| | 1 | {{{ |
| | 2 | #!html |
| | 3 | |
| | 4 | <h1> |
| | 5 | Chimera Change Log |
| | 6 | </h1> |
| | 7 | |
| | 8 | <p> |
| | 9 | This page lists changes to Chimera that are visible to users, including the |
| | 10 | date and Chimera version when the change was checked in, and who made the |
| | 11 | change (TG = Tom Goddard, AL = Andrew Ling). |
| | 12 | </p> |
| | 13 | |
| | 14 | <p> |
| | 15 | Ideally this log would record all changes, but we are currently seeing |
| | 16 | how difficult it is to keep it up to date. |
| | 17 | </p> |
| | 18 | |
| | 19 | <p><b>November 21, 2008. Version 1.2577.</b></p> |
| | 20 | |
| | 21 | <ul type=None> |
| | 22 | <li><p>Made initial volume viewer thresholds symmetric about 0 for |
| | 23 | electrostatic potential data and other polar data. TG |
| | 24 | <li><p>Added gaussian and laplacian filters to vop command. TG |
| | 25 | </ul> |
| | 26 | |
| | 27 | <p><b>November 20, 2008. Version 1.2576.</b></p> |
| | 28 | |
| | 29 | <ul type=None> |
| | 30 | <li><p>Made per-model clipping work with solid volume rendering where |
| | 31 | projection mode is perpendicular to view (uses 3d textures). |
| | 32 | </ul> |
| | 33 | |
| | 34 | <p><b>November 19, 2008. Version 1.2576.</b></p> |
| | 35 | |
| | 36 | <ul type=None> |
| | 37 | <li><p>Fixed error reading mrc file > 2 Gbytes. TG |
| | 38 | </ul> |
| | 39 | |
| | 40 | <p><b>November 18, 2008. Version 1.2575.</b></p> |
| | 41 | |
| | 42 | <ul type=None> |
| | 43 | <li><p>Fixed hkcage command error when invoked second time with surface |
| | 44 | capping enabled. TG |
| | 45 | <li><p>Added planes keyword to volume command to show sequence of planes. TG |
| | 46 | <li><p>Made turn, move, ... not raise error if model deleted during motion. TG |
| | 47 | <li><p>Added volume outline box linewidth setting. TG |
| | 48 | <li><p>Fixed reset command to preserve relative orientations. TG |
| | 49 | </ul> |
| | 50 | |
| | 51 | <p><b>November 17, 2008. Version 1.2575.</b></p> |
| | 52 | |
| | 53 | <ul type=None> |
| | 54 | <li><p>Fixed bug that caused extra frames during movie capture scripts |
| | 55 | that read volume data, caused by progress messages. TG |
| | 56 | <li><p>Made movie encode command print status messages on main status line. TG |
| | 57 | </ul> |
| | 58 | |
| | 59 | <p><b>November 14, 2008. Version 1.2575.</b></p> |
| | 60 | |
| | 61 | <ul type=None> |
| | 62 | <li><p>Fixed incorrect center of rotation when a model is closed where another |
| | 63 | model has the same id. TG |
| | 64 | <li><p>Made actions / focus with nothing selected turn of near/far clipping. TG |
| | 65 | </ul> |
| | 66 | |
| | 67 | <p><b>November 13, 2008. Version 1.2574.</b></p> |
| | 68 | |
| | 69 | <ul type=None> |
| | 70 | <li><p>Suppress Mac 10.5 crash report dialog when molecular surface |
| | 71 | calculation mscalc program crashes. TG |
| | 72 | <li><p>Fixed volume command bug setting color of solid rendering. TG |
| | 73 | </ul> |
| | 74 | |
| | 75 | <p><b>November 12, 2008. Version 1.2574.</b></p> |
| | 76 | |
| | 77 | <ul type=None> |
| | 78 | <li><p>Fixed bugs writing image stacks as single hdf (*.cmap) files. TG |
| | 79 | </ul> |
| | 80 | |
| | 81 | <p><b>November 11, 2008. Version 1.2574.</b></p> |
| | 82 | |
| | 83 | <ul type=None> |
| | 84 | <li><p>Made molecule bounds include atom radii to avoid clipping atom spheres |
| | 85 | when near/far clipping is turned off. TG |
| | 86 | |
| | 87 | <li><p>Fixed error closing volumes when new session opened. TG |
| | 88 | <li><p>Fixed bug where distant opaque solid volume models appeared in front of |
| | 89 | closer opaque soild volume models. TG |
| | 90 | <li><p>Fixed bug where restored traced surface not saved in subsequent sessions. |
| | 91 | TG |
| | 92 | </ul> |
| | 93 | |
| | 94 | <p><b>November 10, 2008. Version 1.2574.</b></p> |
| | 95 | |
| | 96 | <ul type=None> |
| | 97 | <li><p>Added warning when restoring a session file written by a newer chimera |
| | 98 | version. TG |
| | 99 | <li><p>Fixed bug restoring volume / surface coloring from session files written |
| | 100 | by Chimera version more than 1 year old. TG |
| | 101 | </ul> |
| | 102 | |
| | 103 | <p><b>November 6, 2008. Version 1.2573.</b></p> |
| | 104 | |
| | 105 | <ul type=None> |
| | 106 | |
| | 107 | <li><p>Fixed volume eraser bug introduce Sept 30. TG |
| | 108 | </ul> |
| | 109 | |
| | 110 | <p><b>November 4, 2008. Version 1.2573.</b></p> |
| | 111 | |
| | 112 | <ul type=None> |
| | 113 | <li><p>Made surface capping on by default. TG |
| | 114 | <li><p>Made space navigator preserve front-center rotation point during |
| | 115 | rotation. TG |
| | 116 | </ul> |
| | 117 | |
| | 118 | <p><b>November 3, 2008. Version 1.2573.</b></p> |
| | 119 | |
| | 120 | <ul type=None> |
| | 121 | <li><p>Made near/far clip planes off by default. TG |
| | 122 | </ul> |
| | 123 | |
| | 124 | <p><b>October 31, 2008. Version 1.2572.</b></p> |
| | 125 | |
| | 126 | <ul type=None> |
| | 127 | <li><p>Made surface bounds calculation use bounding sphere instead of box |
| | 128 | resulting in tighter bounds for sphere-like surfaces. Effects amount of camera |
| | 129 | zoom when the first model show is a surface. TG |
| | 130 | </ul> |
| | 131 | |
| | 132 | <p><b>October 29, 2008. Version 1.2572.</b></p> |
| | 133 | |
| | 134 | <ul type=None> |
| | 135 | <li><p>Changed default surface transparency blend model to dim (alpha,1-alpha). |
| | 136 | TG |
| | 137 | <li><p>Added center of rotation mode name options "fixed", "front", "models", |
| | 138 | and "independent" to cofr command. TG |
| | 139 | <li><p>Made coordinateSystem arguments to movement commands work without '#'. TG |
| | 140 | </ul> |
| | 141 | |
| | 142 | <p><b>October 28, 2008. Version 1.2571.</b></p> |
| | 143 | |
| | 144 | <ul type=None> |
| | 145 | <li><p>Fixed failure to hide clicked triangle using pick blobs tool. TG |
| | 146 | <li><p>Cleared surface visibility/color atom attributes when surface closed. TG |
| | 147 | </ul> |
| | 148 | |
| | 149 | <p><b>October 27, 2008. Version 1.2571.</b></p> |
| | 150 | |
| | 151 | <ul type=None> |
| | 152 | <li><p>Fixed bug where hiding a molecular surface piece made subsequent surface |
| | 153 | show not work. TG |
| | 154 | </ul> |
| | 155 | |
| | 156 | <p><b>October 24, 2008. Version 1.2571.</b></p> |
| | 157 | |
| | 158 | <ul type=None> |
| | 159 | <li><p>Changed the default center of rotation mode to front-center. TG |
| | 160 | <li><p>Fixed multiscale session save error that happened after chain deleted. TG |
| | 161 | </ul> |
| | 162 | |
| | 163 | <p><b>October 22, 2008. Version 1.2569.</b></p> |
| | 164 | |
| | 165 | <ul type=None> |
| | 166 | <li><p>Added front-center center of rotation mode. TG |
| | 167 | <li><p>Added coordinate system, center, models arguments to turn, roll, rock, |
| | 168 | and move commands. TG |
| | 169 | <li><p>Made benchmark dialog show warning if models are open. TG |
| | 170 | <li><p>Allowed move command to move along all 3 axes at once. TG |
| | 171 | <li><p>Made cofr command accept point coordinates and coord sys arguments. TG |
| | 172 | <li><p>Added center, coord system, model id args to shape command. TG |
| | 173 | </ul> |
| | 174 | |
| | 175 | <p><b>October 20, 2008. Version 1.2567.</b></p> |
| | 176 | |
| | 177 | <ul type=None> |
| | 178 | <li><p>Made options panel for morph map and added roundtrip option. TG |
| | 179 | </ul> |
| | 180 | |
| | 181 | <p><b>October 15, 2008. Version 1.2566.</b></p> |
| | 182 | |
| | 183 | <ul type=None> |
| | 184 | <li><p>Fixed actions menu entries focus, set pivot, surface |
| | 185 | hide/show/repr/tranparency and color when a molecular surface is selected |
| | 186 | but not its atoms. TG |
| | 187 | </ul> |
| | 188 | |
| | 189 | <p><b>October 14, 2008. Version 1.2566.</b></p> |
| | 190 | |
| | 191 | <ul type=None> |
| | 192 | <li><p>Made focus command and action use center-of-models when nothing selected. |
| | 193 | TG |
| | 194 | <li><p>Fixed session saving error after closing traced surface model. TG |
| | 195 | </ul> |
| | 196 | |
| | 197 | <p><b>October 10, 2008. Version 1.2566.</b></p> |
| | 198 | |
| | 199 | <ul type=None> |
| | 200 | <li><p>Fixed model panel configure dialog bug, pmw tabs not raising in |
| | 201 | Mac Aqua Chimera. TG |
| | 202 | </ul> |
| | 203 | |
| | 204 | <p><b>October 1, 2008. Version 1.2561.</b></p> |
| | 205 | |
| | 206 | <ul type=None> |
| | 207 | |
| | 208 | <li><p>Made molecular surface show "all components" false in selection |
| | 209 | inspector if all-component calculation failed and instead used single-component. |
| | 210 | TG |
| | 211 | <li><p>Fixed volume show/hide icon update error on model close. TG |
| | 212 | </ul> |
| | 213 | |
| | 214 | <p><b>September 29, 2008. Version 1.2561.</b></p> |
| | 215 | |
| | 216 | <ul type=None> |
| | 217 | <li><p>Added memory checking to c++ python array allocation used in volume |
| | 218 | and surface calculations. TG |
| | 219 | </ul> |
| | 220 | |
| | 221 | <p><b>September 25, 2008. Version 1.2561.</b></p> |
| | 222 | |
| | 223 | <ul type=None> |
| | 224 | <li><p>Added ls keyboard shortcut to open last session file. TG |
| | 225 | </ul> |
| | 226 | |
| | 227 | <p><b>September 23, 2008. Version 1.2560.</b></p> |
| | 228 | |
| | 229 | <ul type=None> |
| | 230 | <li><p>Fixed volume solid color mode and projection mode bugs. TG |
| | 231 | </ul> |
| | 232 | |
| | 233 | <p><b>September 19, 2008. Version 1.2559.</b></p> |
| | 234 | |
| | 235 | <ul type=None> |
| | 236 | <li><p>Added out-of-memory test for large surfaces. TG |
| | 237 | <li><p>Turn off mesh lighting for single plane volume display. TG |
| | 238 | <li><p>Made volume planes switch to solid style only when "one" button pressed. |
| | 239 | TG |
| | 240 | <li><p>Made single plane volume contour surface without capping render with |
| | 241 | mesh to show 2d contours. TG |
| | 242 | </ul> |
| | 243 | |
| | 244 | <p><b>September 12, 2008. Version 1.2558.</b></p> |
| | 245 | |
| | 246 | <ul type=None> |
| | 247 | <li><p>Added fourier transform to vop command, removed fourier transform |
| | 248 | menu entry. TG |
| | 249 | </ul> |
| | 250 | |
| | 251 | <p><b>September 11, 2008. Version 1.2558.</b></p> |
| | 252 | |
| | 253 | <ul type=None> |
| | 254 | <li><p>Made volume square mesh option show box cap diagonals. |
| | 255 | The square mesh code that excluded box cap diagonals also excluded all |
| | 256 | contours for single data planes. TG |
| | 257 | <li><p>Added volume planes cycle option with plane count and speed control. |
| | 258 | Replaces "play" button. TG |
| | 259 | <li><p>Added button to volume planes panel to preload data. Allows faster |
| | 260 | moving through planes. TG |
| | 261 | </ul> |
| | 262 | |
| | 263 | <p><b>September 10, 2008. Version 1.2558.</b></p> |
| | 264 | |
| | 265 | <ul type=None> |
| | 266 | <li><p>Fixed volume tracer bug where first marker on empty space mispositioned |
| | 267 | if no models are opened. TG |
| | 268 | </ul> |
| | 269 | |
| | 270 | <p><b>September 9, 2008. Version 1.2558.</b></p> |
| | 271 | |
| | 272 | <ul type=None> |
| | 273 | <li><p>Changed volume dialog origin field to show index of xyz origin instead |
| | 274 | of xyz coordinates of index 0,0,0. Allows changing voxel size without altering |
| | 275 | xyz origin position within array. TG |
| | 276 | <li><p>Added originIndex keyword to volume command for specifying the xyz origin |
| | 277 | in grid index units. Changing voxelSize with volume command now preserves |
| | 278 | index of xyz 0,0,0 rather than xyz of index 0,0,0. TG |
| | 279 | <li><p>Added single volume plane surface and mesh display. Allows drawing |
| | 280 | 2d contour lines. Formerly surface and mesh style volume display showed |
| | 281 | nothing for single planes. TG |
| | 282 | </ul> |
| | 283 | |
| | 284 | <p><b>September 8, 2008. Version 1.2557.</b></p> |
| | 285 | |
| | 286 | <ul type=None> |
| | 287 | <li><p>Made solid volume rendering status messages about color appear |
| | 288 | only once per frame. Were showing for every data plane. TG |
| | 289 | <li><p>Fixed erratic incorrect use of x or y projection axes in solid |
| | 290 | rendering. TG |
| | 291 | <li><p>Fixed netcdf out of memory error message. TG |
| | 292 | <li><p>Fixed bugs where volume dialog did not update display style and |
| | 293 | hide/show icon when solid style hidden (and hence solid model closed). TG |
| | 294 | </ul> |
| | 295 | |
| | 296 | <p><b>September 5, 2008. Version 1.2557.</b></p> |
| | 297 | |
| | 298 | <ul type=None> |
| | 299 | <li><p>Added luminance color for volume rendering so single color modes need |
| | 300 | not display white. TG |
| | 301 | <li><p>Added auto projection mode that chooses 2d z planes rendering volume |
| | 302 | slabs with aspect 4:1 or greater, otherwise xyz planes (using more memory). TG |
| | 303 | </ul> |
| | 304 | |
| | 305 | <p><b>September 3, 2008. Version 1.2554.</b></p> |
| | 306 | |
| | 307 | <ul type=None> |
| | 308 | <li><p>Removed colormap mode from solid style volume rendering. TG |
| | 309 | </ul> |
| | 310 | |
| | 311 | <p><b>September 2, 2008. Version 1.2554.</b></p> |
| | 312 | |
| | 313 | <ul type=None> |
| | 314 | <li><p>Changed electrostatic surface coloring to be opaque red/white/blue. TG |
| | 315 | </ul> |
| | 316 | |
| | 317 | <p><b>August 29, 2008. Version 1.2554.</b></p> |
| | 318 | |
| | 319 | <ul type=None> |
| | 320 | <li><p>Added volume projection mode option for tomogram viewing using solid |
| | 321 | style. Allows only showing z planes. 3x less memory use versus xyz mode |
| | 322 | where planes most parallel to screen used. More memory efficient. TG |
| | 323 | |
| | 324 | <li><p>Change volume solid style rendering to not make full 3-d temporary color |
| | 325 | array. Instead computes only 2-d color planes at a time. Reduces memory use. TG |
| | 326 | </ul> |
| | 327 | |
| | 328 | <p><b>August 28, 2008. Version 1.2554.</b></p> |
| | 329 | |
| | 330 | <ul type=None> |
| | 331 | <li><p>Added support for volume color pixel formats (opengl texture |
| | 332 | format): RGB, luminance/alpha, luminance, 4,8,12 or 16-bit. Formerly |
| | 333 | only RGBA 8-bit used. More memory efficient, faster transfer to |
| | 334 | graphics card, allows display of larger maps. |
| | 335 | </ul> |
| | 336 | |
| | 337 | <p><b>August 27, 2008. Version 1.2554.</b></p> |
| | 338 | |
| | 339 | <ul type=None> |
| | 340 | <li><p>Fixed color zone session restore bug on msms surfaces. TG |
| | 341 | </ul> |
| | 342 | |
| | 343 | <p><b>August 26, 2008. Version 1.2553.</b></p> |
| | 344 | |
| | 345 | <ul type=None> |
| | 346 | <li><p>Updated surface model programmer's guide documentation. TG |
| | 347 | <li><p>Made morph map not report error on reset/cancel movie recording. TG |
| | 348 | </ul> |
| | 349 | |
| | 350 | <p><b>August 25, 2008. Version 1.2552.</b></p> |
| | 351 | |
| | 352 | <ul type=None> |
| | 353 | <li><p>Sped up volume plane display solid rendering 2x by reusing color array. TG |
| | 354 | </ul> |
| | 355 | |
| | 356 | <p><b>August 22, 2008. Version 1.2552.</b></p> |
| | 357 | |
| | 358 | <ul type=None> |
| | 359 | <li><p>Delayed volume dialog histogram and range updates to speed up |
| | 360 | cycling through volume planes. TG |
| | 361 | <li>Optimized speed of volume plane display. TG |
| | 362 | </ul> |
| | 363 | |
| | 364 | <p><b>August 21, 2008. Version 1.2552.</b></p> |
| | 365 | |
| | 366 | <ul type=None> |
| | 367 | <li><p>Added Chimera video documentation to web site. AL |
| | 368 | <li><p>Changed implementation of solid style volume rendering with |
| | 369 | colormaps to not use opengl pixel transfer. Avoids graphics driver |
| | 370 | bug on GeForce 7300 Mac graphics. TG |
| | 371 | <li><p>Made solid volume colormap use 8-bit color values instead of float, |
| | 372 | more memory efficient. TG |
| | 373 | </ul> |
| | 374 | |
| | 375 | <p><b>August 20, 2008. Version 1.2552.</b></p> |
| | 376 | |
| | 377 | <ul type=None> |
| | 378 | <li><p>Made imod file reader to correctly handle open vs closed contours. TG |
| | 379 | <li><p>Added support uint8 rgba color values in solid rendering, more |
| | 380 | memory efficient. TG |
| | 381 | </ul> |
| | 382 | |
| | 383 | <p><b>August 19, 2008. Version 1.2552.</b></p> |
| | 384 | |
| | 385 | <ul type=None> |
| | 386 | <li><p>Removed broken spotlight help/search menu entry on aqua mac 10.5. TG |
| | 387 | <li><p>Fixed color_by_volume() routine used in scripts. TG |
| | 388 | </ul> |
| | 389 | |
| | 390 | <p><b>August 15, 2008. Version 1.2550.</b></p> |
| | 391 | |
| | 392 | <ul type=None> |
| | 393 | <li><p>Added 8-bit color indices for solid volume rendering, more |
| | 394 | memory efficient. Formerly only 16-bit indices used. TG |
| | 395 | </ul> |
| | 396 | |
| | 397 | <p><b>August 14, 2008. Version 1.2550.</b></p> |
| | 398 | |
| | 399 | <ul type=None> |
| | 400 | <li><p>Made surface color tool ignore volume outline boxes. TG |
| | 401 | </ul> |
| | 402 | |
| | 403 | <p><b>August 13, 2008. Version 1.2550.</b></p> |
| | 404 | |
| | 405 | <ul type=None> |
| | 406 | <li><p>Making imod file reader properly skip unused records. TG |
| | 407 | <li><p>Updated tomoplane extension to new surface model api. TG |
| | 408 | |
| | 409 | </ul> |
| | 410 | |
| | 411 | <p><b>August 12, 2008. Version 1.2549.</b></p> |
| | 412 | |
| | 413 | <ul type=None> |
| | 414 | <li><p>Fixed bug where closing volume series removed wrong entry from menu. TG |
| | 415 | </ul> |
| | 416 | |
| | 417 | <p><b>August 1, 2008. Version 1.2549.</b></p> |
| | 418 | |
| | 419 | <ul type=None> |
| | 420 | <li><p>Fixed black covering status line on aqua when graphics window |
| | 421 | resized smaller. TG |
| | 422 | </ul> |
| | 423 | |
| | 424 | <p><b>July 31, 2008. Version 1.2548.</b></p> |
| | 425 | |
| | 426 | <ul type=None> |
| | 427 | <li><p>Added focus follows mouse preference, only shown and used on aqua. TG |
| | 428 | </ul> |
| | 429 | |
| | 430 | <p><b>July 30, 2008. Version 1.2547.</b></p> |
| | 431 | |
| | 432 | <ul type=None> |
| | 433 | <li><p>Fixed pif map bug where integer file values scaled by floating point |
| | 434 | scale factor remained as an integer map. Caused sparse histograms. TG |
| | 435 | <li><p>Made volume cap facing initially off for PIF maps since they are |
| | 436 | most often inverted. TG |
| | 437 | <li><p>Made marker resize mouse mode use caps lock instead of alt key. TG |
| | 438 | <li><p>Added option to hide in-window menus on aqua. TG |
| | 439 | </ul> |
| | 440 | |
| | 441 | |
| | 442 | <p><b>July 29, 2008. Version 1.2546.</b></p> |
| | 443 | |
| | 444 | <ul type=None> |
| | 445 | <li><p>Moved create color key button to options panel. TG |
| | 446 | </ul> |
| | 447 | |
| | 448 | |
| | 449 | <p><b>July 28, 2008. Version 1.2546.</b></p> |
| | 450 | |
| | 451 | <ul type=None> |
| | 452 | <li><p>Put new movie making tutorial on chimera tutorials and |
| | 453 | animations web pages. TG |
| | 454 | </ul> |
| | 455 | |
| | 456 | <p><b>July 23, 2008. Version 1.2544.</b></p> |
| | 457 | |
| | 458 | <ul type=None> |
| | 459 | |
| | 460 | <li><p>Made volume series update histograms for all series. Was only updating |
| | 461 | one when multiple series played simultaneosly. TG |
| | 462 | <li><p> |
| | 463 | </ul> |
| | 464 | |
| | 465 | <p><b>July 22, 2008. Version 1.2544.</b></p> |
| | 466 | |
| | 467 | <ul type=None> |
| | 468 | <li><p>Made volume series tool handle multiwavelength priism data. TG |
| | 469 | <li><p>Made volume series tool allow playing all series at once. TG |
| | 470 | <li><p>Fixed memory leak when volumes created and closed. Data array |
| | 471 | was deallocated but not surface model and volume python object. TG |
| | 472 | <li><p>Added showDialog option to molmap command to suppress display of |
| | 473 | volume dialog (useful in MD trajectory per-frame scripts). TG |
| | 474 | <li><p>Made fetch eds able to set model id on command-line. TG |
| | 475 | </ul> |
| | 476 | |
| | 477 | <p><b>July 21, 2008. Version 1.2544.</b></p> |
| | 478 | |
| | 479 | <ul type=None> |
| | 480 | <li><p>Fixed bug when volume data read canceled on opening, |
| | 481 | session save failed. TG |
| | 482 | </ul> |
| | 483 | |
| | 484 | <p><b>July 18, 2008. Version 1.2544.</b></p> |
| | 485 | |
| | 486 | <ul type=None> |
| | 487 | <li><p>Made volume series tool copy changes in voxel size and volume origin. TG |
| | 488 | <li><p>Fixed bug saving volume over original file on a different file system |
| | 489 | than /tmp (file move didn't work). TG |
| | 490 | <li><p>Fixed bug where msms calculation says it succeeded but actually returns |
| | 491 | an incorrect empty surface. TG |
| | 492 | <li><p>Fixed movie recorder ffmpeg encoding on aqua, trouble reporting status |
| | 493 | from non-gui thread. Disabled status reporting on aqua. TG |
| | 494 | <li><p>Made movie recorder not raise main window when doing image capture. TG |
| | 495 | </ul> |
| | 496 | |
| | 497 | <p><b>July 15, 2008. Version 1.2542.</b></p> |
| | 498 | |
| | 499 | <ul type=None> |
| | 500 | <li><p>Fixed bug, surface color wrong if volume moved while data is being |
| | 501 | read. TG |
| | 502 | <li><p>Fixed space navigator lag on aqua. TG |
| | 503 | </ul> |
| | 504 | |
| | 505 | <p><b>July 9, 2008. Version 1.2540.</b></p> |
| | 506 | |
| | 507 | <ul type=None> |
| | 508 | <li><p>Production release Chimera 1.2540. |
| | 509 | </ul> |
| | 510 | |
| | 511 | <p><b>July 8, 2008. Version 1.2540.</b></p> |
| | 512 | |
| | 513 | <ul type=None> |
| | 514 | |
| | 515 | <li><p>Fixed bug where NaN volume normals caused raytracing failure. TG |
| | 516 | </ul> |
| | 517 | |
| | 518 | <p><b>July 7, 2008. Version 1.2540.</b></p> |
| | 519 | |
| | 520 | <ul type=None> |
| | 521 | <li><p>Made vop resample command undisplay original instead of |
| | 522 | grid volume. TG |
| | 523 | <li><p>Fixed volume dialog shown/hidden indicator updating for new volumes. TG |
| | 524 | <li><p>Made crash report dialog on mac not appear for |
| | 525 | mscalc crashes (msms surface calculation). TG |
| | 526 | </ul> |
| | 527 | |
| | 528 | <p><b>July 2, 2008. Version 1.2540.</b></p> |
| | 529 | |
| | 530 | <ul type=None> |
| | 531 | <li><p>Fixed aqua bug: patched pmw to make open dialog history popup menus |
| | 532 | appear on top. TG |
| | 533 | |
| | 534 | </ul> |
| | 535 | |
| | 536 | <p><b>July 1, 2008. Version 1.2537.</b></p> |
| | 537 | |
| | 538 | <ul type=None> |
| | 539 | <li><p>Made volume solid style coloring properly color min/max data values. In |
| | 540 | some cases the data values corresponding to the end nodes on the volume |
| | 541 | histogram were not colored. TG |
| | 542 | <li><p>Fixed molecule copies behavior of crystal contacts tool |
| | 543 | and added command version. TG |
| | 544 | </ul> |
| | 545 | |
| | 546 | <p><b>June 30, 2008. Version 1.2537.</b></p> |
| | 547 | |
| | 548 | <ul type=None> |
| | 549 | <li><p>Optimized morph map, 8x faster linear combination on 256^3 array. TG |
| | 550 | <li><p>Made vop resample command use better name for new volume. TG |
| | 551 | <li><p>Fixed aqua bug: patched pmw notebook bubble buttons and borders for |
| | 552 | aqua tk 8.5.2. TG |
| | 553 | |
| | 554 | </ul> |
| | 555 | |
| | 556 | <p><b>June 27, 2008. Version 1.2537.</b></p> |
| | 557 | |
| | 558 | <ul type=None> |
| | 559 | <li><p>Fixed aqua bug: clipped volume plane button text and feature buttons. TG |
| | 560 | <li><p>Fixed volume show/hide icon in volume dialog in solid mode. Sometimes |
| | 561 | showed incorrect display state. TG |
| | 562 | </ul> |
| | 563 | |
| | 564 | <p><b>June 26, 2008. Version 1.2537.</b></p> |
| | 565 | |
| | 566 | <ul type=None> |
| | 567 | <li><p>Added mS shortcut to place markers on selected atoms. TG |
| | 568 | </ul> |
| | 569 | |
| | 570 | <p><b>June 25, 2008. Version 1.2537.</b></p> |
| | 571 | |
| | 572 | <ul type=None> |
| | 573 | <li><p>Added aqua in-window menubars for all dialogs: castp, |
| | 574 | selection workbench, modbase, rotamers, render by attr, viewdock, demo, movie, |
| | 575 | multalign. TG |
| | 576 | </ul> |
| | 577 | |
| | 578 | <p><b>June 24, 2008. Version 1.2535.</b></p> |
| | 579 | |
| | 580 | <ul type=None> |
| | 581 | <li><p>Fixed aqua bug: disappearing bonds (stick style) and vrml cylinders |
| | 582 | when zooming. TG |
| | 583 | <li><p>Fixed aqua bug: playing morph map gave volume dialog focus |
| | 584 | prevented stopping morph playback. TG |
| | 585 | <li><p>Fixed aqua bug: mouse scroll wheel zooming very insensitive. TG |
| | 586 | </ul> |
| | 587 | |
| | 588 | <p><b>June 19, 2008. Version 1.2534.</b></p> |
| | 589 | |
| | 590 | <ul type=None> |
| | 591 | <li><p>Fixed volume dialog surface brightness and transparency sliders. |
| | 592 | They were producing color component values > 1 causing error messages. TG |
| | 593 | <li><p>Made command-q and the main window close button show the quit |
| | 594 | confirmation dialog on aqua. TG |
| | 595 | </ul> |
| | 596 | |
| | 597 | <p><b>June 18, 2008. Version 1.2532.</b></p> |
| | 598 | |
| | 599 | <ul type=None> |
| | 600 | <li><p>Added in-window menu bars to volume and tracer dialog windows in aqua. TG |
| | 601 | <li><p>Added vop subtract operation for making difference maps. TG |
| | 602 | <li><p>Fixed volume histogram flickering on aqua. TG |
| | 603 | </ul> |
| | 604 | |
| | 605 | <p><b>June 17, 2008. Version 1.2531.</b></p> |
| | 606 | |
| | 607 | <ul type=None> |
| | 608 | <li><p>Fixed divide by zero warning message appearing in shell when |
| | 609 | using volume solid style rendering with opacity = 1. TG |
| | 610 | </ul> |
| | 611 | |
| | 612 | <p><b>June 16, 2008. Version 1.2531.</b></p> |
| | 613 | |
| | 614 | <ul type=None> |
| | 615 | <li><p>Fixed error when deleting volumes caused by trying to update |
| | 616 | volume shown indicator (dash icon) after deletion. TG |
| | 617 | <li><p>Added option/command key 3-button mouse emulation in aqua. TG |
| | 618 | </ul> |
| | 619 | |
| | 620 | <p><b>June 13, 2008. Version 1.2531.</b></p> |
| | 621 | |
| | 622 | <ul type=None> |
| | 623 | |
| | 624 | <li><p>Added MacMolPlt/Gamess quantum orbitals volume file reader. TG |
| | 625 | </ul> |
| | 626 | |
| | 627 | <p><b>June 12, 2008. Version 1.2531.</b></p> |
| | 628 | |
| | 629 | <ul type=None> |
| | 630 | <li><p>Made volume viewer and volume tracer show menu bar at top of screen |
| | 631 | on aqua. TG |
| | 632 | </ul> |
| | 633 | |
| | 634 | <p><b>June 11, 2008. Version 1.2529.</b></p> |
| | 635 | |
| | 636 | <ul type=None> |
| | 637 | <li><p>Fixed display of headings in preferences tools pane on aqua. TG |
| | 638 | <li><p>Added focus follow mouse mode for aqua. TG |
| | 639 | </ul> |
| | 640 | |
| | 641 | <p><b>June 10, 2008. Version 1.2527.</b></p> |
| | 642 | |
| | 643 | <ul type=None> |
| | 644 | <li><p>Made opening electrostatic potential file formats (delphi, apbs, uhbd) |
| | 645 | and molecular orbital file formats (gaussian, gopenmol) turn of box face |
| | 646 | surface capping so that negative threshold levels do not result in box surface. |
| | 647 | TG |
| | 648 | <li><p>Fixed actions menu surface transparency on molecular surfaces colored |
| | 649 | by molecule. TG |
| | 650 | <li><p>Made in-memory writable volumes created by volume eraser have names |
| | 651 | ending in "copy" to distinguish them from original volumes. TG |
| | 652 | <li><p>Made opening volume file not use data from already opened writable |
| | 653 | volume since that data may be modified later. TG |
| | 654 | <li>Fixed aqua 60% cpu usage when showing model panel, but in tix |
| | 655 | scrolledhlist with headers. TG |
| | 656 | </ul> |
| | 657 | |
| | 658 | <p><b>June 9, 2008. Version 1.2527.</b></p> |
| | 659 | |
| | 660 | <ul type=None> |
| | 661 | <li><p>Made model menus use multiple columns on x11 if they have more than |
| | 662 | 35 entries to avoid inaccessible entries off bottom of screen. TG |
| | 663 | |
| | 664 | <li><p>Made saving volume data update the volume name in volume dialog |
| | 665 | and menus. TG |
| | 666 | </ul> |
| | 667 | |
| | 668 | <p><b>June 6, 2008. Version 1.2525.</b></p> |
| | 669 | |
| | 670 | <ul type=None> |
| | 671 | <li><p>Made surface display use opengl vertex buffer objects instead of display |
| | 672 | lists, leading to 2x faster rendering on two tested graphics cards. TG |
| | 673 | </ul> |
| | 674 | |
| | 675 | <p><b>June 5, 2008. Version 1.2525.</b></p> |
| | 676 | |
| | 677 | <ul type=None> |
| | 678 | <li><p>Made priism volume file reader set correct voxel size. TG |
| | 679 | <li><p>Made molecular surface display for a set of atoms not override |
| | 680 | partial surface display done with surface zone tool. TG |
| | 681 | <li><p>Made active volume name highlighting on aqua use blue color. Was using |
| | 682 | white which was identical to inactive background. TG |
| | 683 | |
| | 684 | <li><p>Made main window have focus at startup on aqua. TG |
| | 685 | </ul> |
| | 686 | |
| | 687 | <p><b>June 3, 2008. Version 1.2525.</b></p> |
| | 688 | |
| | 689 | <ul type=None> |
| | 690 | <li><p>Fixed hang on aqua caused by benchmark dialog horizontal scrollbar |
| | 691 | display/undisplay. TG |
| | 692 | <li><p>Fixed aqua bug where movie recorder could not be stopped because |
| | 693 | graphics window was given focus at each frame preventing pressing the Stop |
| | 694 | button. TG |
| | 695 | <li><p>Fixed aqua bug where movie recorder could not find ffmpeg executable. TG |
| | 696 | </ul> |
| | 697 | |
| | 698 | <p><b>June 2, 2008. Version 1.2525.</b></p> |
| | 699 | |
| | 700 | <ul type=None> |
| | 701 | <li><p>Made priism volume file reader handle xywzt and xyzwt data orders |
| | 702 | (w = wavelength, t = time). TG |
| | 703 | |
| | 704 | </ul> |
| | 705 | |
| | 706 | <p><b>May 30, 2008. Version 1.2524.</b></p> |
| | 707 | |
| | 708 | <ul type=None> |
| | 709 | <li><p>Fixed molecular surface bug where closing surface model and then |
| | 710 | reshowing surface for subset of atoms showed entire surface. TG |
| | 711 | <li><p>Made toolbar and model panel balloons not take focus in aqua. TG |
| | 712 | </ul> |
| | 713 | |
| | 714 | <p><b>May 28, 2008. Version 1.2523.</b></p> |
| | 715 | |
| | 716 | <ul type=None> |
| | 717 | <li><p>Padded selection button in lower right corner of main window so that |
| | 718 | text is not clipped on aqua. TG |
| | 719 | <li><p>Made atom spec balloons on aqua not have window frame, and not take |
| | 720 | focus. TG |
| | 721 | <li><p>Added apple application menu entries for About Chimera... and |
| | 722 | Preferences... on aqua. TG |
| | 723 | |
| | 724 | <li><p>Made model panel Select button work on molecular surfaces. TG |
| | 725 | </ul> |
| | 726 | |
| | 727 | <p><b>May 27, 2008. Version 1.2522.</b></p> |
| | 728 | |
| | 729 | <ul type=None> |
| | 730 | <li><p>Fixed volume image stack session saving bug. TG |
| | 731 | <li><p>Fixed recently introduced bug where color byatom with a surface shown |
| | 732 | generated an error. TG |
| | 733 | <li><p>Fixed aqua chimera crash when any dialog shown by disabling apple event |
| | 734 | handling code. TG |
| | 735 | </ul> |
| | 736 | |
| | 737 | <p><b>May 26, 2008. Version 1.2522.</b></p> |
| | 738 | |
| | 739 | <ul type=None> |
| | 740 | <li><p>Made actions atom/ribbon/surface menus work with multiscale models. TG |
| | 741 | |
| | 742 | </ul> |
| | 743 | |
| | 744 | <p><b>May 22, 2008. Version 1.2517.</b></p> |
| | 745 | |
| | 746 | <ul type=None> |
| | 747 | <li><p>Made space navigator work with independent center of rotation mode. TG |
| | 748 | <li><p>Made select command on surfaces select all the surface pieces. TG |
| | 749 | </ul> |
| | 750 | |
| | 751 | <p><b>May 21, 2008. Version 1.2517.</b></p> |
| | 752 | |
| | 753 | <ul type=None> |
| | 754 | <li><p>Fixed recently introduced bug where cofr command did not work on |
| | 755 | undisplayed selected surfaces. TG |
| | 756 | </ul> |
| | 757 | |
| | 758 | <p><b>May 20, 2008. Version 1.2514.</b></p> |
| | 759 | |
| | 760 | <ul type=None> |
| | 761 | <li><p>Made selecting molecular surface select atoms and bonds. TG |
| | 762 | <li><p>Made action menu set pivot work on selected surfaces. TG |
| | 763 | <li><p>Made volume viewer detect surface color/style changes made from Actions menu or by other means. TG |
| | 764 | </ul> |
| | 765 | |
| | 766 | <p><b>May 19, 2008. Version 1.2511.</b></p> |
| | 767 | |
| | 768 | <ul type=None> |
| | 769 | <li><p>Fixed fit map error when no atoms selected and simulated map enabled. TG |
| | 770 | </ul> |
| | 771 | |
| | 772 | <p><b>May 15, 2008. Version 1.2511.</b></p> |
| | 773 | |
| | 774 | <ul type=None> |
| | 775 | <li><p>Made Actions / Focus menu entry work for selected surfaces. TG |
| | 776 | <li><p>Fixed volume series error when playing series when active volume |
| | 777 | in not in series. TG |
| | 778 | <li><p>Fixed volume series bug undisplaying surfaces when caching off. TG |
| | 779 | </ul> |
| | 780 | |
| | 781 | <p><b>May 13, 2008. Version 1.2510.</b></p> |
| | 782 | |
| | 783 | <ul type=None> |
| | 784 | <li><p>Made Actions menu entries work when molecular surfaces are selected. |
| | 785 | Formerly they only worked when atoms were selected. TG |
| | 786 | <li><p>Made selecting a surface in mesh or dot style require clicking on |
| | 787 | a mesh line or dot. Formerly any area of the surface could be clicked. |
| | 788 | The new behavior allows selecting molecules within surfaces. TG |
| | 789 | <li><p>Made volume surfaces selectable. TG |
| | 790 | <li><p>Made Actions / Surface and Actions / Color menu entries work on |
| | 791 | non-molecular surfaces. TG |
| | 792 | <li><p>Removed Actions / Target menu. TG |
| | 793 | </ul> |
| | 794 | |
| | 795 | <p><b>May 12, 2008. Version 1.2510.</b></p> |
| | 796 | |
| | 797 | <ul type=None> |
| | 798 | <li><p>Fixed crash at startup on mac when remote displaying caused by |
| | 799 | space navigator tool. Same problem when --nogui mode used and the user |
| | 800 | is not logged in to the mac console. TG |
| | 801 | </ul> |
| | 802 | |
| | 803 | <p><b>May 9, 2008. Version 1.2510.</b></p> |
| | 804 | |
| | 805 | <ul type=None> |
| | 806 | <li><p>Made molecular surface calculation report the number of surface |
| | 807 | components and the solvent excluded and solvent accessible surface areas. TG |
| | 808 | <li><p>Fixed error in surface color tool when surface is colored by volume |
| | 809 | value and the volume is closed and then the surface is changed. TG |
| | 810 | </ul> |
| | 811 | |
| | 812 | <p><b>May 8, 2008. Version 1.2510.</b></p> |
| | 813 | |
| | 814 | <ul type=None> |
| | 815 | <li><p>Removed accelerators on/off menu entries from Tools / General Controls |
| | 816 | menu and renamed Accelerators List entry to Keyboard Shortcuts. Keyboard |
| | 817 | shortcuts are now enabled with a switch on the dialog and that setting is now |
| | 818 | saved in preferences automatically. TG |
| | 819 | </ul> |
| | 820 | |
| | 821 | <p><b>May 7, 2008. Version 1.2510.</b></p> |
| | 822 | |
| | 823 | <ul type=None> |
| | 824 | <li><p>Made Fetch Structure by ID report download progress in status line. TG |
| | 825 | </ul> |
| | 826 | |
| | 827 | <p><b>May 6, 2008. Version 1.2510.</b></p> |
| | 828 | |
| | 829 | <ul type=None> |
| | 830 | <li><p>Fixed recently introduced bug in model panel Tile button where models |
| | 831 | were placed in random order on screen. Fixed ordering is by model id number. TG |
| | 832 | |
| | 833 | </ul> |
| | 834 | |
| | 835 | <p><b>May 5, 2008. Version 1.2510.</b></p> |
| | 836 | |
| | 837 | <ul type=None> |
| | 838 | <li><p>Put least used controls of surface color dialog in options panel. TG |
| | 839 | <li><p>Made surface color dialog use a separate volume menu that is displayed |
| | 840 | when color method is by volume data value. Formerly every volume appeared as |
| | 841 | an entry in the coloring method menu. TG |
| | 842 | <li><p>Added electrostatic coloring method to surface color dialog. This is |
| | 843 | the same as coloring by volume data value, only with dialog text specialized |
| | 844 | to save "electrostatic potential" to reduce confusion. TG |
| | 845 | <li><p> Fixed session saving bug with custom colored molecular surface models. |
| | 846 | Bug introduced in past month. TG |
| | 847 | </ul> |
| | 848 | |
| | 849 | <p><b>May 2, 2008. Version 1.2510.</b></p> |
| | 850 | |
| | 851 | <ul type=None> |
| | 852 | |
| | 853 | <li><p>Made benchmark tool draw models on screen to avoid inflated frame rates. |
| | 854 | Formerly drawing was done in an internal buffer and not shown and newer drivers |
| | 855 | shortcut the rendering leading to frame rates sometimes 2x higher than in |
| | 856 | actual use. TG |
| | 857 | <li><p>Added "report scores" button to benchmark tool to send scores to |
| | 858 | RBVI for posting on web. TG |
| | 859 | <li><p>Simplified benchmark dialog to show only the commonly used controls, |
| | 860 | with others hidden in an options panel. TG |
| | 861 | <li><p>Fixed bug in benchmark tool with solid rendering where volume was not |
| | 862 | in field of view so some graphics drivers rendered nothing leading to very |
| | 863 | large test cases which caused memory errors. TG |
| | 864 | </ul> |
| | 865 | |
| | 866 | <p><b>April 30, 2008. Version 1.2508.</b></p> |
| | 867 | |
| | 868 | <ul type=None> |
| | 869 | <li><p>Fixed bug in crystal contacts tool where contacts between a crystal |
| | 870 | asymmetric unit and copies translated by unit cell translations were not |
| | 871 | detected. TG |
| | 872 | <li><p>Added option to crystal contacts tool to create moleucule models for |
| | 873 | contacting copies. TG |
| | 874 | </ul> |
| | 875 | |
| | 876 | <p><b>April 28, 2008. Version 1.2506.</b></p> |
| | 877 | |
| | 878 | <ul type=None> |
| | 879 | <li><p>Made volume eraser radius slider resize when the dialog is resized. TG |
| | 880 | </ul> |
| | 881 | |
| | 882 | <p><b>April 25, 2008. Version 1.2506.</b></p> |
| | 883 | |
| | 884 | <ul type=None> |
| | 885 | <li><p>Made model panel Tile button highlight when non-molecule models selected. TG |
| | 886 | </ul> |
| | 887 | |
| | 888 | <p><b>April 24, 2008. Version 1.2506.</b></p> |
| | 889 | |
| | 890 | <ul type=None> |
| | 891 | <li><p>Made model panel Tile button work with all models, not just molecules. TG |
| | 892 | </ul> |
| | 893 | |
| | 894 | <p><b>April 18, 2008. Version 1.2505.</b></p> |
| | 895 | |
| | 896 | <ul type=None> |
| | 897 | <li><p>Made phantom force feedback tool volume aligned cross-hair display |
| | 898 | correctly when local volume coordinates are rotated. TG |
| | 899 | </ul> |
| | 900 | |
| | 901 | <p><b>April 17, 2008. Version 1.2504.</b></p> |
| | 902 | |
| | 903 | <ul type=None> |
| | 904 | <li><p>Added color palette option menu and a button to reverse color order |
| | 905 | to surface color tool. TG |
| | 906 | </ul> |
| | 907 | |
| | 908 | <p><b>April 16, 2008. Version 1.2503.</b></p> |
| | 909 | |
| | 910 | <ul type=None> |
| | 911 | <li><p>Made multiscale tool with surface resolution = 0 (solvent excluded |
| | 912 | surface) use probe radius, vertex density and disjoint component preference |
| | 913 | settings. Formerly it used values that could not be changed. TG |
| | 914 | <li><p>Made relative orientation schematic shortcut "ai" not give an error |
| | 915 | when rotation angle is zero. TG |
| | 916 | </ul> |
| | 917 | |
| | 918 | <p><b>April 15, 2008. Version 1.2503.</b></p> |
| | 919 | |
| | 920 | <ul type=None> |
| | 921 | <li><p>Made phantom force feedback tool handle volume step change, and |
| | 922 | made move marker warn if no marker is under cursor. TG |
| | 923 | </ul> |
| | 924 | |
| | 925 | <p><b>April 11, 2008. Version 1.2503.</b></p> |
| | 926 | |
| | 927 | <ul type=None> |
| | 928 | |
| | 929 | <li><p>Simplified Phantom Force Feedback dialog. Made key commands work from |
| | 930 | main Chimera window. Changed move models, zoom, contour level, move marker |
| | 931 | keyboard commands to press once to activate, again to deactivate. Formerly key |
| | 932 | had to be held down. TG |
| | 933 | <li><p>Included Phantom force feedback OpenHaptics event handling in Windows |
| | 934 | Chimera distribution. User is required to install OpenHaptics driver. TG |
| | 935 | </ul> |
| | 936 | |
| | 937 | <p><b>April 10, 2008. Version 1.2503.</b></p> |
| | 938 | |
| | 939 | <ul type=None> |
| | 940 | <li><p>Fixed bug where molecular surface calculation for zero atoms failed. TG |
| | 941 | </ul> |
| | 942 | |
| | 943 | <p><b>April 8, 2008. Version 1.2503.</b></p> |
| | 944 | |
| | 945 | <ul type=None> |
| | 946 | <li><p>Made "ac" command accept arguments which are keyboard shortcuts to run. |
| | 947 | Without arguments it still enables typing keyboard shortcuts to main window. TG |
| | 948 | </ul> |
| | 949 | |
| | 950 | <p><b>April 7, 2008. Version 1.2503.</b></p> |
| | 951 | |
| | 952 | <ul type=None> |
| | 953 | <li><p>Added support for Space Navigator six degree-of-freedom input device |
| | 954 | to Windows Chimera versions. TG |
| | 955 | </ul> |
| | 956 | |
| | 957 | <p><b>April 4, 2008. Version 1.2503.</b></p> |
| | 958 | |
| | 959 | <ul type=None> |
| | 960 | <li><p>Made molecular surface calculation not show a console window on Windows. |
| | 961 | TG |
| | 962 | </ul> |
| | 963 | |
| | 964 | <p><b>April 3, 2008. Version 1.2503.</b></p> |
| | 965 | |
| | 966 | <ul type=None> |
| | 967 | <li><p>Fixed molecular surface calculation on Windows. Was interpreting ctrl-z |
| | 968 | as end of input. Also mscalc program was not started correctly. TG |
| | 969 | </ul> |
| | 970 | |
| | 971 | <p><b>April 2, 2008. Version 1.2502.</b></p> |
| | 972 | |
| | 973 | <ul type=None> |
| | 974 | <li><p>Added support for Space Navigator six degree-of-freedom input device |
| | 975 | to Mac Chimera versions. TG |
| | 976 | </ul> |
| | 977 | |
| | 978 | <p><b>April 1, 2008. Version 1.2502.</b></p> |
| | 979 | |
| | 980 | <ul type=None> |
| | 981 | <li><p>Fixed bug where enabling surface capping and surface coloring caused |
| | 982 | continuous recalculation of cap and colors. TG |
| | 983 | |
| | 984 | <li><p>Made surface cap color not flicker to solid color when moving cap. TG |
| | 985 | </ul> |
| | 986 | |
| | 987 | <p><b>March 27, 2008. Version 1.2502.</b></p> |
| | 988 | |
| | 989 | <ul type=None> |
| | 990 | <li><p>Made multiscale dialog use stand-alone program molecular surface |
| | 991 | calculation when resolution set to zero for solvent excluded surface. TG |
| | 992 | </ul> |
| | 993 | |
| | 994 | <p><b>March 26, 2008. Version 1.2501.</b></p> |
| | 995 | |
| | 996 | <ul type=None> |
| | 997 | <li><p>Optimized surface distance calculation (keyboard shortcut "sd") by |
| | 998 | translating Python code to C++. Several hundred times faster. TG |
| | 999 | </ul> |
| | 1000 | |
| | 1001 | <p><b>March 25, 2008. Version 1.2501.</b></p> |
| | 1002 | |
| | 1003 | <ul type=None> |
| | 1004 | <li><p>Changed solvent excluded/accessible surface area calculation to use |
| | 1005 | analytical values instead of approximate values calculated from the triangulated |
| | 1006 | surface (which depended on vertex density). TG |
| | 1007 | <li><p>Added per-residue solvent excluded/accessible surface area (areaSES, |
| | 1008 | areaSAS) attributes viewable with Render by Attribute tool. TG |
| | 1009 | <li><p>Added solvent excluded/accessible surface area in Reply Log |
| | 1010 | output when molecular surface is calculated. |
| | 1011 | <li><p>Made up and down arrow keys work with selected surface pieces. TG |
| | 1012 | <li><p>Fixed bug in IMOD mesh file reader where normal vectors appeared in |
| | 1013 | the surface vertex array resulting in wrong inertia calculation. TG |
| | 1014 | <li><p>Added "ra" keyboard shortcut for showing render-by-attribute dialog. TG |
| | 1015 | <li><p>Added "se" keyboard shortcut for toggling silhouette edge display. TG |
| | 1016 | <li><p>Fixed bug in surface distance calculation where distance to an |
| | 1017 | edge was used when the closest distance was actually to a vertex. TG |
| | 1018 | </ul> |
| | 1019 | |
| | 1020 | <p><b>March 20, 2008. Version 1.2501.</b></p> |
| | 1021 | |
| | 1022 | <ul type=None> |
| | 1023 | <li><p>Fixed meshmol command on molecular surfaces, "truth value ambiguous" |
| | 1024 | error. TG |
| | 1025 | <li><p>Fixed error in Measure and Color Blobs, "array cannot be safely |
| | 1026 | cast to required type" on 64-bit Chimera versions. TG |
| | 1027 | <li><p>Made Color Zone, Surface Zone and Surface Color work on MSMS surface |
| | 1028 | caps. TG |
| | 1029 | </ul> |
| | 1030 | |
| | 1031 | <p><b>March 18, 2008. Version 1.2500.</b></p> |
| | 1032 | |
| | 1033 | <ul type=None> |
| | 1034 | <li><p>Made Chimera calculate solvent excluded molecular surfaces using a |
| | 1035 | standalone application so crashes do not crash Chimera. TG |
| | 1036 | <li><p>Made molecular surface calculation assign per-atom solvent excluded |
| | 1037 | surface area (areaSES) and solvent accessible surface area (areaSAS) values |
| | 1038 | that can be used with Render by Attribute dialog or the "select" command. TG |
| | 1039 | <li><p>Molecular surfaces now are implemented using SurfaceModel. Some |
| | 1040 | new attributes of this type of model are visible in the selection and model |
| | 1041 | attribute inspector dialogs. TG |
| | 1042 | <li><p>Eliminated warning messages that appeared in the Chimera reply log |
| | 1043 | on Mac OS 10.5 about an unhandled apple event. TG |
| | 1044 | <li><p>Changed Benchmark molecule tests to only time one molecule instead of |
| | 1045 | six. |
| | 1046 | <li><p>Fixed ribbon benchmark timing, previous scores invalid. TG |
| | 1047 | </ul> |
| | 1048 | |
| | 1049 | <p><b>March 17, 2008. Version 1.2500.</b></p> |
| | 1050 | |
| | 1051 | <ul type=None> |
| | 1052 | <li><p>Fixed a triangle template allocation bug in MSMS molecular surface |
| | 1053 | calculation reducing number of crash cases in half. Also changed to allow |
| | 1054 | surface calculation when one atom is entirely inside of another. TG |
| | 1055 | <li><p>Made Movie Recorder respect preference for saving POVray files. TG |
| | 1056 | <li><p>Fixed InterSurf to use new SurfaceModel Python names. TG |
| | 1057 | </ul> |
| | 1058 | |
| | 1059 | <p><b>March 11, 2008. Version 1.2500.</b></p> |
| | 1060 | |
| | 1061 | <ul type=None> |
| | 1062 | <li><p>Renamed Surface_Model to SurfaceModel and changed Python method |
| | 1063 | names and attributes to eliminated underscore characters. TG |
| | 1064 | </ul> |
| | 1065 | |
| | 1066 | <p><b>March 5, 2008. Version 1.2499.</b></p> |
| | 1067 | |
| | 1068 | <ul type=None> |
| | 1069 | <li><p>Added dot surface display and dot size setting to surface models, |
| | 1070 | settable with selection inspector. TG |
| | 1071 | </ul> |
| | 1072 | |
| | 1073 | <p><b>March 4, 2008. Version 1.2498.</b></p> |
| | 1074 | |
| | 1075 | <ul type=None> |
| | 1076 | <li><p>Reduced memory use of volume solid style rendering in color map |
| | 1077 | mode. Was unnecessarily making floating point copy of map. TG |
| | 1078 | </ul> |
| | 1079 | |
| | 1080 | <p><b>February 29, 2008. Version 1.2497.</b></p> |
| | 1081 | |
| | 1082 | <ul type=None> |
| | 1083 | <li><p>Removed setting to flip surface lighting normals visible in |
| | 1084 | selection inspector dialog. TG |
| | 1085 | </ul> |
| | 1086 | |
| | 1087 | <p><b>February 28, 2008. Version 1.2496.</b></p> |
| | 1088 | |
| | 1089 | <ul type=None> |
| | 1090 | <li><p>Added consistency checking (valid record size) in delphi map |
| | 1091 | file reader. TG |
| | 1092 | </ul> |
| | 1093 | |
| | 1094 | <p><b>February 27, 2008. Version 1.2495.</b></p> |
| | 1095 | |
| | 1096 | <ul type=None> |
| | 1097 | <li><p>Added checkbuttons to volume tracer mouse mode panel that match |
| | 1098 | those in the Mouse menu. TG |
| | 1099 | <li><p>Fixed volume tracer session restore bug where a second traced surfaces |
| | 1100 | model was created after restoring a session containing traced surfaces. TG |
| | 1101 | |
| | 1102 | <li><p>Made volume tracer delete surface panel only delete selected |
| | 1103 | traced surfaces. Was deleting any selected surface. TG |
| | 1104 | <li><p>Made volume tracer continuous marker placement while dragging |
| | 1105 | work with "on spot", "on plane", or "outside data" mouse mode. Was ignoring |
| | 1106 | those settings and always dropping markers on plane. TG |
| | 1107 | </ul> |
| | 1108 | |
| | 1109 | <p><b>February 26, 2008. Version 1.2495.</b></p> |
| | 1110 | |
| | 1111 | <ul type=None> |
| | 1112 | <li><p>Fixed volume tracer bug where traceback given if "marker color |
| | 1113 | matches volume color" enabled and marker is placed. TG |
| | 1114 | <li><p>Made crash dump detection for bug reporting work on Mac OS 10.5. |
| | 1115 | Mac OS 10.5 uses separate file for each crash, while 10.4 used one file |
| | 1116 | for all crashes of the same application. TG |
| | 1117 | </ul> |
| | 1118 | |
| | 1119 | <p><b>February 22, 2008. Version 1.2495.</b></p> |
| | 1120 | |
| | 1121 | <ul type=None> |
| | 1122 | <li><p>Modified per-model clipping command to not modify existing clip |
| | 1123 | plane axis or origin unless explicit options are given. TG |
| | 1124 | |
| | 1125 | </ul> |
| | 1126 | |
| | 1127 | <p><b>February 21, 2008. Version 1.2495.</b></p> |
| | 1128 | |
| | 1129 | <ul type=None> |
| | 1130 | <li><p>Added option to create simulated map (uses molmap command) |
| | 1131 | to the fit map dialog. TG |
| | 1132 | </ul> |
| | 1133 | |
| | 1134 | <p><b>February 20, 2008. Version 1.2495.</b></p> |
| | 1135 | |
| | 1136 | <ul type=None> |
| | 1137 | <li><p>Added per-model clipping command mclip. TG |
| | 1138 | <li><p>Fixed volume eraser bug that gave traceback when erasing done |
| | 1139 | with eraser sphere entirely outside of volume. TG |
| | 1140 | <li><p>Fixed bug on movement mouse mode where no translation was possible |
| | 1141 | if near clip plane was at or in front of eye position. Changed behavior |
| | 1142 | so amount of translation is based on dragging center of rotation of object. |
| | 1143 | TG |
| | 1144 | </ul> |
| | 1145 | |
| | 1146 | <p><b>February 19, 2008. Version 1.2494.</b></p> |
| | 1147 | |
| | 1148 | <ul type=None> |
| | 1149 | <li><p>Added zflip option to vop (volume operation) command to change |
| | 1150 | the hand of a map by reversing the order of the z planes. TG |
| | 1151 | </ul> |
| | 1152 | |
| | 1153 | <p><b>February 15, 2008. Version 1.2493.</b></p> |
| | 1154 | |
| | 1155 | <ul type=None> |
| | 1156 | <li><p>Added IMOD map file reader, file suffix ".rec". These are MRC maps |
| | 1157 | but signed 8-bit mode is interpreted as unsigned. TG |
| | 1158 | <li><p>Changed volume solid style transparency modulation from |
| | 1159 | t -> t ** (1.0/planes) to t -> t ** (1.0/(planes*t)). Here planes |
| | 1160 | = minimum number of planes along each axis times the transparency factor |
| | 1161 | and the initial transparency t is the height of the transfer function on |
| | 1162 | the histogram (0-1 range). For transparent voxels the change is minor. |
| | 1163 | For opaque voxels it makes the effective thickness smaller and avoids |
| | 1164 | a large brightness jump between opacity 0.99 and 1.0. TG |
| | 1165 | |
| | 1166 | </ul> |
| | 1167 | |
| | 1168 | <p><b>February 13, 2008. Version 1.2493.</b></p> |
| | 1169 | |
| | 1170 | <ul type=None> |
| | 1171 | <li><p>Fixed bug where deleting volume tracer links by means other than |
| | 1172 | the "delete links" menu entry would later cause session saving to fail. TG |
| | 1173 | <li><p>Made session saving for volume opens put paths in the session file |
| | 1174 | that are relative to the session file directory if the volume data lies |
| | 1175 | within or below that directory. This allows restoring the session file after |
| | 1176 | moving a directory containing session files and volume data. TG |
| | 1177 | <li><p>Added linewidth option to shape command for meshes. TG |
| | 1178 | <li><p>Made shape command show mesh by default only for icosahedron |
| | 1179 | (not sphere) with lattice option specified. TG |
| | 1180 | <li><p>Changed shape command default color to "gray". TG |
| | 1181 | </ul> |
| | 1182 | |
| | 1183 | <p><b>February 12, 2008. Version 1.2493.</b></p> |
| | 1184 | |
| | 1185 | <ul type=None> |
| | 1186 | |
| | 1187 | <li><p>Added displayThreshold option to molmap command to set the initial |
| | 1188 | contour level of the new map so that the specified fraction of total mass |
| | 1189 | is contained within the contour. Default value 0.95. TG |
| | 1190 | <li><p>Changed effect of volume solid style transparency slider so that |
| | 1191 | it modulates transparency even when factor times depth in planes is less |
| | 1192 | than 1. This allows making completely opaque single planes. TG |
| | 1193 | </ul> |
| | 1194 | |
| | 1195 | <p><b>February 8, 2008. Version 1.2493.</b></p> |
| | 1196 | |
| | 1197 | <ul type=None> |
| | 1198 | <li><p>Reduced memory use when saving a volume zone. For maps larger than |
| | 1199 | 16 Mvoxels the map mask is computed plane by plane. Smaller maps use 12 |
| | 1200 | bytes per voxel overhead. TG |
| | 1201 | </ul> |
| | 1202 | |
| | 1203 | <p><b>February 7, 2008. Version 1.2493.</b></p> |
| | 1204 | |
| | 1205 | <ul type=None> |
| | 1206 | <li><p>Fixed split map button in color zone dialog. TG |
| | 1207 | </ul> |
| | 1208 | |
| | 1209 | <p><b>January 31, 2008. Version 1.2492.</b></p> |
| | 1210 | |
| | 1211 | <ul type=None> |
| | 1212 | <li><p>Combined "fit model in map" and "fit map in map" dialogs into a single |
| | 1213 | dialog, and combined menu entries into one entry. Dialog has new layout but |
| | 1214 | same functionality as original two dialogs. TG |
| | 1215 | <li><p>Added option for real-time updating of correlation and average map |
| | 1216 | value to fit map dialog. TG |
| | 1217 | </ul> |
| | 1218 | |
| | 1219 | <p><b>January 30, 2008. Version 1.2486.</b></p> |
| | 1220 | |
| | 1221 | <ul type=None> |
| | 1222 | <li><p>Added ability to create surfaces from stacks of loops and curves |
| | 1223 | with the volume path tracer tool. Uses the new Surface panel of the volume |
| | 1224 | path tracer dialog. TG |
| | 1225 | <li><p>Renamed "volume path tracer" to "volume tracer". TG |
| | 1226 | <li><p>Reordered volume tools menu to put more frequently useful tools near |
| | 1227 | the top and group them by functionality. TG |
| | 1228 | <li><p>Added split map button to color zone dialog and eliminated separate |
| | 1229 | volume tools menu entry for split map. TG |
| | 1230 | |
| | 1231 | <li><p>Changed molmap ratio of resolution to Gaussian standard deviation |
| | 1232 | to be 1/(pi*sqrt(2)) (~0.225) from former value of 1/(2*sqrt(pi)) (~0.282). TG |
| | 1233 | <li>Made split map by color zone give proper alignment when map coordinates |
| | 1234 | involve a rotation. |
| | 1235 | </ul> |
| | 1236 | |
| | 1237 | <p><b>January 29, 2008. Version 1.2485.</b></p> |
| | 1238 | |
| | 1239 | <ul type=None> |
| | 1240 | <li><p>Added keyboard shortcut "or" to toggle orthographic projection. TG |
| | 1241 | </ul> |
| | 1242 | |
| | 1243 | <p><b>January 25, 2008. Version 1.2485.</b></p> |
| | 1244 | |
| | 1245 | <ul type=None> |
| | 1246 | <li><p>Added ability to export surfaces in Wavefront OBJ format using |
| | 1247 | File / Export Scene. TG |
| | 1248 | <li><p>Optimized "split map by color zone" to use less memory. Operates |
| | 1249 | plane by plane for maps larger than 16 Mvoxels. TG |
| | 1250 | |
| | 1251 | <li><p>Added mouse mode to resize a selected surface by dragging. Enabled |
| | 1252 | for one drag use by keyboard shortcut sz. TG |
| | 1253 | <li><p>Added keyboard shortcut "ao" to activate only selected surfaces. TG |
| | 1254 | <li><p>Added keyboard shortcut "oc" to allow typing one command and then |
| | 1255 | automatically return to entering keyboard shortcuts. TG |
| | 1256 | <li><p>Allowed resizing volume path tracer markers by dragging the mouse |
| | 1257 | while holding the Alt key down if the move/resize mode is enabled. TG |
| | 1258 | </ul> |
| | 1259 | |
| | 1260 | <p><b>January 24, 2008. Version 1.2485.</b></p> |
| | 1261 | |
| | 1262 | <ul type=None> |
| | 1263 | <li><p>Added "resample" operation to vop command to resample one volume |
| | 1264 | data set on the grid of a second volume data set. TG |
| | 1265 | </ul> |
| | 1266 | |
| | 1267 | <p><b>January 23, 2008. Version 1.2485.</b></p> |
| | 1268 | |
| | 1269 | <ul type=None> |
| | 1270 | |
| | 1271 | <li><p>Fixed incorrect rainbow colormap direction for volumes with |
| | 1272 | rotated local coordinates. TG |
| | 1273 | <li><p>Made "measure and color blobs" dialog and mask command ignore |
| | 1274 | outline boxes around volume data. TG |
| | 1275 | <li><p>Added "shape" command that makes surfaces having standard geometric |
| | 1276 | shapes. Handles cylinder, sphere, and icosahedron. Includes icosahedral |
| | 1277 | mesh capabilities of hkcage command. Includes interpolating icosahedron |
| | 1278 | with sphere and alternate coordinates systems as in the Icosahedron surface |
| | 1279 | dialog. TG |
| | 1280 | <li><p>Changed vm keyboard shortcut to mask active volume using selected |
| | 1281 | surfaces. Formerly it masked volume using volume contour surface. TG |
| | 1282 | </ul> |
| | 1283 | |
| | 1284 | <p><b>January 22, 2008. Version 1.2485.</b></p> |
| | 1285 | |
| | 1286 | <ul type=None> |
| | 1287 | <li><p>Made volume contour surfaces have correct lighting when the voxel |
| | 1288 | size along an axis is made negative to flip the hand of the map. Formerly |
| | 1289 | two sided lighting gave dark surface in this case. TG |
| | 1290 | <li><p>Made image stack volume reader handle multi-page tiff images. TG |
| | 1291 | <li><p>Fixed surface capping bug when new surface created while capping is |
| | 1292 | enabled. TG |
| | 1293 | </ul> |
| | 1294 | |
| | 1295 | <p><b>January 18, 2008. Version 1.2485.</b></p> |
| | 1296 | |
| | 1297 | <ul type=None> |
| | 1298 | <li><p>Added molmap command to make volume from a molecule by summing |
| | 1299 | Gaussians at each atom position. TG |
| | 1300 | </ul> |
| | 1301 | |
| | 1302 | <p><b>January 16, 2008. Version 1.2483.</b></p> |
| | 1303 | |
| | 1304 | <ul type=None> |
| | 1305 | <li><p>Made opening tiff image stacks work by selecting all images in the |
| | 1306 | open dialog. Formerly only one image was selected and others that had the |
| | 1307 | same prefix and different numeric suffix were inferred. TG |
| | 1308 | <li><p>Made image stack reader handle image types other than TIFF. Can |
| | 1309 | handle any image format understood by the Python image library (e.g. png, |
| | 1310 | jpeg). TG |
| | 1311 | </ul> |
| | 1312 | |
| | 1313 | <p><b>January 15, 2008. Version 1.2483.</b></p> |
| | 1314 | |
| | 1315 | <ul type=None> |
| | 1316 | |
| | 1317 | <li><p>Fixed chimera "--send" startup option on mac. Was always starting |
| | 1318 | a new instance of chimera. TG |
| | 1319 | </ul> |
| | 1320 | |
| | 1321 | <p><b>January 11, 2008. Version 1.2483.</b></p> |
| | 1322 | |
| | 1323 | <ul type=None> |
| | 1324 | <li><p>Removed marker set models closed with the file menu entry in |
| | 1325 | the volume path tracer dialog. Formerly the models were just emptied |
| | 1326 | of markers. TG |
| | 1327 | <li><p>Changed mask command sandwich option default value to true. TG |
| | 1328 | <li><p>Changed mask command fullmap option to require a true/false value. |
| | 1329 | Formerly the option took no value. TG |
| | 1330 | </ul> |
| | 1331 | |
| | 1332 | <p><b>January 10, 2008. Version 1.2483.</b></p> |
| | 1333 | |
| | 1334 | <ul type=None> |
| | 1335 | <li><p>Made default projection axis for mask command y instead of z. TG |
| | 1336 | |
| | 1337 | <li><p>Renamed "pick surface pieces" dialog and menu entry to the more |
| | 1338 | descriptive "measure and color blobs". TG |
| | 1339 | <li><p>Added slab option to mask command to mask using a slab of specified |
| | 1340 | thickness created by thickening a surface. TG |
| | 1341 | </ul> |
| | 1342 | |
| | 1343 | <p><b>January 9, 2008. Version 1.2483.</b></p> |
| | 1344 | |
| | 1345 | <ul type=None> |
| | 1346 | <li><p>Added selection inspector attributes for surface pieces: |
| | 1347 | surface piece count, line thickness, line smoothing, lighting, two |
| | 1348 | sided lighting, lighting normal direction, transparency brightness. TG |
| | 1349 | <li><p>Made selection inspector attributes for surface models and pieces |
| | 1350 | update when changed using other dialogs or commands. TG |
| | 1351 | </ul> |
| | 1352 | |
| | 1353 | <p><b>January 8, 2008. Version 1.2481.</b></p> |
| | 1354 | |
| | 1355 | <ul type=None> |
| | 1356 | <li><p>Added attributes to selection inspector dialog for surfaces and |
| | 1357 | surface pieces. Attributes: color, display style (mesh/solid), displayed, |
| | 1358 | triangle count, active, selectable with mouse. TG |
| | 1359 | |
| | 1360 | <li><p>Made selected surfaces show green outline even when "selectable with |
| | 1361 | mouse" is turned off. TG |
| | 1362 | <li><p>Made keyboard shortcuts work on surfaces selected with select command. |
| | 1363 | The select command selects the surface model but not the surface components. |
| | 1364 | TG |
| | 1365 | </ul> |
| | 1366 | |
| | 1367 | <p><b>January 7, 2008. Version 1.2481.</b></p> |
| | 1368 | |
| | 1369 | <ul type=None> |
| | 1370 | <li><p>Made surfnet tool create a surface model instead of a vrml model. |
| | 1371 | Allows measuring enclosed volume, coloring, splitting disjoint components, |
| | 1372 | .... TG |
| | 1373 | <li><p>Eliminated _cubes contour calculation module. TG |
| | 1374 | </ul> |
| | 1375 | |
| | 1376 | <p><b>January 2, 2008. Version 1.2481.</b></p> |
| | 1377 | |
| | 1378 | <ul type=None> |
| | 1379 | <li><p>Added fill value option to vop command. Large negative fill values |
| | 1380 | can produce flat cut faces when erasing an octant. TG |
| | 1381 | |
| | 1382 | </ul> |
| | 1383 | |
| | 1384 | <p><b>December 21, 2007. Version 1.2480.</b></p> |
| | 1385 | |
| | 1386 | <ul type=None> |
| | 1387 | <li><p>Made help command show documentation for commands volume, topo, sym, |
| | 1388 | bondzone, split, msc, meshmol, mask, hkcage, crystalcontacts. TG |
| | 1389 | <li><p>Added vop (volume operation command) to erase an octant. Plan to |
| | 1390 | support many other volume modifying operations (gaussian filter, erase |
| | 1391 | outside sphere, interpolate, ...) as options to this command in the future. |
| | 1392 | TG |
| | 1393 | <li><p>Changed volume suffixes from <N> format (e.g. "map.mrc <1>") |
| | 1394 | to instead append model id number. Previous suffix number was not the |
| | 1395 | model id number. TG |
| | 1396 | </ul> |
| | 1397 | |
| | 1398 | <p><b>December 20, 2007. Version 1.2480.</b></p> |
| | 1399 | |
| | 1400 | <ul type=None> |
| | 1401 | <li><p>Made meshmol command work when surface has the same model id number |
| | 1402 | as an existing molecule. TG |
| | 1403 | <li><p>Fixed bug in multiscale tool where molecule copies were not closed |
| | 1404 | when multiscale model deleted. TG |
| | 1405 | </ul> |
| | 1406 | |
| | 1407 | <p><b>December 18, 2007. Version 1.2479.</b></p> |
| | 1408 | |
| | 1409 | <ul type=None> |
| | 1410 | <li><p>Made changing volume step size with step menu not turn off automatic |
| | 1411 | step size adjustment. Now the voxel limit for automatic step adjustment is |
| | 1412 | instead changed to the number of voxels shown with the chosen step. TG |
| | 1413 | <li><p>Changed default volume solid threshold brightness at 99% rank data |
| | 1414 | value from 1.0 to 0.99 to avoid completely opaque voxels. TG |
| | 1415 | <li><p>Reduced memory allocation used to zero volume solid 3-d texture from |
| | 1416 | 4*(number of voxels) bytes to 4*(number of voxels in one xy plane). TG |
| | 1417 | <li><p>Optimized pick surface piece tool. About 10x faster in typical case. |
| | 1418 | TG |
| | 1419 | <li><p>Added Tools / Volume Data menu entry that adds Volume menu to main |
| | 1420 | window menu bar, and remembers this setting for future sessions. TG |
| | 1421 | </ul> |
| | 1422 | |
| | 1423 | <p><b>December 14, 2007. Version 1.2476.</b></p> |
| | 1424 | |
| | 1425 | <ul type=None> |
| | 1426 | <li><p>Fixed toggle surface selectability keyboard shortcut ts. TG |
| | 1427 | </ul> |
| | 1428 | |
| | 1429 | <p><b>December 12, 2007. Version 1.2476.</b></p> |
| | 1430 | |
| | 1431 | <ul type=None> |
| | 1432 | <li><p>Made topography command work with yz and xz planes. Formerly only |
| | 1433 | handled xy planes. TG |
| | 1434 | <li><p>Added topography command "replace" option to replace the existing |
| | 1435 | topography surface rather than create a new one. TG |
| | 1436 | <li><p>Made volume planes show the correct depth after All planes button is |
| | 1437 | pressed when step size is greater than 1. TG |
| | 1438 | <li><p>Fixed volume command writing brix, mrc and netcdf formats. |
| | 1439 | Was giving an error message and not writing file. TG |
| | 1440 | </ul> |
| | 1441 | |
| | 1442 | <p><b>December 11, 2007. Version 1.2476.</b></p> |
| | 1443 | |
| | 1444 | <ul type=None> |
| | 1445 | <li><p>Made volume solid rendering model have same id number as volume |
| | 1446 | surface model. Wasn't doing that when solid was shown first. TG |
| | 1447 | </ul> |
| | 1448 | |
| | 1449 | <p><b>December 7, 2007. Version 1.2476.</b></p> |
| | 1450 | |
| | 1451 | <ul type=None> |
| | 1452 | <li>Fixed bug where volume data set menu and list box contained deleted |
| | 1453 | volumes. TG |
| | 1454 | <li><p>Fixed error in session restore where multiscale models of volume |
| | 1455 | path tracer marker sets were present. TG |
| | 1456 | </ul> |
| | 1457 | |
| | 1458 | <p><b>December 5, 2007. Version 1.2476.</b></p> |
| | 1459 | |
| | 1460 | <ul type=None> |
| | 1461 | |
| | 1462 | <li><p>Removed checkbutton volume planes panel of volume dialog and added |
| | 1463 | "one", "all" buttons to control display of single plane or all planes. |
| | 1464 | New interface makes it clearer that plane display is not a mode, and makes |
| | 1465 | display of all planes more reliable. TG |
| | 1466 | <li><p>Made sessions include derived maps (e.g. Gaussian filter) that have |
| | 1467 | been saved to a separate volume file. TG |
| | 1468 | </ul> |
| | 1469 | |
| | 1470 | <p><b>December 4, 2007. Version 1.2476.</b></p> |
| | 1471 | |
| | 1472 | <ul type=None> |
| | 1473 | <li><p>Fixed bug that caused volume histogram to be off by a few percent |
| | 1474 | in number of voxels counts per value bin. TG |
| | 1475 | <li><p>Added threshold normalization to morph map dialog. Adjusts volume |
| | 1476 | threshold to keep a fixed number of grid points within the contour surface |
| | 1477 | for all interpolated maps. TG |
| | 1478 | </ul> |
| | 1479 | |
| | 1480 | <p><b>November 30, 2007. Version 1.2475.</b></p> |
| | 1481 | |
| | 1482 | <ul type=None> |
| | 1483 | <li><p>Added key shortcuts to create a new volume using the zone display of |
| | 1484 | the active volume (zv), and the region outside the zone (ez, erase zone). TG |
| | 1485 | |
| | 1486 | </ul> |
| | 1487 | |
| | 1488 | <p><b>November 29, 2007. Version 1.2475.</b></p> |
| | 1489 | |
| | 1490 | <ul type=None> |
| | 1491 | <li><p>Added topography command which creates a surface corresponding to |
| | 1492 | a volume data plane. The surface height above the volume plane is |
| | 1493 | proportional to the volume data value. TG |
| | 1494 | </ul> |
| | 1495 | |
| | 1496 | <p><b>November 27, 2007. Version 1.2473.</b></p> |
| | 1497 | |
| | 1498 | <ul type=None> |
| | 1499 | <li><p>Made Chimera compatible with 2 year old Chimera 1.2154 preferences files. |
| | 1500 | Showing volume with new Chimera and old preferences file caused error. TG |
| | 1501 | <li><p>Made restoring a session that uses the Surface Color tool not display |
| | 1502 | the Surface Color dialog unless it was displayed when the session was saved. |
| | 1503 | TG |
| | 1504 | <li><p>Added TIFF volume file reader support for 16-bit unsigned integer, |
| | 1505 | 32 bit floating point, and 32 bit integer pixel values. TG |
| | 1506 | <li><p>Added volume file writing in BRIX format (used by crystallography |
| | 1507 | program O). TG |
| | 1508 | |
| | 1509 | </ul> |
| | 1510 | |
| | 1511 | <p><b>November 15, 2007. Version 1.2470.</b></p> |
| | 1512 | |
| | 1513 | <ul type=None> |
| | 1514 | <li><p>Chimera production release 1.2470. |
| | 1515 | </ul> |
| | 1516 | |
| | 1517 | <p><b>November 13, 2007. Version 1.2469.</b></p> |
| | 1518 | |
| | 1519 | <ul type=None> |
| | 1520 | <li><p>Made Gaussian filter copy the local coordinate rotation of original |
| | 1521 | map. TG |
| | 1522 | <li><p>Made volume subregion resampling pad by half a voxel between the |
| | 1523 | displayed outline box and the resampling grid. This allows resampling on |
| | 1524 | the exact grid of a second map by clicking outside that map to outline it |
| | 1525 | (which includes a half voxel padding). TG |
| | 1526 | <li><p>Added display full volume keyboard shortcut fv. Useful after |
| | 1527 | showing a subregion for returning to full map display. TG |
| | 1528 | </ul> |
| | 1529 | |
| | 1530 | <p><b>November 8, 2007. Version 1.2468.</b></p> |
| | 1531 | |
| | 1532 | <ul type=None> |
| | 1533 | <li><p>Fixed priism volume file reader byte order detection code. Did |
| | 1534 | not work correctly with 8-bit data values. TG |
| | 1535 | </ul> |
| | 1536 | |
| | 1537 | <p><b>November 7, 2007. Version 1.2468.</b></p> |
| | 1538 | |
| | 1539 | <ul type=None> |
| | 1540 | <li><p>Added options to the Gaussian filter dialog to use only the displayed |
| | 1541 | subsampling, and to use only the displayed subregion. TG |
| | 1542 | <li><p>Fixed volume caching bug that sometimes caused single plane volume |
| | 1543 | data display to be blank. TG |
| | 1544 | <li><p>Fixed bug in morph map where the first map was modified instead of |
| | 1545 | creating a new interpolated map when the first map was writable. TG |
| | 1546 | </ul> |
| | 1547 | |
| | 1548 | <p><b>November 6, 2007. Version 1.2468.</b></p> |
| | 1549 | |
| | 1550 | <ul type=None> |
| | 1551 | <li><p>Made Chimera start correctly on Mac OS 10.5 (Leopard) by preventing |
| | 1552 | Chimera from trying to automatically start the X server, since that is now |
| | 1553 | done by the operating system. TG |
| | 1554 | <li><p>Fixed bug in error message displayed when reading truncated XPLOR |
| | 1555 | volume files. TG |
| | 1556 | </ul> |
| | 1557 | |
| | 1558 | <p><b>November 5, 2007. Version 1.2468.</b></p> |
| | 1559 | |
| | 1560 | <ul type=None> |
| | 1561 | <li><p>Made BRIX/DSN6 (O map) volume file reader apply scale and shift from |
| | 1562 | file header to 8-bit values to produce floating point values. TG |
| | 1563 | </ul> |
| | 1564 | |
| | 1565 | <p><b>October 31, 2007. Version 1.2467.</b></p> |
| | 1566 | |
| | 1567 | <ul type=None> |
| | 1568 | <li><p>Made mask command handle degenerate cases where projected grid lines |
| | 1569 | exactly intersect surface vertices or edges. TG |
| | 1570 | </ul> |
| | 1571 | |
| | 1572 | <p><b>October 29, 2007. Version 1.2466.</b></p> |
| | 1573 | |
| | 1574 | <ul type=None> |
| | 1575 | <li><p>Added "sandwich" option to mask command for extracting the volume |
| | 1576 | between two surfaces along a projection axis. Without this option regions |
| | 1577 | between one surface and the volume box boundary are also included. TG |
| | 1578 | </ul> |
| | 1579 | |
| | 1580 | <p><b>October 26, 2007. Version 1.2466.</b></p> |
| | 1581 | |
| | 1582 | <ul type=None> |
| | 1583 | <li><p>Changed hkcage command which makes icosahedral cages use keyword |
| | 1584 | options instead of requiring options to be in fixed order. Added "replace" |
| | 1585 | keyword option to replace the existing cage instead of creating a new model. |
| | 1586 | TG |
| | 1587 | |
| | 1588 | </ul> |
| | 1589 | |
| | 1590 | <p><b>October 24, 2007. Version 1.2465.</b></p> |
| | 1591 | |
| | 1592 | <ul type=None> |
| | 1593 | <li><p>Made MRC volume files written by Chimera contain the Chimera version |
| | 1594 | and date. TG |
| | 1595 | <li><p>Made split command which places chains of an atomic model in separate |
| | 1596 | models do nothing when applied to a single chain. TG |
| | 1597 | </ul> |
| | 1598 | |
| | 1599 | <p><b>October 23, 2007. Version 1.2465.</b></p> |
| | 1600 | |
| | 1601 | <ul type=None> |
| | 1602 | <li><p>Added mask command which creates a volume data set containing |
| | 1603 | only the values within a surface. TG |
| | 1604 | <li><p>Fixed bug in close points calculation used by Find Clashes, |
| | 1605 | Color Zone and Surface Zone tools which in rare cases may have led to |
| | 1606 | incorrect neighbor calculation or hanging. TG |
| | 1607 | </ul> |
| | 1608 | |
| | 1609 | <p><b>October 22, 2007. Version 1.2465.</b></p> |
| | 1610 | |
| | 1611 | <ul type=None> |
| | 1612 | <li><p>Fixed bug where meshmol command would create a model aligned |
| | 1613 | with the model with lowest id number instead of the original mesh model. TG |
| | 1614 | <li><p>Fixed bug where resampled volume had no name in volume dialog and |
| | 1615 | model panel. TG |
| | 1616 | <li><p>Made volume display tolerate externally deleted contour surface groups, |
| | 1617 | for example with Ds keyboard shortcut. TG |
| | 1618 | </ul> |
| | 1619 | |
| | 1620 | <p><b>October 18, 2007. Version 1.2463.</b></p> |
| | 1621 | |
| | 1622 | <ul type=None> |
| | 1623 | <li><p>Fixed volume series bug opening priism format data. TG |
| | 1624 | </ul> |
| | 1625 | |
| | 1626 | <p><b>October 17, 2007. Version 1.2463.</b></p> |
| | 1627 | |
| | 1628 | <ul type=None> |
| | 1629 | <li><p>Made morph map volume browse button display the opened data. TG |
| | 1630 | </ul> |
| | 1631 | |
| | 1632 | <p><b>October 11, 2007. Version 1.2458.</b></p> |
| | 1633 | |
| | 1634 | <ul type=None> |
| | 1635 | <li><p>Made calculation of volume enclosed in a surface handle surface holes |
| | 1636 | but placing a point at the center of each boundary curve and making a triangle |
| | 1637 | fan to cover the hole. TG |
| | 1638 | <li><p>Add split map and fourier transform menu entries (Tools / Volume Data). |
| | 1639 | TG |
| | 1640 | </ul> |
| | 1641 | |
| | 1642 | <p><b>October 10, 2007. Version 1.2456.</b></p> |
| | 1643 | |
| | 1644 | <ul type=None> |
| | 1645 | <li><p>Added several tools from experimental features web page to the |
| | 1646 | distribution: morph map, transform molecule coordinates, mesh to molecule, |
| | 1647 | icosahedral cage (hkcage command), surface distance, crystal contacts, volume |
| | 1648 | series, movement mouse mode, flatten icosahedron, split molecule, multiscale |
| | 1649 | color command, pick surface pieces, symmetry copies command (sym). TG |
| | 1650 | <li><p>Added Tools menu to volume dialog. TG |
| | 1651 | <li><p>Optimized speed of Find Clashes tool. TG |
| | 1652 | <li><p>Added version number to Chimera HDF map file format. TG |
| | 1653 | </ul> |
| | 1654 | |
| | 1655 | <p><b>October 9, 2007. Version 1.2455.</b></p> |
| | 1656 | |
| | 1657 | <ul type=None> |
| | 1658 | <li><p>Added "cap high values at box faces" volume surface rendering option. TG |
| | 1659 | <li><p>Made popup balloons for IMOD object surfaces give object name. |
| | 1660 | Mousing over other selectable surfaces will also show names. TG |
| | 1661 | <li>Add keyboard shortcut Ds to delete selected surfaces and Sc to split |
| | 1662 | selected surfaces into one surface for each connected component. TG |
| | 1663 | </ul> |
| | 1664 | |
| | 1665 | <p><b>October 6, 2007. Version 1.2454.</b></p> |
| | 1666 | |
| | 1667 | <ul type=None> |
| | 1668 | <li><p>Made volume contour surfaces use lighting normals parallel to data |
| | 1669 | gradient instead of averaged surface triangle normals. Gives less faceted |
| | 1670 | apperance. TG |
| | 1671 | <li><p>Made multiscale model tool use surface lighting normals based on |
| | 1672 | gradient of atom density rather than average normal of surface triangles. |
| | 1673 | Small improvement in surface smoothness. TG |
| | 1674 | </ul> |
| | 1675 | |
| | 1676 | <p><b>October 5, 2007. Version 1.2454.</b></p> |
| | 1677 | |
| | 1678 | <ul type=None> |
| | 1679 | <li><p>Added IMOD mesh file reader. TG |
| | 1680 | <li><p>Added Gaussian filter tool to smooth volume data by convolving with |
| | 1681 | a gaussian. TG |
| | 1682 | <li><p>Added Fourier transform keyboard shortcut FT to display 3-dimensional |
| | 1683 | Fourier transform of volume data. TG |
| | 1684 | <li><p>Added keyboard shortcut sm to split a volume data set into multiple |
| | 1685 | data sets, one for each color of the original volume, as colored by the |
| | 1686 | color zone tool. TG |
| | 1687 | <li><p>Made multiscale model tool not change the display style of the original |
| | 1688 | molecule used in building multimeric assembly. Only displays new copies as |
| | 1689 | surfaces. TG |
| | 1690 | |
| | 1691 | </ul> |
| | 1692 | |
| | 1693 | <p><b>October 4, 2007. Version 1.2454.</b></p> |
| | 1694 | |
| | 1695 | <ul type=None> |
| | 1696 | <li><p>Made surface capping not show a cap for a clipped unit cell outline box. |
| | 1697 | (Bug 4605). TG |
| | 1698 | <li><p>Made unit cell tool pack asymmetric unit in single unit cell even when |
| | 1699 | molecule atoms/ribbon is undisplayed (as when using Multiscale). Now uses |
| | 1700 | center of all atoms rather than center of displayed atoms for packing. |
| | 1701 | (Bug 4606). TG |
| | 1702 | </ul> |
| | 1703 | |
| | 1704 | <p><b>October 3, 2007. Version 1.2454.</b></p> |
| | 1705 | |
| | 1706 | <ul type=None> |
| | 1707 | <li><p>Added tool to print mean, standard deviation and RMS for volume data |
| | 1708 | (Tools / Volume Data / Volume Mean, SD, RMS). TG |
| | 1709 | <li><p>Made color zone slider range equal to diagonal size of surface bounding |
| | 1710 | box. Formerly maximum slider value was always 30. TG |
| | 1711 | <li><p>Made surface capping not create a cap for clipped volume outline box. TG |
| | 1712 | |
| | 1713 | </ul> |
| | 1714 | |
| | 1715 | <p><b>October 2, 2007. Version 1.2451.</b></p> |
| | 1716 | |
| | 1717 | <ul type=None> |
| | 1718 | <li><p>Made volume contour surfaces cover volume box faces where high |
| | 1719 | density is exposed. TG |
| | 1720 | </ul> |
| | 1721 | |
| | 1722 | <p><b>September 26, 2007. Version 1.2450.</b></p> |
| | 1723 | |
| | 1724 | <ul type=None> |
| | 1725 | <li><p>Made volume contour calculation work on volumes up to size 4 Gvoxels. |
| | 1726 | Formerly the limit was 4/3 Gvoxels. TG |
| | 1727 | </ul> |
| | 1728 | |
| | 1729 | <p><b>September 20, 2007. Version 1.2448.</b></p> |
| | 1730 | |
| | 1731 | <ul type=None> |
| | 1732 | <li><p>Added series of 10 initial volume colors to volume data display |
| | 1733 | options panel. Opened data sets are shown in different colors. TG |
| | 1734 | </ul> |
| | 1735 | |
| | 1736 | <p><b>September 19, 2007. Version 1.2448.</b></p> |
| | 1737 | |
| | 1738 | <ul type=None> |
| | 1739 | <li><p>Made volume data saving use a temporary file if map is written back |
| | 1740 | over itself. Formerly this would cause an error if the map was not entirely |
| | 1741 | cached in memory because the source file would be erased before all the |
| | 1742 | needed data was obtained. TG |
| | 1743 | </ul> |
| | 1744 | |
| | 1745 | <p><b>September 18, 2007. Version 1.2448.</b></p> |
| | 1746 | |
| | 1747 | <ul type=None> |
| | 1748 | <li><p>Added "compress" option to volume command to compress data when |
| | 1749 | saving in Chimera map format. Useful for mask files. TG |
| | 1750 | |
| | 1751 | <li><p>Made volume command region option accept "all" or "full" value |
| | 1752 | to set region display to show the full data set. TG |
| | 1753 | <li><p>Fixed bug where volume command did not accept upper case boolean values |
| | 1754 | True, TRUE, False, .... TG |
| | 1755 | <li><p>Fixed volume command so that model id numbers of "solid" models can |
| | 1756 | be used. Formerly the model id of the volume surface model was required. TG |
| | 1757 | <li><p>Made default solid volume rendering thresholds use only 2 nodes for |
| | 1758 | mask data sets having just two values 0/1. TG |
| | 1759 | <li><p>Made Chimera map file include original file names with suffix stripped |
| | 1760 | off when multiple maps are written to one file. TG |
| | 1761 | </ul> |
| | 1762 | |
| | 1763 | <p><b>September 17, 2007. Version 1.2448.</b></p> |
| | 1764 | |
| | 1765 | <ul type=None> |
| | 1766 | <li><p>Added "symmetry" option to volume command that assigns symmetry |
| | 1767 | matrices to a volume data set. It takes an argument "icos,XXX" where XXX |
| | 1768 | is one of 222, 2n5, n25, 2n3, 222r, 2n5r, n25r, 2n3r to specify icosahedral |
| | 1769 | symmetry in one of the standard coordinate frames as in the icosahedron |
| | 1770 | tool. Future additions will support space and point group and screw symmetries |
| | 1771 | and BIOMT PDB matrices. TG |
| | 1772 | </ul> |
| | 1773 | |
| | 1774 | <p><b>September 15, 2007. Version 1.2448.</b></p> |
| | 1775 | |
| | 1776 | <ul type=None> |
| | 1777 | <li><p>Made experimental "sym" command use symmetries associated with volume |
| | 1778 | data set. If there are none it uses BIOMT matrices from PDB model as |
| | 1779 | previously. Not yet on web. TG |
| | 1780 | <li><p>Added "contact" and "range" options to "sym" command to make molecule |
| | 1781 | copies only when it is near the original copy. Both parameters take a |
| | 1782 | distance. Contact requires a pair of atoms within the threshold distance |
| | 1783 | while range requires the center of the molecule bounding boxes to be within |
| | 1784 | the specified range. Not yet on web. TG |
| | 1785 | <li>Added keyboard shortcut "ic" to assign icosahedral 222 symmetry to the |
| | 1786 | active volume data set. TG |
| | 1787 | </ul> |
| | 1788 | |
| | 1789 | <p><b>September 12, 2007. Version 1.2446.</b></p> |
| | 1790 | |
| | 1791 | <ul type=None> |
| | 1792 | <li><p>Added volume command chunkShape option for writing map files that |
| | 1793 | allow fast access to yz planes. TG |
| | 1794 | </ul> |
| | 1795 | |
| | 1796 | <p><b>September 11, 2007. Version 1.2445.</b></p> |
| | 1797 | |
| | 1798 | <ul type=None> |
| | 1799 | |
| | 1800 | <li><p>Made CCP4 and MRC separate file formats in File / Open dialog. |
| | 1801 | Formerly they were treated as one format. CCP4 reader now will not |
| | 1802 | incorrectly interpret xorigin, yorigin, zorigin parameters found only |
| | 1803 | in MRC2000 files. TG |
| | 1804 | <li><p>Changed CCP4 and MRC file readers heuristic for deciding whether |
| | 1805 | origin header values (ncstart, nrstart, nsstart) are valid. Now requires |
| | 1806 | that they have magnitude no larger than 10 times the maximum data size along |
| | 1807 | the 3 axes. Formerly use limit of 1 times original axis data size for each |
| | 1808 | axis. Fixes bug 4473. TG |
| | 1809 | <li><p>Replaced HDF file reader with two file readers that use HDF: 1) EMAN HDF |
| | 1810 | and 2) Chimera map format. TG |
| | 1811 | <li><p>Added Chimera map file writer. |
| | 1812 | <li><p>Made movie recorder encode from jpeg images. Fixes bug 4284. TG |
| | 1813 | <li><p>Made surface color properly handle volume data set that is closed |
| | 1814 | while it is being used for automatic color updates. TG |
| | 1815 | </ul> |
| | 1816 | |
| | 1817 | <p><b>September 10, 2007. Version 1.2445.</b></p> |
| | 1818 | |
| | 1819 | <ul type=None> |
| | 1820 | <li><p>Clamped colormap size for solid rendering of volumes to maximum |
| | 1821 | reported by OpenGL. Fixed bug 4324. TG |
| | 1822 | <li><p>Fixed volume path tracer bug where adding third marker set sometimes |
| | 1823 | caused dialog to go into infinite resizing loop adding and removing a |
| | 1824 | scrollbar. Fixes bug 3305. TG |
| | 1825 | </ul> |
| | 1826 | |
| | 1827 | <p><b>September 7, 2007. Version 1.2445.</b></p> |
| | 1828 | |
| | 1829 | <ul type=None> |
| | 1830 | <li><p>Made opening volume data set with a Chimera command or on the Chimera |
| | 1831 | command-line give a explanatory error message instead of a Python traceback. |
| | 1832 | Fixes bug 4450. TG |
| | 1833 | </ul> |
| | 1834 | |
| | 1835 | <p><b>September 5, 2007. Version 1.2445.</b></p> |
| | 1836 | |
| | 1837 | <ul type=None> |
| | 1838 | <li><p>Made volume command keywords not have underscores, and not be |
| | 1839 | case sensitive, and allow unique prefix abbreviations. TG |
| | 1840 | <li><p>Made volume command color |
| | 1841 | options accept values "colorpanel", "fromeditor", or "editor" in which |
| | 1842 | case color is taken from color dialog. Also can now use color names |
| | 1843 | defined with Chimera colordef command. TG |
| | 1844 | <li><p>Made volume command save path option accept |
| | 1845 | "browse" or "browser" in which case a modal save file dialog is opened |
| | 1846 | to choose the file. TG |
| | 1847 | <li><p>Fixed bug saving sessions when volume dialog shown but no volumes |
| | 1848 | are opened. TG |
| | 1849 | <li><p>Made volume crop button use a circumscribing data axis aligned box |
| | 1850 | when selection box has been rotated. TG |
| | 1851 | </ul> |
| | 1852 | |
| | 1853 | <p><b>September 4, 2007. Version 1.2443.</b></p> |
| | 1854 | |
| | 1855 | <ul type=None> |
| | 1856 | <li><p>Added subregion selection panel controls to copy subregions that |
| | 1857 | are not aligned with the data axes. New controls are "rotate selection box" |
| | 1858 | switch, "resample voxel size" entry, and "resample" button. TG |
| | 1859 | <li><p>Made mrc, netcdf and hdf file reader and writer code save and |
| | 1860 | restore data rotation. TG |
| | 1861 | <li><p>Made solid style volume rendering correctly display skewed data, |
| | 1862 | common with crystallographic density maps. TG |
| | 1863 | <li><p>Eliminated "double" and "half" button on subregion selection panel |
| | 1864 | to reduce crowding. Rarely used. TG |
| | 1865 | <li><p>Allow unicode volume files names. Fixes bug 4433. TG |
| | 1866 | </ul> |
| | 1867 | |
| | 1868 | <p><b>August 24, 2007. Version 1.2442.</b></p> |
| | 1869 | |
| | 1870 | <ul type=None> |
| | 1871 | <li><p>Added "volume" command to change all rendering settings of volume |
| | 1872 | data, that can be changed with the volume dialog. TG |
| | 1873 | <li><p>Made volume object a subclass of surface model. This allows |
| | 1874 | extension code to more easily obtain the volume object from the list |
| | 1875 | of open models with chimera.openModels.list(). TG |
| | 1876 | </ul> |
| | 1877 | |
| | 1878 | <p><b>August 23, 2007. Version 1.2441.</b></p> |
| | 1879 | |
| | 1880 | <ul type=None> |
| | 1881 | <li><p>Changed volume code so that Chimera "open" command can assign model |
| | 1882 | id numbers when opening volume data. TG |
| | 1883 | <li><p>Simplified volume data python interface so extensions do not need |
| | 1884 | to use volume viewer dialog. TG |
| | 1885 | </ul> |
| | 1886 | |
| | 1887 | <p><b>August 10, 2007. Version 1.2437.</b></p> |
| | 1888 | |
| | 1889 | <ul type=None> |
| | 1890 | <li><p>Made volume dialog display histograms for multiple data sets. |
| | 1891 | A single line above each histogram shows the data name, size, step menu, |
| | 1892 | visibility (eye icon) and close map button (dash icon). Up to 3 histograms |
| | 1893 | are shown, and this limit can be changed with a new display options setting. |
| | 1894 | The "active" data set has a white background behind its name. The level |
| | 1895 | entry field and color button and rendering options shown in the dialog |
| | 1896 | effect only the active data set. There is no provision for changing the |
| | 1897 | settings for multiple data sets at the same time. TG |
| | 1898 | <li><p>Removed Show and Unshow buttons from bottom of dialog. Replaced |
| | 1899 | by "eye" icon button above each data histogram to show/unshow data. |
| | 1900 | Eye icon has white background when data is shown. TG |
| | 1901 | <li><p>Eliminated data menu panel which also showed data size and step. Added a |
| | 1902 | Data menu to the dialog menu bar. The size and step is now shown above each |
| | 1903 | histogram. TG |
| | 1904 | <li><p>Moved display style panel (surface/mesh/solid) below histograms. Formerly |
| | 1905 | it was above histograms. Better to put the most useful data sets info at |
| | 1906 | the top. Display style is now closer to color and threshold settings. TG |
| | 1907 | |
| | 1908 | <li><p>Changed display stye heading from "Show: *surface *mesh *solid" to |
| | 1909 | "Style: *surface *mesh *solid". |
| | 1910 | <li><p>Fixed newly introduced bug in UHBD volume file reader. TG |
| | 1911 | </ul> |
| | 1912 | |
| | 1913 | <p><b>August 9, 2007. Version 1.2436.</b></p> |
| | 1914 | |
| | 1915 | <ul type=None> |
| | 1916 | <li><p>Made volume data size show as a single number with superscript 3 |
| | 1917 | if size is the same along all three axes. TG |
| | 1918 | <li><p>Made moving volume plane slider or changing plane axis not automatically |
| | 1919 | activate plane display. Avoids unintended switch into plane mode. TG |
| | 1920 | <li><p>Made sample grid points always have indices that are multiples of |
| | 1921 | step size. Formerly if a volume subregion had an origin that was not a |
| | 1922 | multiple of the step size then the sample point included that origin. |
| | 1923 | This change makes precomputed subsamples behave the same way as |
| | 1924 | subsamples extracted from full resolution arrays. TG |
| | 1925 | </ul> |
| | 1926 | |
| | 1927 | <p><b>August 8, 2007. Version 1.2436.</b></p> |
| | 1928 | |
| | 1929 | <ul type=None> |
| | 1930 | |
| | 1931 | <li><p>Made volume plane display checkbutton update when volume region |
| | 1932 | changed using other interfaces such as subregion selection "Full" |
| | 1933 | button. TG |
| | 1934 | <li><p>Made volume dialog File / Open map dialog close as soon as file |
| | 1935 | is chosen. Formerly it waited to see if the open succeeded. TG |
| | 1936 | </ul> |
| | 1937 | |
| | 1938 | <p><b>August 6, 2007. Version 1.2434.</b></p> |
| | 1939 | |
| | 1940 | <ul type=None> |
| | 1941 | <li><p>Made volume plane display to respect auto step size adjustment to |
| | 1942 | achieve the user-requested voxel limit. Formerly plane display did not adjust |
| | 1943 | the step size. TG |
| | 1944 | <li><p>Fixed newly introduce volume data caching bug seen when requested |
| | 1945 | data and cache data have different origins and step sizes. TG |
| | 1946 | </ul> |
| | 1947 | |
| | 1948 | <p><b>August 3, 2007. Version 1.2434.</b></p> |
| | 1949 | |
| | 1950 | <ul type=None> |
| | 1951 | <li><p>Added volume file reader for HDF5 format used by EMAN and SPARX. TG |
| | 1952 | |
| | 1953 | <li><p>Added third party HDF5 library and PyTables 2.0 python module |
| | 1954 | (interface to hdf5) to the Chimera distribution. TG |
| | 1955 | </ul> |
| | 1956 | |
| | 1957 | <p><b>August 2, 2007. Version 1.2434.</b></p> |
| | 1958 | |
| | 1959 | <ul type=None> |
| | 1960 | <li><p>Changed volume solid rendering transparency so that voxel brightness |
| | 1961 | is now multiplied by opacity. This makes more transparent voxels dimmer. |
| | 1962 | This mode is now the default. The former mode can be enabled by turning off |
| | 1963 | the new "Dim transparent voxels" setting under "Solid rendering options". TG |
| | 1964 | <li><p>Changed the effect of the transparency slider for solid volume |
| | 1965 | rendering. It now is a fraction of displayed data thickness while formerly |
| | 1966 | it was a thickness value. The fraction times the number of planes (minimum |
| | 1967 | for 3 axes) gives a depth in planes that is used as an exponent to modulate |
| | 1968 | transparency. Transfer function (1-alpha) is mapped to (1-alpha)**(1/planes). |
| | 1969 | If the planes values is 2 this means that the new transparency will require |
| | 1970 | 2 planes to block as much light as the same amount of light as one plane |
| | 1971 | using the unmodified transfer function. TG |
| | 1972 | <li>Changed default solid rendering transfer function ramp. Now |
| | 1973 | starts at rank 10% data value ramping up to full brightness at rank |
| | 1974 | 99% and continuing to the maximum data value at full brightness. |
| | 1975 | With new default transparency mode this provides reasonable |
| | 1976 | brightness views of single planes or full maps. TG |
| | 1977 | <li><p>Renamed volume viewer "Transparency Factor" (surface rendering) and |
| | 1978 | "Transparency Depth" (solid rendering) slider headings to "Transparency". TG |
| | 1979 | </ul> |
| | 1980 | |
| | 1981 | <p><b>July 31, 2007. Version 1.2430.</b></p> |
| | 1982 | |
| | 1983 | <ul type=None> |
| | 1984 | |
| | 1985 | <li><p>Made reading volume data with step size greater than 1 only allocate |
| | 1986 | space for the subsampled data. Formerly the full size data set would be |
| | 1987 | read into memory. The new behavior permits display of data sets larger than |
| | 1988 | will fit in memory. TG |
| | 1989 | <li><p>Made reading binary volume files report progress every 0.2 seconds |
| | 1990 | or every data z plane read, which ever is longer. Previously used a less |
| | 1991 | reliable estimate for frequency of messages based on bytes of data read. TG |
| | 1992 | <li><p>Fixed bug where scale bar value-changed callback occurs when scale |
| | 1993 | limits are updated if the old scale value does not lie within the limits. |
| | 1994 | Observed for volume z plane slider when switching between data sets. TG |
| | 1995 | </ul> |
| | 1996 | |
| | 1997 | <p><b>July 27, 2007. Version 1.2430.</b></p> |
| | 1998 | |
| | 1999 | <ul type=None> |
| | 2000 | <li><p>Made movie recorder turn off raytrace preview overriding the |
| | 2001 | user preference. TG |
| | 2002 | <li><p>Made "movie encode" command implicitly do a "movie stop" before |
| | 2003 | encoding. Formerly, frame capture continued while encoding was done. TG |
| | 2004 | </ul> |
| | 2005 | |
| | 2006 | <p><b>July 26, 2007. Version 1.2430.</b></p> |
| | 2007 | |
| | 2008 | <ul type=None> |
| | 2009 | |
| | 2010 | <li><p>Added z plane panel to volume viewer. Allows quick switching between |
| | 2011 | individual data z planes shown using solid rendering by moving a slider. TG |
| | 2012 | <li><p>Added volume viewer option to initially display a single z plane when |
| | 2013 | opening data sets larger than 256 Mvoxels. TG |
| | 2014 | </ul> |
| | 2015 | |
| | 2016 | <p><b>July 25, 2007. Version 1.2430.</b></p> |
| | 2017 | |
| | 2018 | <ul type=None> |
| | 2019 | <li><p>Made volume dialog not transiently resize when displayed for the first |
| | 2020 | time. TG |
| | 2021 | <li><p>Made volume "show data when opened if smaller than X Mvoxels" use |
| | 2022 | size of subsampled data if a precomputed subsample file is being read. TG |
| | 2023 | </ul> |
| | 2024 | |
| | 2025 | <p><b>July 24, 2007. Version 1.2430.</b></p> |
| | 2026 | |
| | 2027 | <ul type=None> |
| | 2028 | <li><p>Made volume step size menu add entries for new step sizes that are |
| | 2029 | entered using the region bounds panel. TG |
| | 2030 | |
| | 2031 | <li><p>Made volume region bounds panel not deactivate auto-step adjustment |
| | 2032 | when new bounds are entered by step values are left the same. TG |
| | 2033 | <li><p>Added user-friendly error message when allocating an array for |
| | 2034 | reading a volume data set fails. TG |
| | 2035 | </ul> |
| | 2036 | |
| | 2037 | <p><b>July 23, 2007. Version 1.2430.</b></p> |
| | 2038 | |
| | 2039 | <ul type=None> |
| | 2040 | <li><p>Made each volume have its own auto-adjust step size setting. Formerly |
| | 2041 | all volumes used the dialog setting. TG |
| | 2042 | <li><p>Made newly opened volumes use the default rendering options instead |
| | 2043 | of the options currently set in the volume dialog. Definitely want this |
| | 2044 | behavior for auto-adjust step, but no so clear for smoothing, outline box, |
| | 2045 | others. TG |
| | 2046 | <li><p>Fixed bug where canceling volume file read disabled updates of volume |
| | 2047 | display when threshold or step size changed. TG |
| | 2048 | </ul> |
| | 2049 | |
| | 2050 | <p><b>July 21, 2007. Version 1.2430.</b></p> |
| | 2051 | |
| | 2052 | <ul type=None> |
| | 2053 | |
| | 2054 | <li><p>Added volume file reader for stacks of TIFF images. TG |
| | 2055 | <li><p>Added progress report status-line messages when reading volume files. |
| | 2056 | <li><p>Added cancel link (in blue) in volume progress status messages. TG |
| | 2057 | <li><p>Added support for multi-color status-line messages and detecting |
| | 2058 | mouse clicks on parts of status-line messages. TG |
| | 2059 | <li><p>Made writing MRC or NetCDF volume file read and write one z-plane |
| | 2060 | at a time to allow writing files larger than can fit in memory. TG |
| | 2061 | <li><p>Changed volume viewer dialog "step" menu entries to be just a single |
| | 2062 | number instead of 3 numbers if steps along all 3 axes are the same |
| | 2063 | (e.g. 2 instead of 2 2 2). TG |
| | 2064 | <li><p>Eliminated parentheses around volume size shown in volume dialog. TG |
| | 2065 | <li><p>Eliminated "ctrl-click on histogram to add or delete thresholds" message |
| | 2066 | from volume dialog. Not worth the dialog space. TG |
| | 2067 | <li><p>Multi-component volume data files are now appear as separate data sets |
| | 2068 | for each component. This effects multi-wavelength optical microscopy files |
| | 2069 | in Priism format. One histogram is displayed in the volume dialog instead |
| | 2070 | of multiple histograms. TG |
| | 2071 | </ul> |
| | 2072 | |
| | 2073 | <p><b>July 17, 2007. Version 1.2430.</b></p> |
| | 2074 | |
| | 2075 | <ul type=None> |
| | 2076 | <li><p>Fixed movie recorder bug when using raytracing and encoding with |
| | 2077 | "play forward and backward". GNAT 4208. TG |
| | 2078 | </ul> |
| | 2079 | |
| | 2080 | <p><b>July 7, 2007. Version 1.2425.</b></p> |
| | 2081 | |
| | 2082 | <ul type=None> |
| | 2083 | <li><p>Made single plane volume data sets display using "solid" rendering |
| | 2084 | style even if dialog is set to surface or mesh. Helpful for looking at EM |
| | 2085 | micrographs. TG |
| | 2086 | </ul> |
| | 2087 | |
| | 2088 | <p><b>July 2, 2007. Version 1.2425.</b></p> |
| | 2089 | |
| | 2090 | <ul type=None> |
| | 2091 | <li><p>Made volume and multiscale surface models allow variable thickness |
| | 2092 | silhouette edges. TG |
| | 2093 | </ul> |
| | 2094 | |
| | 2095 | <p><b>June 1, 2007. Version 1.2417.</b></p> |
| | 2096 | |
| | 2097 | <ul type=None> |
| | 2098 | <li><p>Fixed volume path tracer marker placement when per-model clipping |
| | 2099 | and solid rendering used. Was ignoring per-model clip plane. TG |
| | 2100 | <li><p>Made volume path tracer marker placement with solid rendering use |
| | 2101 | threshold level given by the lowest node in the solid transfer function |
| | 2102 | with brightness > 0. Formerly was using surface threshold. TG |
| | 2103 | <li><p>Made volume gOpenMol file reader provide a user-friendly error |
| | 2104 | message when reading an empty file. GNAT 3952. TG |
| | 2105 | </ul> |
| | 2106 | |
| | 2107 | <p><b>May 24, 2007. Version 1.2416.</b></p> |
| | 2108 | |
| | 2109 | <ul type=None> |
| | 2110 | <li><p>Fixed volume path tracer test suite test. Use of deprecated Python |
| | 2111 | os.tmpnam() on Windows Vista gave unwritable file. TG |
| | 2112 | </ul> |
| | 2113 | |
| | 2114 | <p><b>May 17, 2007. Version 1.2412.</b></p> |
| | 2115 | |
| | 2116 | <ul type=None> |
| | 2117 | <li><p>Fixed mesh benchmark divide by zero that occured with defective |
| | 2118 | graphics driver that could not render mesh. TG |
| | 2119 | </ul> |
| | 2120 | |
| | 2121 | <p><b>May 15, 2007. Version 1.2411.</b></p> |
| | 2122 | |
| | 2123 | <ul type=None> |
| | 2124 | <li><p>Fixed 64-bit Linux dependency on system lapack / blas libraries. TG |
| | 2125 | </ul> |
| | 2126 | |
| | 2127 | <p><b>May 14, 2007. Version 1.2410.</b></p> |
| | 2128 | |
| | 2129 | <ul type=None> |
| | 2130 | <li><p>Fixed movie command bug where (unnecessary) movie reset command |
| | 2131 | issued after movie encode command which was still working in background. |
| | 2132 | GNAT 3873. TG |
| | 2133 | </ul> |
| | 2134 | |
| | 2135 | <p><b>May 9, 2007. Experimental feature.</b></p> |
| | 2136 | |
| | 2137 | <ul type=None> |
| | 2138 | <li><p>Enhanced IMOD segmentation file reader to read contours and points, |
| | 2139 | creating a volume path tracer model. TG |
| | 2140 | </ul> |
| | 2141 | |
| | 2142 | <p><b>May 8, 2007. Version 1.2399.</b></p> |
| | 2143 | |
| | 2144 | <ul type=None> |
| | 2145 | <li><p>Made closing volume path tracer dialog turn off the marker placement |
| | 2146 | mouse mode. Reshowing the dialog turns the mouse mode back on. TG |
| | 2147 | <li><p>Renamed button on movie recorder output path browse dialog |
| | 2148 | from Save to Set Movie Path. Bug #2270. TG |
| | 2149 | <li><p>Fixed bug #3833 where volume menu it fit map in map tool did not update |
| | 2150 | after a volume was closed. Made volume menus in fit map, values at atom |
| | 2151 | positions, and morph map dialog automatically update as soon as a volume data |
| | 2152 | set is opened or closed. TG |
| | 2153 | </ul> |
| | 2154 | |
| | 2155 | <p><b>May 1, 2007. Version 1.2392.</b></p> |
| | 2156 | |
| | 2157 | <ul type=None> |
| | 2158 | <li><p>Fixed bug in bondzone command where "if array:" construct used to |
| | 2159 | test if array is non-empty. Bug introduced with switch from Numeric to |
| | 2160 | Numpy library. TG |
| | 2161 | </ul> |
| | 2162 | |
| | 2163 | <p><b>April 30, 2007. Version 1.2388.</b></p> |
| | 2164 | |
| | 2165 | <ul type=None> |
| | 2166 | <li><p>Fixed bug opening biological unit model from PQS database using |
| | 2167 | id on command-line (e.g. "open pqsID:104l") TG |
| | 2168 | </ul> |
| | 2169 | |
| | 2170 | <p><b>April 27, 2007. Version 1.2388.</b></p> |
| | 2171 | |
| | 2172 | <ul type=None> |
| | 2173 | <li><p>Added code to check the Mac Python crash log to see if the last |
| | 2174 | invocation of Chimera ended in a crash. If so, a dialog appears the next |
| | 2175 | time they run Chimera allowing them to report the crash including the |
| | 2176 | crash log. TG |
| | 2177 | <li><p>Added xray fo-fc difference maps from the Uppsala Electron |
| | 2178 | Density Server to File / Fetch by Id. TG |
| | 2179 | <li><p>Added biological unit PDB files from the Probably Quaternary Structure |
| | 2180 | (PQS) server to File / Fetch by Id. TG |
| | 2181 | </ul> |
| | 2182 | |
| | 2183 | <p><b>April 26, 2007. Version 1.2388.</b></p> |
| | 2184 | |
| | 2185 | <ul type=None> |
| | 2186 | <li><p>Fixed bug #3808 where movie recorder "play forward then backward" |
| | 2187 | option caused error on Windows. TG |
| | 2188 | <li><p>Fixed bug #3812 where default movie recorder output movie file location |
| | 2189 | is unwritable on Windows Vista. TG |
| | 2190 | </ul> |
| | 2191 | |
| | 2192 | <p><b>April 25, 2007. Version 1.2384.</b></p> |
| | 2193 | |
| | 2194 | <ul type=None> |
| | 2195 | <li><p>Made opening APBS, DelPhi, or UBHD electrostatic potential files |
| | 2196 | show surface color dialog instead of volume viewer. TG |
| | 2197 | </ul> |
| | 2198 | |
| | 2199 | <p><b>April 11, 2007. Version 1.2375.</b></p> |
| | 2200 | |
| | 2201 | <ul type=None> |
| | 2202 | <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 |
| | 2203 | <li><p>Bug fix. Nucleic acid blobs reschains.py error when scale bar shown. TG |
| | 2204 | <li><p>Bug #3775 fixed. Fit model in map when map not shown. TG |
| | 2205 | </ul> |
| | 2206 | |
| | 2207 | <p><b>April 9, 2007. Version 1.2373.</b></p> |
| | 2208 | |
| | 2209 | <ul type=None> |
| | 2210 | |
| | 2211 | <li><p>Added button to movie recorder to show raytracing preferences. TG |
| | 2212 | <li><p>Suppressed image saving status messages when capturing with movie recorder. TG |
| | 2213 | <li><p>Change movie command "loop" keyword to "roundtrip". TG |
| | 2214 | </ul> |
| | 2215 | |
| | 2216 | <p><b>April 6, 2007. Version 1.2372.</b></p> |
| | 2217 | |
| | 2218 | <ul type=None> |
| | 2219 | <li><p>Included C++ header files in Chimera distributions. TG |
| | 2220 | <li><p>Restricted movie recorder to PNG image format when raytracing. TG |
| | 2221 | </ul> |
| | 2222 | |
| | 2223 | <p><b>April 5, 2007. Version 1.2370.</b></p> |
| | 2224 | |
| | 2225 | <ul type=None> |
| | 2226 | |
| | 2227 | <li><p>Added movie recorder option to play frames forward then backward when encoding. Also added movie command "loop" option to permit this. TG |
| | 2228 | <li><p>Added raytracing option to movie recorder. TG |
| | 2229 | </ul> |
| | 2230 | |
| | 2231 | <p><b>April 3, 2007. Version 1.2369.</b></p> |
| | 2232 | |
| | 2233 | <ul type=None> |
| | 2234 | <li><p>Added supersampling option to movie recorder. TG |
| | 2235 | </ul> |
| | 2236 | |
| | 2237 | <p><b>March 28, 2007. Version 1.2366.</b></p> |
| | 2238 | |
| | 2239 | <ul type=None> |
| | 2240 | <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 |
| | 2241 | <li><p>Made scale bar, path tracer, and multiscale preserve model numbers when |
| | 2242 | session is restored. TG |
| | 2243 | |
| | 2244 | </ul> |
| | 2245 | |
| | 2246 | <p><b>March 27, 2007. Version 1.2365.</b></p> |
| | 2247 | |
| | 2248 | <ul type=None> |
| | 2249 | <li><p>Made measure volume/area tool automatically update as surface changes. TG |
| | 2250 | </ul> |
| | 2251 | |
| | 2252 | <p><b>March 9, 2007. Version 1.2354.</b></p> |
| | 2253 | |
| | 2254 | <ul type=None> |
| | 2255 | <li><p>Made session restore of volume data sets use original model numbers. TG |
| | 2256 | </ul> |
| | 2257 | |
| | 2258 | }}} |
![[Chimera Issue Tracking System]](/trac/chimera/chrome/site/chimera_logo.png){kind=logo}
