Hi Angel,
would it be too much if I ask you a favor (since you are already playing
with VRML ;-) to export attached molecule to vrml (just, please, if you
could zoom it to 100% first)?
The vrml files I exported from Jmol were...hmmmm....unreadable by vrml
programs. I have followed your suggestions, but it seems that I have three
left hands ;-)
(BTW, you can see from attachment that I've become more knowledgeable Jmol
user, thank you! There was no way I could do this before your
instructions!)
Thank you in advance,
Marko
> Today I am playing with VRML export. Models export very nicely
> (restricted to atoms and bonds, it seems; not a complain, I knew that
> features were limited).
> Jmol offers by default the .vrml extension for files.
>
> To see the vrml files, I have installed Flux Player (application and
> browser plug-in), but it only accepts files with .wrl extension.
>
> I am not used to vrml, so would like to get some feedback from savvy
> users about which is the most common extension. Depending on that
> feedback, maybe the default for Jmol could be changed to wrl?
>
> BTW, I have just added info about VRML, Maya and POV-Ray export in
> the Wiki for future reference. Contributions are welcome.
> http://wiki.jmol.org/index.php/File_formats
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
# Jmol state version 11.6.8 2008-11-24 13:39;
function _setWindowState();
# height 885;
# width 1276;
stateVersion = 1106008;
backgroundColor = "[x000000]";
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
ambientPercent = 45;
diffusePercent = 84;
specular = true;
specularPercent = 22;
specularPower = 40;
specularExponent = 6;
statusReporting = true;
end function;
function _setFileState();
set allowEmbeddedScripts false;
set autoBond true;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultDirectory "";
set defaultLattice {0.0 0.0 0.0};
set defaultLoadScript "";
set defaultVDW Jmol;
set forceAutoBond false;
set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set minBondDistance 0.4;
set pdbSequential false;
set pdbGetHeader false;
set percentVdwAtom 20;
set smartAromatic true;
load /*file*/"C:/Users/Reza/Desktop/mol molekula/IBOGAINE.MOL";
end function;
function _setVariableState();
set defaultanglelabel "%VALUE %UNITS";
set defaultcolorscheme "jmol";
set defaultdirectory "";
set defaultdistancelabel "%VALUE %UNITS";
set defaultdrawarrowscale 0.5;
set defaultlattice "{0.0 0.0 0.0}";
set defaultloadscript "";
set defaulttorsionlabel "%VALUE %UNITS";
set defaulttranslucent 0.5;
set defaultvdw "Jmol";
set allowembeddedscripts true;
set allowrotateselected false;
set appletproxy "";
set applysymmetrytobonds false;
set atompicking true;
set autobond true;
set autofps false;
set axes window;
set axesmode 0;
set axesscale 2.0;
set bondmodeor false;
set bondpicking false;
set bondradiusmilliangstroms 150;
set bondtolerance 0.45;
set cartoonrockets false;
set chaincasesensitive false;
set dataseparator "~~~";
set delaymaximumms 0;
set dipolescale 1.0;
set disablepopupmenu false;
set displaycellparameters true;
set dotdensity 2;
set dotsselectedonly false;
set dotsurface true;
set drawhover false;
set drawpicking false;
set dynamicmeasurements false;
set ellipsoidarcs false;
set ellipsoidaxes false;
set ellipsoidaxisdiameter 0.02;
set ellipsoidball true;
set ellipsoiddotcount 200;
set ellipsoiddots false;
set ellipsoidfill false;
set forceautobond false;
set greyscalerendering false;
set hbondsbackbone false;
set hbondssolid false;
set helppath "http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm";;
set hermitelevel 0;
set hidenameinpopup false;
set hidenavigationpoint false;
set highresolution false;
set historylevel 0;
set hoverdelay 0.5;
set isosurfacepropertysmoothing true;
set justifymeasurements false;
set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set measureallmodels false;
set measurementlabels true;
set messagestylechime false;
set minbonddistance 0.4;
set navigationperiodic false;
set navigationspeed 5.0;
set pdbgetheader false;
set pdbsequential false;
set percentvdwatom 20;
set pickingspinrate 10;
set picklabel "";
set pointgroupdistancetolerance 0.2;
set pointgrouplineartolerance 8.0;
set propertyatomnumbercolumncount 0;
set propertyatomnumberfield 0;
set propertycolorscheme "roygb";
set propertydatacolumncount 0;
set propertydatafield 0;
set quaternionframe "c";
set rangeselected false;
set ribbonaspectratio 16;
set ribbonborder false;
set rocketbarrels false;
set selectallmodels true;
set selecthetero true;
set selecthydrogen true;
set sheetsmoothing 1.0;
set showhiddenselectionhalos false;
set showhydrogens true;
set showmeasurements true;
set showmultiplebonds true;
set shownavigationpointalways false;
set smartaromatic true;
set solventprobe false;
set solventproberadius 1.2;
set ssbondsbackbone false;
set stereodegrees -5.0;
set strandcountformeshribbon 7;
set strandcountforstrands 5;
set testflag1 false;
set testflag2 false;
set testflag3 false;
set testflag4 false;
set tracealpha true;
set usenumberlocalization true;
set vectorscale 1.0;
set vibrationperiod 0.5;
set vibrationscale 0.5;
set wireframerotation false;
set zoomlarge true;
set zshade false;
#user-defined variables;
# --none--;
# label defaults;
select none;
color label none;
background label none;
set labelOffset 4 4;
set labelAlignment left;
set labelPointer off;
font label 13.0 SansSerif Plain;
end function;
function _setModelState();
select ({0:48});
Spacefill 0.0;
select BONDS ({0:52});
wireframe 0.03;
select ({6 11 18});
label "%e";
measures delete;
select *; set measures nanometers;
font measures 15.0 SansSerif Plain;
select measures ({null});
dots 0 radius 1.95 ({2 6 7 9 14 23 24 33 36 39:41 48 50 53 54 79 80 82:85 88
100:102 117:121 128 133 135 140:143 146:148 150 155:157 159:161 180:182 184:187
194 195 199 200 202:205 216 299:304 306:324 326 327 331:333 342 377:379 381 384
423 444:465 488 489 514 522:527 541 542 544 546 548:552 557 565:572 574:576 579
582 584 586 595 596 599 604:610 612:615 621:623 628:641});
dots 1 radius 1.95 ({2 9 15 41 48:50 53 54 57 83 84 100 119 121 127 128 135
136 139 157 159 161 180:185 187 199:204 212 214 308 309 318 319 321 323 324 377
379 451:454 465 488 489 492:494 507 522:528 609 610 612:614 626:628 634:639
641});
dots 2 radius 1.95 ({2 9 14 36 44 48 50 53 54 82 84 85 100:102 128 135 136
156 157 161 168 180:187 192 194 195 199:205 216 219 308 309 311 318:321 323 324
342 377:382 384 393 395 488 489 514 522:527 609 610 612:615 623 630 634
636:638});
dots 3 radius 1.95 ({0 2 4 5 9 12 14:17 28 29 41:44 48:56 61 64 69 71 72 74
83 84 96:104 119 127:129 134:136 157 161:170 179:185 187 189:207 209:217 220
221 226:231 234 238 240 242 243 258:260 263 264 270:276 278 280 281 284 289 290
308 309 318 319 323 360:365 370:396 451 453 454 488:491 493 495:499 508 509
517:520 522:528 531 609 610 612:614 628 634:639});
dots 4 radius 1.95 ({2:4 9 14:16 28 35 36 48 50:58 60:63 67 82:85 89:91
98:102 127 128 135 156 157 161 180:182 184 185 187 194 196:217 220 221 224:237
239:243 251 252 308 309 311 313 318:321 323 324 334:337 339 341:345 370:375
377:379 381 383:385 394 451 473 488:495 498 499 502 504 507 508 514 522 523 525
526 609:615 620:623 630 631 634:638 641});
dots 5 radius 1.95 ({2 9 15 35 41 48:50 53 54 83:85 100 102 119 127 128 135
136 154 156 157 161 180:185 187 189:191 199:205 212:214 217 308 309 318:324 336
341 377:379 451 453:455 463 464 488 489 491:494 522:528 531 604 606 609:615 622
624 627 628 634:637 639});
dots 6 radius 1.85 ({2 4 9 12 14 16 28 29 41:44 46 48:54 56 58 61 63 73 75 84
98:105 128 134:136 157 161 163:170 177 179:185 187:205 209:211 214:217 220 221
231:234 236 239 241:243 251 274 275 277 279 284 285 288 289 291 309 318 319 323
361 370:375 377:385 387 390:397 399:401 451 454 488:491 495 498 499 517:531 609
610 613 634:637});
dots 7 radius 1.95 ({2 9 15 35 53 54 83 84 100 102 128 135 157 161 180 194
199:205 216 309 312 314 318 319 321 323 324 336 377:382 384 451 453 488 489 492
493 522 523 525:527 609:614 630 634:641});
dots 8 radius 1.95 ({2 9 24 36 41 48 50 53 54 84 85 100 102 128 135 155:157
161 180:182 184 185 187 188 199:205 216 217 309 318:324 332 333 377:379 384 451
488 489 514 516 522:527 604 608:610 612:615 622 630 634:638});
dots 9 radius 1.95 ({9:11 15 24 25 29 33 35 37 40 85 87:90 100 109 117 118
128 130 132 136:140 142:146 148:150 152 155 156 158 201 212 214 320 324 328 329
331:334 336:343 377:379 382 403:405 434 444 446:450 467 474 488 489 492:494
500:504 510 511 513 515 523 527:540 545 547:564 567 568 571 573 574 576:585 587
588 591:593 602 603 605 607:609 611 612 616:623 629});
dots 10 radius 1.95 ({2 7 11 22:25 32 38 39 50 52 58 59 61 79:88 90 112 113
117:119 121 125 126 139 142:144 147 159 160 180:182 192 193 199 218:226 242
299:309 311:314 316:322 325:333 335 338:340 342:344 422 424:428 444:447 449:455
461:465 473:475 478 479 481 483 484 532:534 538:540 543 550:555 557 558 562 565
566 569 570 586 594:597 624:626 632 633 638 640 641});
dots 11 radius 1.85 ({6 11 32 37 38 41 112 113 115 116 120 121 137:143 154
159 160 299 301 422 423 425:428 434 436:438 440:443 456 457 459 532:557 572:575
602 604:606 615 622 624:633 635 639:641});
dots 12 radius 1.95 ({9 11 38 41 100 102 135 139 149 154 157 159 161 377:382
384 392 488 489 491 522 523 525:527 532:534 538:540 555 558 580 581 602 603 606
609 610 613 624:628 633:641});
dots 13 radius 1.95 ({5 9 18 29 62 68:71 73 100 104 105 128 134:136 156 157
232 235:237 241 246 252:254 256:269 275 276 278 280 377 382 386 387 389:391 396
397 399 400 489 493 517:531 609 610 612:615 634 636 637});
dots 14 radius 1.95 ({0 2 4 7 12 14 15 17:19 24 25 42:44 48 53 54 59 62 64:68
70 71 84:92 96 97 99 103 104 124:126 147 162:170 180 183:185 189 199:205 212
219 222 232:239 244:247 249:257 264:270 273 318:350 360:363 365 367 370 371 373
375 376 386 388:391 393 444:447 455 473:479 481 483 484 487 495 566 594 596});
dots 15 radius 1.95 ({1 2 13 15 22 45 47 50 53 56 57 59 66 72 77 78 80 82:85
89 112 114 171:173 175 176 180 182 186 196 198:203 209 212:215 217:219 244
247:250 271 272 282:285 289 292:298 305 307:311 313:319 321 323 324 336 337
339:341 343 413 424 429 432 433 441 442 451});
dots 16 radius 1.95 ({0 5 6 12 13 20:22 28:32 42:44 46 47 49 52 59 65 66 69
71:76 78:82 97 100:108 110 112:114 116 129 134 136 162:170 172 174:179 183 186
188:193 195:197 218 219 221:224 244 245 247:250 258:263 270:282 284:291 298:303
305:307 310 315:317 378 380:387 389:392 395:402 406:408 411 412 414:428 430
436:443 456 490 491 497:499 508 517:521 527 528 530 531 541:544 572});
dots 17 radius 1.95 ({11 19 22 28 67 71 79:81 98 99 102 103 127 128 144
154:156 251 252 255 264 294 296 300:303 305:307 316 317 371:376 383:385 388 389
393 394 422 424 425 427 432 433 488 490:493 498 499 534 558 580 602:605 612 615
622});
dots 18 radius 1.7 ({2 6 7 9 11 23 24 33 37:41 48 53 79 80 82:85 88 113
117:121 135 137:150 153:157 159:161 180:182 199 200 202 204 205 299:304 306 308
309 312:314 317:323 325:327 331:333 377 378 422 423 444:465 478 489 522 532:547
550:552 555:586 594:597 599 600 602:610 613:615 621 622 624:628 630 632:641});
dots 19 radius 1.95 ({0 2:4 8 9 11 13 17 18 24:27 33 35 36 40 41 43 48:50 53
59 60 62:65 67 68 83:85 87:98 117:119 124 127:131 135 144:146 149 152 154:159
161:163 166 169 170 174 180:184 186:191 199 200 219 222 224 225 227:229 232:241
243:247 251:254 256 257 268 308:313 318:324 326:371 374 444:455 458 463:465 468
469 473:477 488:509 516 522 524 526 532 534 558:563 565 567 568 570 571 578:581
583:585 588 591 602:624 626:628 630 634:641});
dots 20 radius 1.2 ({6 11 32 33 37:41 113 115 118 120 137:151 153:155 159:161
423 426:428 438 448 456 460 532:586 591:608 613 615 617 621:633 635 636
639:641});
dots 21 radius 1.2 ({0 4 5 16:20 42 44 51 52 58:72 74 96:99 103 104 162:164
166 167 169 192 193 195:198 209 211 218:224 226:276 278 280 281 289:291 350
360:365 370:376 386:389 391:395 495 497 498});
dots 22 radius 1.2 ({3 4 17 26:28 35 60:64 67 90:94 96:98 127 129 131 206
225:230 232:243 251 252 256 335 344:352 354:375 383 473 476 490:499 501:509
611});
dots 23 radius 1.2 ({0 4 5 12 14 16:21 28 29 42:44 46 47 51 52 58 59 61:76
97:99 101 103:106 134 162:170 173 177:179 189 190 192:198 209 211 215 218:224
227 228 230:291 360:363 365 370:376 380:382 384:402 414 415 419 420 495 497:499
517:521 528});
dots 24 radius 1.2 ({9:11 29 35 36 38 41 100 102 109 115 128 132:139 142 143
149 154:161 377:379 381 382 384 403 405 409 434 488 489 491:494 510:516 518
522:534 536 538:540 548:553 555 558 580 581 584 602:615 617 620:641});
dots 25 radius 1.2 ({7 8 24 25 33 34 39 40 86:90 117 118 122:126 130 144:147
149:153 158 320 325:335 338:343 351 353 444:450 466:487 500 501 558:563 565:571
576:601 607 608 616:619});
dots 26 radius 1.2 ({6 7 11 23 32 33 37:39 79:81 88 112 113 115 117:121
137:141 143:150 153 154 299:307 327 422:428 436 438 441 444:450 452 456:465 478
532:547 549:583 585 586 594:597 599 602 603 624:626});
dots 27 radius 1.2 ({0 2 3 14:17 24 25 42:44 48:61 63 83:85 87 89:92 124
162:164 166 168:170 180:189 191:231 240:243 245 308 309 318:324 328:345 347:350
451 453:455 473:476 484});
dots 28 radius 1.2 ({9 11 28 35 40 41 102 127:131 135 149 154:159 161 377:379
383 384 488:494 499:505 507:509 522 532 534 558 580 581 584 602:624 626:628
634:637 639});
dots 29 radius 1.2 ({4 5 9 19 28 29 35 62 67 68 70 71 97:104 127:129 134:136
156 157 232:234 236 237 251:257 259 260 262 264:269 361 370:395 488:499 507:509
517:519 522 523 525 527 528 531 609:612 614 634});
dots 30 radius 1.2 ({0 3 4 14:18 26 42:44 48 51:66 68 85 89:92 96 124 162:170
180 183:185 189 192:250 252 256 257 267 268 270 272 273 319 323 324 334:341
343:350 360 362 363 365 367:369 473:477});
dots 31 radius 1.2 ({0 5 12 18:20 42:44 47 59 65 66 68:72 74 75 103 162:167
169 170 177 179 189 190 193 218 219 222 244:250 253:274 276:278 280 281 284 285
289:291 376 380 386 388 389 391:393 395});
dots 32 radius 1.2 ({0:2 12:16 18 20 42:59 61 65 66 72 74:78 82:85 162:205
207 209:224 230 231 241 242 244:250 261 263 267 270:274 277 280:293 295 297 298
308:319 321 323 324 336 412 413 451 453});
dots 33 radius 1.2 ({1 13 22 31 45:47 76:78 111 114 171:176 178 282 283 285
287 292:298 305 307 315 316 412 413 415:418 424 429:433 442 443});
dots 34 radius 1.2 ({0 4 5 18:20 27:29 58 59 62:71 96:99 101:104 127 129 193
218:224 232:269 271 272 275 276 280 281 354 360:366 369:376 378 380:396 490 491
495:499 506:509 517 519});
dots 35 radius 1.95 ({4 6 8 11 18 23 27 33 35 38:41 50 59 62 64 67 68 79 82
83 93 97 113 121 123 130 131 135 139 143 147 149:161 222 224 232:237 239 246
251 252 254:257 299:304 308 311:314 351:356 360 361 363:366 423 448 450 452 453
457:459 461:463 465 467 492 496 500:506 509 522 523 525 526 534 538 540 543 550
552 565 568:570 580:628 630 633:641});
dots 36 radius 1.2 ({6 11 22 23 32 37 79:81 112 113 120 121 137:141 144 145
148:150 154 299:307 422:428 433 441 442 452 456:462 532:547 554:564 572:585 602
603 605:607 624 626 627});
dots 37 radius 1.2 ({7 8 11 25 26 33 34 39 40 86:88 90 91 93:95 117 118
122:126 130 144:147 149:153 155 158 325:333 338:340 342 343 346 348 351:353 355
357:359 444:450 466:487 500 501 558:563 565:571 576:601 603 607 608 616:621});
dots 38 radius 1.2 ({0 2 3 12 14:18 25 42:44 46 48:66 72 84 85 87 89:92 124
162:170 174 179:231 233 235:250 256 257 268 270 272:274 308 309 318:324 328
333:350 362 367 451 473:476});
dots 39 radius 1.2 ({4 9 19 28 29 35 36 62 67 68 71 97:104 109 127:129
132:136 156 157 161 232:234 237 246 251:257 264 266 268 269 361 370:395 488:499
502 507:531 609:614 630 631 634:638 641});
dots 40 radius 1.95 ({1:3 7 10 13:15 25 31 37 45 46 48:50 53:57 60 77 78 82
85:87 89:91 107 108 111 115 142 143 171:176 180:189 191 194 199:217 225 226 230
283 292 293 295 297 298 308:311 315 316 318:321 323:330 332:348 368 403 404
406:408 412 413 416:418 421 429:432 434 435 439 440 473:476 484 535 545 547:549
551 553 555 556 564 565 573 577 578});
dots 41 radius 1.2 ({4 9 19 27:29 35 36 62 64 67 68 71 93 96:104 127:131 135
136 156 157 161 232:234 236 237 239 251:257 264:266 268 269 354 356 360 361
363:366 370:386 388:395 488:499 501:509 516 518 522:529 531 609:615 619 620 622
623 634:638});
dots 42 radius 1.95 ({0 2 4:6 9 21:23 28:32 37 41 42 44 51:53 61 64 69 71:77
79:81 83 84 98:116 119:121 128 134 137:141 143 148 157 162:164 167 168 192:197
199 200 202 204 205 220 221 234 239 240 242 243 251 258:260 264 270:292 294 296
299:307 309 312 314 316:319 323 361 370:404 406:443 451:454 456:465 488:491 495
498 499 512 517:523 527 528 530 531 533:547 549 550 553:557 564 572:575 606 609
610 613:615 624 627});
dots 43 radius 1.2 ({6 7 11 32 33 37:39 79 81 112 113 115 117 118 120 121
137:150 153 154 159 299:301 303:306 422 423 425:428 436:438 441 444 445 447:450
456:463 465 478 532:547 549:586 594:597 599:603 605:607 624:628 632 633 640});
dots 44 radius 1.2 ({9:11 29 30 32 36 38 41 100 102 107:109 115 128 132:136
138 139 142 143 154:157 159:161 377:382 390 398 400 403:411 434:439 488 489
510:516 518:536 538:540 543 548:557 580 602:607 609 610 612:615 622 624:641});
dots 45 radius 1.2 ({0 4 5 12 16:20 42 44 51 52 58 59 61:74 96:99 103 104
162:164 166:169 192 193 195:198 209 211 218:224 227:278 280 281 284 289:291
360:363 365 370:376 386:389 391:396 495 497 498});
dots 46 radius 1.2 ({0:2 12:14 21:23 42:54 66 72 75:84 110 111 114 119
162:195 197:205 215:217 219 245 270:274 277 282:298 300 302:319 321:323 412:417
424 425 429:433 442 451:454 462 465});
dots 47 radius 1.2 ({2 6 7 13 15 22:25 33 37 39 45 48:50 53 54 77:89 112 113
117:121 125 126 137 138 140 141 144:148 153 174:176 180:188 191 199:204 212
293:333 336:343 422:427 433 444:465 478:484 532 535:537 541:547 556 558:579 585
586 594:599});
dots 48 radius 1.2 ({1 6 10 22 31 32 37 38 45 77:82 107 111:116 120 137 138
140:143 145 148 171 176 292:307 310 311 314:317 403:408 412 413 416:418 422:443
456 457 535:537 539:557 563 564 572:575 577});
boundBox off;
frank on;
font frank 16.0 SansSerif Bold;
set fontScaling false;
end function;
function _setPerspectiveState();
set perspectiveModel 11;
set scaleAngstromsPerInch 0.0;
set perspectiveDepth true;
set visualRange 5.0;
set cameraDepth 3.0;
boundbox corners {-10.9002 -2.1297998 -1.9635} {2.3637 4.6501 3.4523} #
volume = 487.03162;
center {-4.26825 1.2601502 0.7444};
moveto 0.0 {0 0 1 0} 50.0 0.0 0.12 {-4.26825 1.2601502 0.7444} 8.964178 {0.0
0.0 0.0} 11.81489 5.0893216 50.0;;
slab 100;depth 0;
set spinX 0; set spinY 30; set spinZ 0; set spinFps 30;
end function;
function _setSelectionState();
select ({0:48});
set hideNotSelected false;
end function;
function _setState();
initialize;
set refreshing false;
_setWindowState;
_setFileState;
_setVariableState;
_setModelState;
_setPerspectiveState;
_setSelectionState;
set refreshing true;
set antialiasDisplay false;
set antialiasTranslucent true;
set antialiasImages true;
end function;
_setState;------------------------------------------------------------------------------
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