From: Eran H. <era...@we...> - 2007-10-18 16:28:33
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Rolf, You're right. It appears to work in build 11.3.33. I currently have build 11.2.8 loaded. I will try to upgrade. Bob, you requested I send you the state so you can look at it. It appears to be a problem with the older release of Jmol, so perhaps investigating the state printout is not relevant anymore but anyways here it is. # Jmol state version 11.2.8 2007-07-23 12:04; # window state; # height 300; # width 300; initialize; stateVersion = 1102008; refreshing = false; backgroundColor = "[xffffff]"; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; ambientPercent = 45; diffusePercent = 84; specular = true; specularPercent = 22; specularPower = 40; specularExponent = 6; # file state; allowEmbeddedScripts = false; autoBond = true; appendNew = true; applySymmetryToBonds = false; bondRadiusMilliAngstroms = 150; bondTolerance = 0.45; defaultLattice = {0.0 0.0 0.0}; defaultLoadScript = ""; loadFormat = "http://www.rcsb.org/pdb/files/%FILE.pdb"; forceAutoBond = false; minBondDistance = 0.4; percentVdwAtom = 20; load "http://132.77.150.123/cgi-bin/getpdb.pl?1xjo"; # settings; refreshing = false; defaultanglelabel = "%VALUE %UNITS"; defaultcolorscheme = "Jmol"; defaultdistancelabel = "%VALUE %UNITS"; defaultloadscript = ""; defaulttorsionlabel = "%VALUE %UNITS"; defaulttranslucent = 0.5; allowembeddedscripts = true; allowrotateselected = false; applysymmetrytobonds = false; autobond = true; autofps = false; axes = window; axesmode = 0; axesscale = 2.0; bondmodeor = false; bondradiusmilliangstroms = 150; bondtolerance = 0.45; cartoonrockets = false; chaincasesensitive = false; disablepopupmenu = false; displaycellparameters = true; dotsselectedonly = false; dotsurface = true; dynamicmeasurements = false; forceautobond = false; greyscalerendering = false; hbondsbackbone = false; hbondssolid = false; helppath = "http://www.stolaf.edu/academics/chemapps/jmol/docs/ index.htm"; hermitelevel = 0; hidenameinpopup = false; hidenavigationpoint = false; highresolutionflag = false; hoverdelay = 0.5; isspinning = true; justifymeasurements = false; loadformat = "http://www.rcsb.org/pdb/files/%FILE.pdb"; measureallmodels = false; minbonddistance = 0.4; navigationcentered = false; navigationperiodic = false; navigationspeed = 5.0; percentvdwatom = 20; perspectivedepth = true; pickingspinrate = 10; propertyatomnumberfield = 0; propertycolorscheme = "roygb"; propertydatafield = 0; rangeselected = false; ribbonaspectratio = 16; ribbonborder = false; scriptdelay = 0; selecthetero = true; selecthydrogen = true; selectionhalos = false; sheetsmoothing = 1.0; showhiddenselectionhalos = false; showhydrogens = true; showmeasurements = true; showmultiplebonds = true; shownavigationpointalways = false; solvent = false; solventproberadius = 1.2; spinflag = true; ssbondsbackbone = true; testflag1 = false; testflag2 = false; testflag3 = false; testflag4 = false; tracealpha = true; usenumberlocalization = true; vectorscale = 1.0; vibrationperiod = 1.0; vibrationscale = 1.0; zoomlarge = true; zshade = false; # connections; calculate hbonds # label defaults; select none; color label none; background label none; labelOffset = 4 4; labelAlignment = left; labelPointer = off; font label 13 SansSerif Plain; # model state; structure sheet ({0:34}) # model=1 & (1 - 5); structure helix ({35:157}) # model=1 & (6 - 22); structure none ({158:222}) # model=1 & (23 - 31); structure helix ({223:343}) # model=1 & (32 - 47); structure none ({344:352}) # model=1 & (48 - 49); structure sheet ({353:429}) # model=1 & (50 - 58); structure none ({430:443}) # model=1 & (59 - 61); structure sheet ({444:522}) # model=1 & (62 - 71); structure none ({523:560}) # model=1 & (72 - 77); structure sheet ({561:616}) # model=1 & (78 - 85); structure none ({617:624}) # model=1 & (86 - 86); structure sheet ({625:645}) # model=1 & (87 - 89); structure none ({646:702}) # model=1 & (90 - 98); structure helix ({703:805}) # model=1 & (99 - 114); structure none ({806:814}) # model=1 & (115 - 116); structure sheet ({815:842}) # model=1 & (117 - 119); structure none ({843:850}) # model=1 & (120 - 120); structure sheet ({851:932}) # model=1 & (121 - 128); structure none ({933:979}) # model=1 & (129 - 135); structure helix ({980:1052}) # model=1 & (136 - 144); structure none ({1053:1067}) # model=1 & (145 - 146); structure helix ({1068:1112}) # model=1 & (147 - 152); structure none ({1113:1125}) # model=1 & (153 - 154); structure sheet ({1126:1168}) # model=1 & (155 - 159); structure none ({1169:1218}) # model=1 & (160 - 166); structure sheet ({1219:1271}) # model=1 & (167 - 172); structure none ({1272:1295}) # model=1 & (173 - 175); structure helix ({1296:1402}) # model=1 & (176 - 188); structure none ({1403:1418}) # model=1 & (189 - 190); structure sheet ({1419:1448}) # model=1 & (191 - 194); structure none ({1449:1466}) # model=1 & (195 - 203); structure helix ({1467:1524}) # model=1 & (204 - 210); structure none ({1525:1535}) # model=1 & (211 - 212); structure sheet ({1536:1556}) # model=1 & (213 - 215); structure none ({1557:1560}) # model=1 & (216 - 216); structure sheet ({1561:1583}) # model=1 & (217 - 219); structure none ({1584:1603}) # model=1 & (220 - 223); structure sheet ({1604:1630}) # model=1 & (224 - 227); structure helix ({1631:1672}) # model=1 & (228 - 233); structure none ({1673:1852}) # model=1 & (234 - 257); structure helix ({1853:1994}) # model=1 & (258 - 276); structure none ({1995:2000}) # model=1 & (277 - 277); select ({2008}); Spacefill 1.973; select ({0:1176 1186:2000}); color atoms opaque [xadd8e6]; select ({2001 2002}); Spacefill 1.39; select ({1184 1185}); Spacefill 1.7; select ({1177}); Spacefill 1.85; select ({0:1176 1186:2000}); Spacefill 0.0; select ({1178:1180 1182 1183}); Spacefill 1.95; select ({1181}); Spacefill 2.0; select BONDS ({16}); color bonds opaque [xffff00]; wireframe 0.2; select BONDS ({5 7:15 26:2232}); wireframe 0.0; measures = nanometers; font measures 15 SansSerif Plain; select measures ({null}); select ({0:2000}); Cartoon on; boundBox off; ; unitcell off; ; frank on; font frank 16 SansSerif Bold; # orientation/center/spin state; set refreshing false; perspectiveModel = 11; cameraDepth = 3.0; center {19.550499 14.5795 45.547005}; moveto /* time, axisAngle */ 0.0 { 0 1000 0 20.17} /* zoom, translation */ 100.0 0.0 0.0 /* center, rotationRadius */ {19.550499 14.5795 45.547005} 31.976118 /* navigation center, translation, depth */ {0.0 0.0 0.0} -45.40585 19.49943 50.0;; slab 100;depth 0; spinX = 0;spinY = 5;spinZ = 0;spinFps = 30; refreshing = true;refresh; spin on; # selection state; select ({2009:2257}); hide selected; select ({0:2257}); refreshing = true; Best, Eran |