The
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 and uses
Javascript 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
buttons.
You will need to be comfortable using the command line interface to use
the tools described here. Eventually, I hope to create a GUI
using something reasonably portable like java, but for now you need a
computer capable of running
perl scripts
from the command line. Essentially all *NIX systems have this
capability (LINUX, BSD, MacOS X). I do not believe perl is
normally installed on MS Windows, but can be added.
Step 1: Gather all the files
you will need into one directory.
Atom
coordinate file: 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
.cube
format. 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 and
convert them using my perl script
MacMolPltgridtocube.pl.
Again,
I recommend that all these files should be gzipped. 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.
Step 2: Generate the raw page
using my
orbtohtml.pl
script.
A) If you only have a few orbitals skip
this step. Create a text file with one file name per line.
The first line should contain the name of the file with the atom
coordinates. The file names of the .cube files should follow in
the order you wish them to appear in the menus.
B) Within the directory containing the files run the orbtohtml.pl perl
script. With the following command:
perl [path to script]/orbtohtml.pl
name_of_file_created_in_step_A >name_of_html_file_you_want_created
or
perl [path to script]/orbtohtml.pl
name_of_coordinate_file name_of_orb1_file [name_of_orb2_file...]
>name_of_html_file_you_want_created
The ">" symbol before the name of
the file you want the data to go to is necessary.
Step 3: Edit the .html file
created in step 2.
A) Set the relative path to the Jmol
installation on your server. Search for the following lines in
the page source and adjust appropriately.
<script src="../../Applets/Java/Jmol/Jmol.js"></script>
jmolInitialize("../../Applets/Java/Jmol");
B) Add explanatory text using your favorite .html editor.
C) If adjustments need to be made to the magnitude of function where
the surfaces are drawn, I suggest searching the page source by orbital
name and replacing the 0.06 in the isosurface command with an
appropriate value.
Step 4: 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
server.
Last Updated: 5/24/06