# Jmol state version 13.1.12 2013-01-17 18:33; function _setWindowState() { # width 508; # height 507; stateVersion = 1301012; 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 zShadePower 3; statusReporting = true; } 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 0.0 0.0}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultStructureDssp true; set defaultVDW Auto; set forceAutoBond false; #set defaultDirectory "/Users/gutow/Documents/Programming/Java_Code/Jmol/build/dist/jmol-13.1.12"; #set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz"; #set loadLigandFormat "http://www.rcsb.org/pdb/files/ligand/%FILE.cif"; #set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"; #set nihResolverFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE"; #set pubChemFormat "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; #set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap"; #set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]"; set legacyAutoBonding false; set minBondDistance 0.4; set minimizationCriterion 0.001; set minimizationSteps 100; set pdbAddHydrogens false; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 23; set smallMoleculeMaxAtoms 40000; set smartAromatic true; load /*file*/"1crn.pdb"; } function _setVariableState() { 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 0.0 0.0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Auto"; set allowembeddedscripts true; set allowmoveatoms false; set allowrotateselected false; set appletproxy ""; set applysymmetrytobonds false; set atompicking true; set atomtypes ""; 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 cartoonbaseedges false; set cartoonfancy false; set cartoonrockets 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 drawhover false; set drawpicking false; set dsspcalculatehydrogenalways true; 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 energyunits "kJ"; set forceautobond false; set fractionalrelative false; set gestureswipefactor 1.0; set greyscalerendering false; set hbondsangleminimum 90.0; set hbondsbackbone false; set hbondsdistancemaximum 3.25; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm"; set hermitelevel 0; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set historylevel 0; set hoverdelay 0.5; set imagestate true; set iskiosk false; set isosurfacekey false; set isosurfacepropertysmoothing true; set isosurfacepropertysmoothingpower 7; 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 monitorenergy false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigationperiodic false; set navigationspeed 5.0; set nmrurlformat "http://www.nmrdb.org/predictor?smiles="; set partialdots false; set pdbaddhydrogens false; set pdbgetheader false; set pdbsequential false; set percentvdwatom 23; 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 "p"; set rangeselected false; set ribbonaspectratio 16; set ribbonborder false; set rocketbarrels false; set saveproteinstructurestate true; set selectallmodels true; set selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showkeystrokes true; set showmeasurements true; set showmultiplebonds true; set shownavigationpointalways false; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone false; 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 testflag1 false; set testflag2 false; set testflag3 false; set testflag4 false; set tracealpha true; set usearcball false; set useminimizationthread true; set usenumberlocalization true; set vectorscale 1.0; set vectorsymmetry false; set vibrationscale 0.5; set waitformoveto true; set wireframerotation false; set zdepth 0; set zoomlarge true; set zslab 50; # 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; } function _setModelState() { select ({3 5 10 12 17 23 29 36 38 42 50 57 62 73 75 79 82 87 98 101 106 113 119 130 138 145 149 151 156 163 167 168 172 177 185 191 196 198 203 211 215 217 222 226 232 240 248 256 263 267 272 274 279 285 292 296 299 300 304 312 316 321 324 326}); Spacefill 1.7; select ({0 7 14 20 26 33 39 47 54 59 66 68:70 76 83 84 95 102 103 110 116 123 125:127 135 142 146 153 160 169 174 182 188 193 200 212 219 223 229 237 245 253 260 264 269 276 282 289 293 301 313 318 325}); Spacefill 1.85; select ({1 2 4 6 8 9 11 13 15 16 18 21 22 24 27 28 30:32 34 35 37 40 41 43:46 48 49 51:53 55 56 58 60 61 63:65 67 71 72 74 77 78 80 81 85 86 88:94 96 97 99 100 104 105 107:109 111 112 114 117 118 120:122 124 128 129 131:134 136 137 139:141 143 144 147 148 150 152 154 155 157:159 161 162 164:166 170 171 173 175 176 178:181 183 184 186 189 190 192 194 195 197 199 201 202 204:210 213 214 216 218 220 221 224 225 227 230 231 233:236 238 239 241:244 246 247 249:252 254 255 257:259 261 262 265 266 268 270 271 273 275 277 278 280 283 284 286:288 290 291 294 295 297 298 302 303 305:311 314 315 317 319 320 322 323}); Spacefill 1.95; select ({19 25 115 187 228 281}); Spacefill 2.0; select BONDS ({0:336}); wireframe 0.0; measures delete; select *; set measures nanometers; font measures 15.0 SansSerif Plain; boundBox off; font boundBox 14.0 SansSerif Plain; boundBox off; unitcell off; font unitcell 14.0 SansSerif Plain; unitcell off; frank on; font frank 16.0 SansSerif Plain; select *; frame 1.1; set unitcell {0.0 0.0 0.0}; unitcell off; font unitcell 14.0 SansSerif Plain; unitcell off; select *; set fontScaling false; } function _setPerspectiveState() { set perspectiveModel 11; set scaleAngstromsPerInch 0.0; set perspectiveDepth true; set visualRange 5.0; set cameraDepth 3.0; boundbox corners {-3.0970001 -0.51600075 -7.421999} {24.284 20.937 19.58} # volume = 15861.099; center {10.5935 10.2105 6.079}; moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0 0.0 0.0} -28.891575 27.901945 0.0; save orientation "default"; moveto 0.0 { 0 -1000 0 118.0} 100.0 0.0 0.0 {10.5935 10.2105 6.079} 17.392593 {0.0 0.0 0.0} 28.454279 27.849842 0.0;; slab 100;depth 0; set slabRange 0.0; set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10; spin on; } function _setSelectionState() { select ({0:326}); set hideNotSelected false; } function _setState() { initialize; set refreshing false; _setWindowState; _setFileState; _setVariableState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay false; set antialiasTranslucent true; set antialiasImages true; spin on; } _setState;