For those of us who are not on the developers mailing list, I
discovered that the following message, which is archived in the
developers list, is very important
http://www.mail-archive.com/[email protected]/msg04660.html
I couldn't get isosurfaces to work in my web pages until I read the
following comment:
"path/to/filename.cube"
-----------------------
path name to your gaussian .cube file. This *must* be in double quotes (as
with the pmesh command).
I kept trying to create isosurfaces using the following code
<script>
jmolInitialize("../../reuse"); //required to initialize codebase
jmolApplet(400, "load carbocation_LUMO.cub; isosurface pos
0.045 carbocation_LUMO.cub;", "carbocation")
</script>
But of course it wouldn't work because my path was not in double
quotes. After finding a pmesh example I realized that I should use
single quotes around my script, and double quotes around the path.
So, the following code did work...
<script>
jmolInitialize("../../reuse"); //required to initialize codebase
jmolApplet(400, 'load carbocation_LUMO.cub; isosurface
posSurf 0.06 "carbocation_LUMO.cub"; isosurface negSurf -0.06
"carbocation_LUMO.cub"', "carbocation")
</script>
and then I found out the button code would work too! Of course, this
only works if you remember to use the new Jmol.js file (I had to quit
and restart my browser before the button code would work properly,
but YMMV).
<form>
<script>
jmolInitialize("../../reuse"); //required to initialize codebase
jmolApplet(400, 'load carbocation_LUMO.cub;', "carbocation")
jmolButton('isosurface posSurf 0.06 "carbocation_LUMO.cub";
isosurface negSurf -0.06 "carbocation_LUMO.cub"'," ");
jmolHtml("Show LUMO");
</script>
</form>
Woo hoo! A quick demo of the buttons bringing up different MO's is here.
http://www.wsc.ma.edu/cmasi/organic/carbocation_stabilization/ carbocation.html
Thanks Miguel, Richard, et al.
Chris
On Sep 30, 2005, at 5:22 PM, Miguel wrote:
Jmol prerelease 10.00.42 is now available from
http://www.jmol.org/files
This release features support for coloring .cub file isosurfaces based
upon color mapping from another .cub file.
Surface are colored using a red->orange->yellow->green->blue rainbow,
where red represents minimum values and blue represents maximum values.
If absolute data values are not provided then Jmol will calculate the
range based upon the actual data values calculated for the surface points.
You need to supply your own cube files, presumably from gaussian or equiv.
Example:
load "ch3cl-density.cub"; # read in the molecule - old functionality
isosurface mySurface 0.0004 "ch3cl-density.cub"; # old functionality
isosurface mySurface color "ch3cl-esp.cub"; # new functionality
color isosurface translucent;
OR, put it all on one line:
isosurface mySurface 0.0004 "ch3cl-density.cub" color "ch3cl-esp.cub";
OR, specify your own absolute range for color data values:
isosurface color absolute -0.1 0.5 "ch3cl-esp.cub";
Note that the subcommand names 'color' and 'absolute' are subject to change.
Thanks to Richard Spinney of Ohio State University (USA) for help on this.
It looks pretty cool ... Enjoy!
Miguel
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