# Jmol state version 11.6.RC12_dev 2008-08-14 16:55; # fullName = "html"; # documentBase = "file:/Users/freichsman/Documents/Projects/SAM/revisions/pna-v5/"; # codeBase = "file:/Users/freichsman/Documents/Projects/SAM/revisions/pna-v5/"; function _setWindowState(); # height 300; # width 450; stateVersion = 1106000; backgroundColor = "[x000066]"; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; ambientPercent = 45; diffusePercent = 84; specular = true; specularPercent = 22; specularPower = 40; specularExponent = 6; statusReporting = true; end function; /* * cpk2off */ function cpk2off(); for ( var i=100; i>-1; i = i - 10 ) x = script("cpk " + i + "%; delay 0.1;") end for end function; /* * off2cpk */ function off2cpk(); for ( var i=0; i<101; i = i + 10 ) x = script("cpk " + i + "%; delay 0.1;") end for end function; /* * off2wf */ function off2wf(); for ( var i=0.06; i<0.2; i = i + 0.02 ) x = script("wireframe " + i + "; delay 0.1;") end for end function; /* * wf2off */ function wf2off(); for ( var i=100; i>-1; i = i - 10 ) x = script("cpk " + i + "%; delay 0.1;") end for 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*/"1prn.pdb"; 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}"; 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 autobond true; set autofps false; set axes window; set axesmode 0; set axesscale 2.0; set bondmodeor 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 3; 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 propertyatomnumberfield 0; set propertycolorscheme "roygb"; 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; 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 1.0; set vibrationscale 1.0; set wireframerotation false; set zoomlarge true; set zshade false; #user-defined variables; x = ""; # 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 ({0:69}); color atoms opaque [x0000ff]; select ({943:999}); color atoms opaque [x00ff20]; select ({419:452}); color atoms opaque [x00c0ff]; select ({375 376 378:381 384 385 387:390 392 393 395:397 399 403 404 406 407 409 411 412 414:416}); Spacefill 1.95; select ({1615:1673}); color atoms opaque [xfff000]; select ({579:628}); color atoms opaque [x00ffe0]; select ({1485:1546}); color atoms opaque [xf0f000]; select ({1916:1978}); color atoms opaque [xff6000]; select ({1059:1130}); color atoms opaque [x20ff00]; select ({1131:1190}); color atoms opaque [x40ff00]; select ({1000:1058}); color atoms opaque [x00ff00]; select ({1191:1251}); color atoms opaque [x60ff00]; select ({1252:1313}); color atoms opaque [x80ff00]; select ({1547:1614}); color atoms opaque [xffff00]; select ({395:401}); color atoms opaque [xcc0000]; select ({2034:2090}); color atoms opaque [xff2000]; select ({751:811}); color atoms opaque [x00ff80]; select ({378:382 387:390 406:409 414:418}); color atoms opaque shapely; select ({629:688}); color atoms opaque [x00ffc0]; select ({196:261}); color atoms opaque [x0060ff]; select ({1674:1736}); color atoms opaque [xffe000]; select ({374 382 383 391 398 400:402 410 418}); Spacefill 1.85; select ({1314:1377}); color atoms opaque [xa0ff00]; select ({502:578}); color atoms opaque [x00ffff]; select ({1378:1428}); color atoms opaque [xc0ff00]; select ({1429:1484}); color atoms opaque [xe0ff00]; select ({70:137}); color atoms opaque [x0020ff]; select ({1794:1858}); color atoms opaque [xffa000]; select ({453:501}); color atoms opaque [x00e0ff]; select ({374:377 383:386 391:394 402:405 410:413}); color atoms opaque [x00bbf9]; select ({812:876}); color atoms opaque [x00ff60]; select ({327:373}); color atoms opaque [x00a0ff]; select ({689:750}); color atoms opaque [x00ffa0]; select ({1859:1915}); color atoms opaque [xff8000]; select ({408}); Spacefill 2.0; select ({377 386 394 405 413 417}); Spacefill 1.7; select ({1979:2033}); color atoms opaque [xff4000]; select ({877:942}); color atoms opaque [x00ff40]; select ({262:326}); color atoms opaque [x0080ff]; select ({2091:2163}); color atoms opaque [xff0000]; select ({138:195}); color atoms opaque [x0040ff]; select ({1737:1793}); color atoms opaque [xffc000]; select ({0:373 419:2474}); Spacefill 0.0; select BONDS ({0:2266}); wireframe 0.0; measures delete; select *; set measures nanometers; font measures 15.0 SansSerif Plain; select measures ({null}); Backbone ({369:418}); Backbone 0.4; set echo off; set echo top center; echo "The part that branches out|is called the R group or side chain."; font echo 15.0 SansSerif Bold; color echo [xff0000]; boundBox off; unitcell 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 {-24.436 14.550003 12.019001} {29.404 60.739 59.989002} # volume = 119292.54; center {0.3222499 51.195305 35.675953}; moveto 0.0 { -401 -866 -299 26.62} 200.24 -5.0 -0.1 {0.3222499 51.195305 35.675953} 42.085636 {0.0 0.0 0.0} 3.8536038 174.40295 50.0;; slab 100;depth 0; set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; end function; function _setSelectionState(); select ({374:377}); set hideNotSelected false; end function; function _setState(); initialize; set refreshing false; _setWindowState; _setFileState; _setVariableState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay true; set antialiasTranslucent true; set antialiasImages true; end function; _setState;