instructions here are for semi-automatically creating pages that look
and work like my
chlorine atomic orbital page
. The page contains one Jmol java applet
to allow the user to choose
up to 4 orbitals (isosurfaces) to display simultaneously on the atom or
molecule in Jmol. A limited number of options for color and
surface type are also provided in the form of user selectable radio
These java applications replace the perl scripts that I provided
previously. They are still accessible here
Be aware that the perl script for converting MacMolPlt grid files to
cube files does not correct a scaling error that the java application
does. The grid origin and
increment was a factor of 1.88973 too small in the perl script, because
I was working in Angstroms instead of Bohr.
: Gather all the files
you will need into one directory.
This file can be any of the formats from
which Jmol can read atom coordinates (.pdb, .mol, GAMESS .log,
etc...). To save space on the server and bandwidth these files
should be gzipped.
Surface file for each orbital:
These files must be in the Gaussian
. Gaussian can generate these directly. If
you use GAMESS
you will need to do some conversion. One route for GAMESS is to
export the surfaces you want from MacMolPlt
convert them using my java application MacMolPlt_Surface_to_Gaussian_Cube.jar
(link should download zip archive).
I recommend that all these files should be gzipped (the java
application does this automatically). Choose the
names for these files carefully. The basename of the file will be
used as the text for the menu item used to display this orbital.
The script assumes that the best display level is (+/-)0.06 for the
isosurface. Optimize your cube file grid size for this, or edit
the resulting page to appropriate levels for your data.
Generate the raw page
using my Orbitals_to_Web.jar
(link should download zip archive) java application.
A) Set the relative path to the Jmol
installation on your server. The default is shown in the text box.
B) Choose the file that contains the atom coordinates.
C) Choose the rendering mode: small dot for just one atom, wireframe
for molecules. There are other options but you will have to
D) Choose the page format. At this point it is just the number of
orbitals that may be simultaneously displayed on the atom or
molecule. Four is the maximum possible.
E) Add the files containing the orbital surfaces to the Orbital Files
list. Drag them to the order you wish them to appear in the
menus. If you pick incorrect files they may be deleted by
selecting them and then clicking on the "Delete Selected" button.
F) To generate the .html file click on the "Save .html as ..."
button. You will get to choose the file name and save location.
Edit the .html file
created in step 2.
A) Add explanatory text using your
favorite .html editor. (look for text between < and > for
suggested places to add stuff.
C) If adjustments need to be made to the magnitude of the function
the surfaces are drawn, I suggest searching the page source by orbital
name and replacing the 0.06 in the isosurface command with an
Put your new page and
all the .gz files on your server in a single directory. Make sure
it has the proper relative relation to the Jmol installation on your
Last Updated: 7/21/06