Hi,
I have a JVXL file containing MO data that I am trying to display. I can see
the molecule, but I can't see the MO. I have tried various scripts to turn on
the MO, to no avail. Below I have copied the relevant part of my Web page. I
am using 'mo HOMO;' as the script, but I have tried several other commands,
including none, to no avail. How do I display the MO? Does the fact that I
load inline prevent the MO from being displayed?
-- Bob
<script type="text/javascript">
// <!--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638,
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ?\n-32
-4.286028 -4.170638 -6.45537 ANGSTROMS\n80 0.12402356 0.0 0.0\n80 0.0 0.184445
0.0\n80 0.0 0.0 0.1257623\n6 6.0 0.0 0.0 0.0\n6 6.0 1.5335295 0.0 0.0\n8 8.0
2.3333447 1.1734227 0.0\n6 6.0 2.3022442 2.08224 -1.0298198\n6 6.0 1.9440373
3.352165 -0.783915\n6 6.0 2.166842 4.391685 -1.8063345\n8 8.0 1.4540279
5.5320063 -1.5695299\n6 6.0 1.4419276 6.5410266 -2.576349\n6 6.0 0.4292079
7.5804462 -2.13194\n1 1.0 0.699213 8.036855 -1.1707217\n1 1.0 0.36370665
8.384962 -2.8751543\n1 1.0 -0.57431144 7.149238 -2.0169382\n1 1.0 2.4541469
6.9775352 -2.6722505\n1 1.0 1.1674224 6.103718 -3.555268\n8 8.0 2.9358563
4.365084 -2.7551525\n1 1.0 1.4746284 3.6545703 0.16250335\n1 1.0 2.660351
1.708333 -1.9975383\n6 6.0 2.025939 -0.95221835 -1.101621\n1 1.0 1.6514318
-1.9706379 -0.937718\n1 1.0 1.6784323 -0.62881225 -2.0926402\n1 1.0 3.1216602
-1.0091194 -1.1394216\n1 1.0 1.869836 -0.3798073 0.9982192\n6 6.0 -0.86121655
0.62561214 -1.0898211\n6 6.0 -0.8380163 2.0938404 -1.2457241\n6 6.0 -0.81681573
2.6353507 -2.5209484\n7 7.0 -0.79011524 3.084059 -3.6053698\n6 6.0 -1.1576223
2.898656 -0.16150327\n7 7.0 -1.4360279 3.5764692 0.75561434\n1 1.0 -0.59091145
0.1594031 -2.0609396\n1 1.0 -1.9027367 0.2891056 -0.885317\n1 1.0 -0.29010567
-1.0688207 0.08750176\n1 1.0 -0.314506 0.47200906 0.95541835\n-1 35 90 35 90
Jmol voxel format version 1.4\n# \n0.05 361 -1362 1362 -1.0 1.0 -1.0 1.0
rendering:isosurface ID "homop" fill noMesh noDots notFrontOnly frontlit\n
117879 5 75 6 74 5 6154 7 72 9 71 9 71 9 72 7 75 3 5915 7 72 9 70 11 69 11 69
11 70 10 71 7 5834 4 74 9 70 11 68 13 67 13 67 13 68 12 69 9 73 5 5754 7 71 11
68 13 67 13 66 14 67 13 67 13 68 11 71 7 5752 8 71 11 68 13 66 14 66 15 65 15
66 13 68 11 71 7 334 2 77 4 77 2 5256 8 70 12 68 13 66 14 66 14 66 14 67 13 68
11 71 7 173 3 75 6 74 7 72 8 73 6 75 4 5176 8 71 11 68 12 67 14 66 14 66 14 67
12 69 10 73 4 173 6 73 8 71 10 70 9 72 8 73 6 5176 6 72 10 69 11 69 12 68 12 68
11 70 9 73 5 175 2 75 7 72 9 71 10 70 10 70 9 72 7 5256 6 72 9 71 9 71 9 72 7
75 2 256 3 75 7 72 9 71 9 71 9 71 9 72 7 5993 7 72 9 71 9 71 9 71 8 74 5 5801 4
74 7 73 7 29 5 39 7 28 7 40 4 28 8 73 7 73 6 5800 5 74 7 72 9 71 9 71 9 28 4 40
7 29 5 75 5 77 1 4709 4 77 3 1008 7 72 9 70 10 70 10 71 9 72 7 75 3 4743 3 76 5
75 5 77 3 928 7 72 9 70 10 70 10 71 9 72 7 75 3 4742 4 76 5 75 5 76 4 928 6 73
8 71 10 70 10 71 9 72 7 4820 3 77 5 75 5 76 4 929 4 75 7 72 8 72 8 73 7 74 5
4822 1 78 4 76 4 77 3 1010 5 74 6 74 6 75 5 4982 2 78 2
279630\nW4?A7Kv(0Dwm)s(RKaX!S@<V0QmxtbS9C3Omxtb9B|#HVR:PQ|RBGb<HJB!-8:#vKSHeHZQ`&a...@t&u(DQOaJ[6>OJRKgiv\'trpm+r...@f7ob*7gzt4@>dX!q:`...@ag|ga{$l{\'-v9-wuv+p2wm...@[s7k>]u[Fw,*\'Lq##%$l|R-5pEO=W?69JmAOWT<W\'_XQcN[n*cJOw\'m31X,GNHDmuXy^Izv+kA2<axMh_lP:ZqF1*-<!,lA;p.)w*)E8BQXQleUe,Z60]N<rx[zeCzs(b;23c`]buFGwJ6\/3cg...@a`tv&vjk4dj4:,+eS\'c\'e5j-mMYzUS>YS*ES9Xc^Hj9!cv|wgBP74=JC\'+g^uny...@kon^c:I2*w,@re<=YqVOVpfMXiEKqP2Tntyt{_e125nBUkx4btL\'&^\'tFOE{#YXCwPuT[HX|;8XXq*P]T\/O4;9TBwZPXsOS.STEk,e*rMsrUZOT^]s.d7GeQvLo8KU!4ql(*(drzx]gjazd...@g8kn@>FWtce=9e2^F<;CSlmC.(\/ErmVLLSazymkr&w+OcjfT\/H6A]^LK+v#w=Q45JQM,UG`631[smx\/9\'-\']3h\'g9{EKKwDX7t\'y#<P^baZLp4S^+DXejjbR6Qx$>R^ecZF##uk(=JOK=%x|m<)&\/K6![mrm[4>TINK2tJrk|pN0G()UDG)N#y.7cro?(3N?QDKA:5m!)>{Wl{yxfSHnw\/BcymJ!Zd-X_ma0_Za6)s46n+]z=eap0dabuyll+gc`e99d].itfk...@lqvz)3$xJgwBo>IiI<C:WTZ;.`\/[;[%o%\/1.1$$)9S4]Yr{pXu2;@^=FxUl^Jh0rFC6VA]Ca;A3B\/u!dz%.rz7L[`=LdD2))1Dfa1ZFI8P>-e(kr-tJc;^rH%|#g$$#8O;In3.;ibxkw)h...@]lqnd\/GICGPinIc!MXjn.bD(Q7Bb[=q]W1%`*45Zz!A1))0a`l...@%w8p$9xr,vxM.MsTf(8\'x#=YN_<];G[vysz96LWZVJ5VT.wqH^r:dd2x7N9sRHX-9[OiXX+tjb0C?EfL<44;Ll{v{jisss1NEPSN@(0HCpc4=_JFE[)u;<&K*9Qv9oKovNQxE|,dD[|bRJIReI,T8;4$\'l#T#rgBYT\'x|diBN^FGWn`HQaA9p7IrX1j:iC|*6N1>DStklvgLFUz)F,^jlfU7NFw6ixct+;6qXN0-k7RG[K733&z%HXj7W;uxg...@zmpfl++n\/&\/6`j(S.tiBS;9qARHJ\/3`8gs...@wkt8hpdf.\/&&*)<;_]snyS6($+?aU+OAqyi>F4bJ&|m\'R`{3YB5ahgED38-C1gBbhXS[o|]MHOap]X^q\n|~1361
\n#-------end of jvxl file data-------\n# cutoff = 0.05; pointsPerAngstrom =
8.062984; nSurfaceInts = 361; nBytesData = 3736; bicolor map\n# created using
Jvxl.java\n# precision: false nColorData 1362\n# isosurface homop cutoff +0.05
mo homo fill;\n# isosurface ID "homop" fill noMesh noDots notFrontOnly
frontlit\n# bytes read: 0; approximate voxel-only input\/output byte ratio:
2794:1\n';
}
// -->
</script>
<table style="margin-left:auto; margin-right:auto;">
<tr><td class="whiteTable" style="text-align:center;">
<script type="text/javascript">
var jmolMol0 = getMol();
var bgcolor = 'white';
var height = 250;
var width = 250;
var addlScripts = 'mo HOMO';
</script>
<!-- method for displaying Jmol, http://jmol.sourceforge.net, in a
jsp page
* Java variables that must be defined in the host page:
* String pathToRoot
* String jmolJSCmds (semicolon-separated list of commands from Jmol
* Javascript library, http://jmol.sourceforge.net/jslibrary/ )
* int jmolNum
* JS variables that must be defined in the host page:
* string variables jmolMol0, bgcolor,
* addlScripts (semicolon-separated list of Jmol scripting
commands)
* int variables width, height
* Use <%@ include page="" %> in the host page.
-->
<script type="text/javascript">
// <!--
function jmolLoaded0() {
jmolLoadInline(jmolMol0, '0');
jmolScript(addlScripts, '0');
}
jmolInitialize('../nosession/jmol');
bgcolor = bgcolor.replace(/#/g, 'x'); // if color has format of HTML tags
if (!isNaN(parseInt(bgcolor, 16))) bgcolor = 'x' + bgcolor; // if color is
hexadecimal only
if (bgcolor.charAt(0) == 'x') bgcolor = '[' + bgcolor + ']'; // if color is
not English
var jmolStartScript = 'background ' + bgcolor
+ '; javascript jmolLoaded0(); ';
jmolApplet([width, height], jmolStartScript, '0');
// -->
</script>
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