exit; # BEGINOFOPTIONS # Options for the scene # caption: Overview of the 1HEW structure. The trace of the protein chain is shown in rainbow colors with the alpha carbons as gray spheres labeled with the residue one letter code. The carbohydrate ligand is shown as ball and stick in CPK colors (carbon: gray, oxygen: red, nitrogen: blue). # spinState: on # doModelReload: false # savePSpeed: -1 # killMove: 1 # killZoom: 1 # animationDirection: 0 # animationMode: PALINDROME # loopPause: 1 # ENDOFOPTIONS # Jmol state version 14.29.16 2018-06-03 23:13; # fullName = "jmolApplet0__3397337520410755__"; # documentBase = "http://proteopedia.org/wiki/index.php?title=Hen_Egg-White_(HEW)_Lysozyme&action=edit"; # codeBase = "http:/wiki/extensions/jsmol/j2s/"; function _setWindowState() { # width 350; # height 350; stateVersion = 1429016; background [x000000]; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; set ambientPercent 45; set diffusePercent 84; set specular true; set specularPercent 22; set specularPower 40; set specularExponent 6; set celShading false; set celShadingPower 10; set zShadePower 3; } function _setFileState() { set allowEmbeddedScripts false; set appendNew true; set appletProxy ""; set applySymmetryToBonds false; set autoBond true; set bondRadiusMilliAngstroms 150; set bondTolerance 0.45; set defaultLattice {0 0 0}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultStructureDssp true; set defaultVDW Jmol; set forceAutoBond false; # set defaultDirectory ""; # set loadFormat "https://files.rcsb.org/download/%FILE.pdb"; # set loadLigandFormat "https://files.rcsb.org/ligands/download/%FILE.cif"; # set smilesUrlFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=true"; # set nihResolverFormat "https://cactus.nci.nih.gov/chemical/structure/%FILE"; # set pubChemFormat "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; set bondingVersion 1; set legacyAutoBonding false; set legacyAutoBonding false; set legacyHAddition false; set legacyJavaFloat true; set minBondDistance 0.4; set minimizationCriterion 0.001; set minimizationSteps 100; set multipleBondBananas false; set pdbAddHydrogens false; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 20; set smallMoleculeMaxAtoms 40000; set smartAromatic true; reloadfile = false; if (loadedfileprev != "2f267243b1cf263a27c03cd5ce051b66"); load /*file*/"/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66"; loadedfileprev = "2f267243b1cf263a27c03cd5ce051b66"; reloadfile = true; endif; } function _setParameterState() { set defaultanglelabel "%VALUE %UNITS"; set defaultcolorscheme "jmol"; set defaultdistancelabel "%VALUE %UNITS"; set defaultdrawarrowscale 0.5; set defaultlabelpdb "%m%r"; set defaultlabelxyz "%a"; set defaultlattice "{0 0 0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Jmol"; set allowembeddedscripts true; set allowmoveatoms false; set allowrotateselected false; set animationmode "once"; set appletproxy ""; set applysymmetrytobonds false; set atomtypes ""; set autobond true; set autofps false; set axes window; set axesmode 0; set axesoffset 0.0; set axesscale 2.0; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonblockheight 0.5; set cartoonblocks false; set cartoonfancy false; set cartoonladders false; set cartoonrockets false; set cartoonsfancy false; set cartoonsteps false; set chaincasesensitive false; set dataseparator "~~~"; set defaultstructuredssp true; set delaymaximumms 0; set dipolescale 1.0; set disablepopupmenu false; set displaycellparameters true; set dotdensity 3; set dotscale 1; set dotsselectedonly false; set dotsurface true; set dragselected false; set drawfontsize 14.0; set drawhover false; set dsspcalculatehydrogenalways true; set ellipsoidarcs false; set ellipsoidarrows false; set ellipsoidaxes false; set ellipsoidaxisdiameter 0.02; set ellipsoidball true; set ellipsoiddotcount 200; set ellipsoiddots false; set ellipsoidfill false; set energyunits "kJ"; set forceautobond false; set gestureswipefactor 1.0; set greyscalerendering false; set hbondsbackbone false; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm"; set hermitelevel 0; set hiddenlinesdashed false; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set hoverdelay 0.5; set infofontsize 20; set isosurfacekey false; set isosurfacepropertysmoothing true; set isosurfacepropertysmoothingpower 7; set jmolinjspecview true; set justifymeasurements false; set loadatomdatatolerance 0.01; set measureallmodels false; set measurementlabels true; set meshscale 1; set messagestylechime false; set minbonddistance 0.4; set minimizationcriterion 0.001; set minimizationrefresh true; set minimizationsilent false; set minimizationsteps 100; set minpixelselradius 6; set modulationscale 1.0; set monitorenergy false; set multiplebondbananas false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigationperiodic false; set navigationspeed 5.0; set nbocharges true; set nmrpredictformat "http://www.nmrdb.org/service/predictor?POST?molfile="; set nmrurlformat "http://www.nmrdb.org/new_predictor?POST?molfile="; set partialdots false; set particleradius 20.0; set pdbaddhydrogens false; set pdbgetheader false; set pdbsequential false; set percentvdwatom 20; set pickingspinrate 10; 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 "p"; set rangeselected false; set ribbonaspectratio 16; set ribbonborder false; set rocketbarrels false; set selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showmeasurements true; set showmodulationvectors false; set showmultiplebonds true; set shownavigationpointalways false; set showunitcelldetails true; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone true; set starwidth 0.05; set stereodegrees -5.0; set strandcountformeshribbon 7; set strandcountforstrands 5; set strutdefaultradius 0.3; set strutlengthmaximum 7.0; set strutsmultiple false; set strutspacing 6; set tracealpha true; set translucent true; set twistedsheets false; set usenumberlocalization true; set vectorscale 1.0; set vectorscentered false; set vectorsymmetry false; set vectortrail 0; set vibrationscale 1.0; set waitformoveto true; set wireframerotation false; set zdepth 0; set zoomheight false; set zoomlarge true; set zslab 50; # user-defined atom sets; @~anomalous_atoms ({}); @~backbone_invisible ({}); @~hydroxy_unchained_nucs ({}); @~nobackbone_aas ({}); @~nophosphorus_nucs ({}); @~protein ({0:1000}); @~unbondable_aas ({}); @~unchained_aas ({}); @~unchained_nucs ({}); # label defaults; select none; color label none; background label none; set labelOffset 4 4; set labelAlignment left; set labelPointer off; font label 13 SansSerif Plain; } function _setModelState() { calculate hbonds; select all; wireframe off; spacefill off; dots off; backbone off; trace off; ribbon off; cartoon off; strands off; rocket off; meshribbon off; isosurface off; halos off; color cpk; hbonds off; select ({4:8 35:41 46 47 52:56 92:96 101:107 112:117 134:137 142:145 162:168 189 190 207:210 236 237 252:256 272:276 281 282 287:290 306:309 314:316 321:325 335:337 342:345 350:356 361:364 369:371 376:379 388 389 394:396 401:404 441:445 458:461 466 467 472:478 511 512 517:520 525:528 537:543 548:550 566 567 572:578 583:586 599 600 605:608 628 629 634 635 661 662 667 668 673:676 689:691 701 702 714:717 722 723 733:737 742:746 766 767 772:775 784:787 804:807 857:863 868:871 876:882 887 888 893:897 906:908 913:916 928:932 964:970 979 980 985:991}); color atoms opaque [xffc0cb]; select ({1 10 13:15 17 20:26 28 32 43 49 58 61:64 66 69 71 74 76 79 81 84:87 89 98 109 119 123 126:129 131 139 147 150:157 159 170 174 177:184 186 192 195:198 200 204 212 215:224 226 229:231 233 239 242 244 247 249 258 261:267 269 278 284 292 295:301 303 311 318 327 330 332 339 347 358 366 373 381 385 391 398 406 409:416 418 422 425:428 430 433:436 438 447 450:453 455 463 469 480 483:492 494 497:506 508 514 522 530 534 545 552 555:557 559 563 569 580 588 591:594 596 602 610 613:616 618 621:623 625 631 637 640 642 645:648 650 653:656 658 664 670 678 681:684 686 693 696 698 704 707:709 711 719 725 728 730 739 748 751:754 756 759:761 763 769 777 781 789 793 796:799 801 809 812 814 817:826 828 831:833 835 838 840 843:852 854 865 873 884 890 899 903 910 918 921:923 925 934 937 939 942:951 953 956:959 961 972 976 982 993 996:999}); color atoms opaque [x808080]; select ({0 2:9 11:16 18:27 29:31 33:42 44:48 50:57 59:65 67:70 72:75 77:80 82:88 90:97 99:108 110:118 120:122 124:130 132:138 140:146 148:158 160:169 171:173 175:185 187:191 193:199 201:203 205:211 213:225 227:232 234:238 240:243 245:248 250:257 259:268 270:277 279:283 285:291 293:302 304:310 312:317 319:326 328:331 333:338 340:346 348:357 359:365 367:372 374:380 382:384 386:390 392:397 399:405 407:417 419:421 423:429 431:437 439:446 448:454 456:462 464:468 470:479 481:493 495:507 509:513 515:521 523:529 531:533 535:544 546:551 553:558 560:562 564:568 570:579 581:587 589:595 597:601 603:609 611:617 619:624 626:630 632:636 638:641 643:649 651:657 659:663 665:669 671:677 679:685 687:692 694:697 699:703 705:710 712:718 720:724 726:729 731:738 740:747 749:755 757:762 764:768 770:776 778:780 782:788 790:792 794:800 802:808 810:813 815:827 829:834 836:839 841:853 855:864 866:872 874:883 885:889 891:898 900:902 904:909 911:917 919:924 926:933 935:938 940:952 954:960 962:971 973:975 977:981 983:992 994:1000 1044:1146}); Spacefill 0; select ({0 2 3 9 11 12 16 18 19 27 29:31 33 34 42 44 45 48 50 51 57 59 60 65 67 68 70 72 73 75 77 78 80 82 83 88 90 91 97 99 100 108 110 111 118 120:122 124 125 130 132 133 138 140 141 146 148 149 158 160 161 169 171:173 175 176 185 187 188 191 193 194 199 201:203 205 206 211 213 214 225 227 228 232 234 235 238 240 241 243 245 246 248 250 251 257 259 260 268 270 271 277 279 280 283 285 286 291 293 294 302 304 305 310 312 313 317 319 320 326 328 329 331 333 334 338 340 341 346 348 349 357 359 360 365 367 368 372 374 375 380 382:384 386 387 390 392 393 397 399 400 405 407 408 417 419:421 423 424 429 431 432 437 439 440 446 448 449 454 456 457 462 464 465 468 470 471 479 481 482 493 495 496 507 509 510 513 515 516 521 523 524 529 531:533 535 536 544 546 547 551 553 554 558 560:562 564 565 568 570 571 579 581 582 587 589 590 595 597 598 601 603 604 609 611 612 617 619 620 624 626 627 630 632 633 636 638 639 641 643 644 649 651 652 657 659 660 663 665 666 669 671 672 677 679 680 685 687 688 692 694 695 697 699 700 703 705 706 710 712 713 718 720 721 724 726 727 729 731 732 738 740 741 747 749 750 755 757 758 762 764 765 768 770 771 776 778:780 782 783 788 790:792 794 795 800 802 803 808 810 811 813 815 816 827 829 830 834 836 837 839 841 842 853 855 856 864 866 867 872 874 875 883 885 886 889 891 892 898 900:902 904 905 909 911 912 917 919 920 924 926 927 933 935 936 938 940 941 952 954 955 960 962 963 971 973:975 977 978 981 983 984 992 994 995 1000}); color atoms translucent 0.5 chain; select ({1 10 17 28 32 43 49 58 66 71 76 81 89 98 109 119 123 131 139 147 159 170 174 186 192 200 204 212 226 233 239 244 249 258 269 278 284 292 303 311 318 327 332 339 347 358 366 373 381 385 391 398 406 418 422 430 438 447 455 463 469 480 494 508 514 522 530 534 545 552 559 563 569 580 588 596 602 610 618 625 631 637 642 650 658 664 670 678 686 693 698 704 711 719 725 730 739 748 756 763 769 777 781 789 793 801 809 814 828 835 840 854 865 873 884 890 899 903 910 918 925 934 939 953 961 972 976 982 993}); Spacefill 0.8; select ({1001:1043}); Spacefill 0.5; select BONDS ({4:48}); wireframe 0.3; select BONDS ({0:3}); color bonds opaque [xffff30]; select BONDS ({49:1069}); wireframe 0; select BONDS ({0:3}); wireframe 0.25; select ({1 10 17 28 32 43 49 58 66 71 76 81 89 98 109 119 123 131 139 147 159 170 174 186 192 200 204 212 226 233 239 244 249 258 269 278 284 292 303 311 318 327 332 339 347 358 366 373 381 385 391 398 406 418 422 430 438 447 455 463 469 480 494 508 514 522 530 534 545 552 559 563 569 580 588 596 602 610 618 625 631 637 642 650 658 664 670 678 686 693 698 704 711 719 725 730 739 748 756 763 769 777 781 789 793 801 809 814 828 835 840 854 865 873 884 890 899 903 910 918 925 934 939 953 961 972 976 982 993}); label "%[group1]"; color label [xffff00]; set labelOffset 0 0; measures delete; select *; set measures angstroms; font measures 15 SansSerif Plain; Backbone ({0:991}); Backbone 0.4; Backbone ({992:1000}); Backbone 0.0; select ({326:345}); color Backbone opaque [x00ffa0]; select ({429:461}); color Backbone opaque [x00ff20]; select ({31:64}); color Backbone opaque [x0020ff]; select ({146:172}); color Backbone opaque [x00a0ff]; select ({883:908}); color Backbone opaque [xff6000]; select ({762:787}); color Backbone opaque [xffe000]; select ({636:662}); color Backbone opaque [xc0ff00]; select ({291:325}); color Backbone opaque [x00ffc0]; select ({405:428}); color Backbone opaque [x00ff40]; select ({238:256}); color Backbone opaque [x00ffff]; select ({529:557}); color Backbone opaque [x40ff00]; select ({257:290}); color Backbone opaque [x00ffe0]; select ({380:404}); color Backbone opaque [x00ff60]; select ({507:528}); color Backbone opaque [x20ff00]; select ({65:79}); color Backbone opaque [x0040ff]; select ({173:202}); color Backbone opaque [x00c0ff]; select ({346:379}); color Backbone opaque [x00ff80]; select ({839:882}); color Backbone opaque [xff8000]; select ({685:709}); color Backbone opaque [xf0f000]; select ({971:1000}); color Backbone opaque [xff0000]; select ({663:684}); color Backbone opaque [xe0ff00]; select ({203:237}); color Backbone opaque [x00e0ff]; select ({80:117}); color Backbone opaque [x0060ff]; select ({558:586}); color Backbone opaque [x60ff00]; select ({933:970}); color Backbone opaque [xff2000]; select ({813:838}); color Backbone opaque [xffa000]; select ({738:761}); color Backbone opaque [xfff000]; select ({118:145}); color Backbone opaque [x0080ff]; select ({609:635}); color Backbone opaque [xa0ff00]; select ({710:737}); color Backbone opaque [xffff00]; select ({0:30}); color Backbone opaque [x0000ff]; select ({909:932}); color Backbone opaque [xff4000]; select ({788:812}); color Backbone opaque [xffc000]; select ({587:608}); color Backbone opaque [x80ff00]; select ({462:506}); color Backbone opaque [x00ff00]; set echo off; hover "%n %r, Chain=%c, Element=%e"; frank on; font frank 16 SansSerif Bold; select *; set fontScaling false; } function _setPerspectiveState() { if (reloadfile) { set perspectiveModel 11; } set scaleAngstromsPerInch 0; set perspectiveDepth true; set visualRange 5; set cameraDepth 3; boundbox corners {-18.918 0.7589989000000017 0.32400129999999905} {22.033 39.8 40.871998} # volume = 64826.84104966273; if (reloadfile) { center {-0.33203837 20.866533 19.55904}; } # removed moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {1.557500000000001 20.2795 20.598} 30.896765908230314 {0 0 0} 0 0 0 3.0 0.0 0.0; # removed save orientation "default"; slab 100;depth 0; set slabRange 0.0; set spinX = 0; set spinY = 5; set spinZ = 0; spinFps = 20; spin axisangle {0.0 1.0 0.0} 10.0; } function _setSelectionState() { select ({4:8 13:15 20:26 35:41 46 47 52:56 61:64 69 74 79 84:87 92:96 101:107 112:117 126:129 134:137 142:145 150:157 162:168 177:184 189 190 195:198 207:210 215:224 229:231 236 237 242 247 252:256 261:267 272:276 281 282 287:290 295:301 306:309 314:316 321:325 330 335:337 342:345 350:356 361:364 369:371 376:379 388 389 394:396 401:404 409:416 425:428 433:436 441:445 450:453 458:461 466 467 472:478 483:492 497:506 511 512 517:520 525:528 537:543 548:550 555:557 566 567 572:578 583:586 591:594 599 600 605:608 613:616 621:623 628 629 634 635 640 645:648 653:656 661 662 667 668 673:676 681:684 689:691 696 701 702 707:709 714:717 722 723 728 733:737 742:746 751:754 759:761 766 767 772:775 784:787 796:799 804:807 812 817:826 831:833 838 843:852 857:863 868:871 876:882 887 888 893:897 906:908 913:916 921:923 928:932 937 942:951 956:959 964:970 979 980 985:991 996:999}); set hideNotSelected false; } function _setState() { # # initialize; # update caption ppdiaCaptionCmd = "changeCaption('Overview of the 1HEW structure. The trace of the protein chain is shown in rainbow colors with the alpha carbons as gray spheres labeled with the residue one letter code. The carbohydrate ligand is shown as ball and stick in CPK colors (carbon: gray, oxygen: red, nitrogen: blue).');"; javascript @ppdiaCaptionCmd; select all; labels off; measurements off; set refreshing false; _setWindowState; _setFileState; _setParameterState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing false; SelectionHalos OFF; delay 1.0; moveto 1.0 { -430 -10 903 146.05} 150.0 0.0 0.0 {-0.33203837 20.866533 19.55904} 31.371292 {0 0 0} 0 0 0 3.0 0.0 0.0;; set refreshing true; if (antialiasDisplayFlag) { antialiasDisplay = true } else { antialiasDisplay = false }; set antialiasTranslucent true; set antialiasImages true; spin on; } _setState;