frequently useful tools near the top and group them by functionality. TG

• Added split map button to color zone dialog and eliminated separate volume tools menu entry for split map. TG

• Changed molmap ratio of resolution to Gaussian standard deviation to be 1/(pi*sqrt(2)) (~0.225) from former value of 1/(2*sqrt(pi)) (~0.282). TG

• Made split map by color zone give proper alignment when map coordinates involve a rotation.

January 29, 2008. Version 1.2485.

• Added keyboard shortcut "or" to toggle orthographic projection. TG

January 25, 2008. Version 1.2485.

• Added ability to export surfaces in Wavefront OBJ format using File / Export Scene. TG

• Optimized "split map by color zone" to use less memory. Operates plane by plane for maps larger than 16 Mvoxels. TG

• Added mouse mode to resize a selected surface by dragging. Enabled for one drag use by keyboard shortcut sz. TG

• Added keyboard shortcut "ao" to activate only selected surfaces. TG

• Added keyboard shortcut "oc" to allow typing one command and then automatically return to entering keyboard shortcuts. TG

• Allowed resizing volume path tracer markers by dragging the mouse while holding the Alt key down if the move/resize mode is enabled. TG

January 24, 2008. Version 1.2485.

• Added "resample" operation to vop command to resample one volume data set on the grid of a second volume data set. TG

January 23, 2008. Version 1.2485.

• Fixed incorrect rainbow colormap direction for volumes with rotated local coordinates. TG

• Made "measure and color blobs" dialog and mask command ignore outline boxes around volume data. TG

• Added "shape" command that makes surfaces having standard geometric shapes. Handles cylinder, sphere, and icosahedron. Includes icosahedral mesh capabilities of hkcage command. Includes interpolating icosahedron with sphere and alternate coordinates systems as in the Icosahedron surface dialog. TG

• Changed vm keyboard shortcut to mask active volume using selected surfaces. Formerly it masked volume using volume contour surface. TG

January 22, 2008. Version 1.2485.

• Made volume contour surfaces have correct lighting when the voxel size along an axis is made negative to flip the hand of the map. Formerly two sided lighting gave dark surface in this case. TG

• Made image stack volume reader handle multi-page tiff images. TG

• Fixed surface capping bug when new surface created while capping is enabled. TG

January 18, 2008. Version 1.2485.

• Added molmap command to make volume from a molecule by summing Gaussians at each atom position. TG

January 16, 2008. Version 1.2483.

• Made opening tiff image stacks work by selecting all images in the open dialog. Formerly only one image was selected and others that had the same prefix and different numeric suffix were inferred. TG

• Made image stack reader handle image types other than TIFF. Can handle any image format understood by the Python image library (e.g. png, jpeg). TG

January 15, 2008. Version 1.2483.

• Fixed chimera "--send" startup option on mac. Was always starting a new instance of chimera. TG

January 11, 2008. Version 1.2483.

• Removed marker set models closed with the file menu entry in the volume path tracer dialog. Formerly the models were just emptied of markers. TG

• Changed mask command sandwich option default value to true. TG

• Changed mask command fullmap option to require a true/false value. Formerly the option took no value. TG

January 10, 2008. Version 1.2483.

• Made default projection axis for mask command y instead of z. TG

• Renamed "pick surface pieces" dialog and menu entry to the more descriptive "measure and color blobs". TG

• Added slab option to mask command to mask using a slab of specified thickness created by thickening a surface. TG

January 9, 2008. Version 1.2483.

• Added selection inspector attributes for surface pieces: surface piece count, line thickness, line smoothing, lighting, two sided lighting, lighting normal direction, transparency brightness. TG

• Made selection inspector attributes for surface models and pieces update when changed using other dialogs or commands. TG

January 8, 2008. Version 1.2481.

• Added attributes to selection inspector dialog for surfaces and surface pieces. Attributes: color, display style (mesh/solid), displayed, triangle count, active, selectable with mouse. TG

• Made selected surfaces show green outline even when "selectable with mouse" is turned off. TG

• Made keyboard shortcuts work on surfaces selected with select command. The select command selects the surface model but not the surface components. TG

January 7, 2008. Version 1.2481.

• Made surfnet tool create a surface model instead of a vrml model. Allows measuring enclosed volume, coloring, splitting disjoint components, .... TG

• Eliminated _cubes contour calculation module. TG

January 2, 2008. Version 1.2481.

• Added fill value option to vop command. Large negative fill values can produce flat cut faces when erasing an octant. TG

December 21, 2007. Version 1.2480.

• Made help command show documentation for commands volume, topo, sym, bondzone, split, msc, meshmol, mask, hkcage, crystalcontacts. TG

• Added vop (volume operation command) to erase an octant. Plan to support many other volume modifying operations (gaussian filter, erase outside sphere, interpolate, ...) as options to this command in the future. TG

• Changed volume suffixes from