Pat Carroll recently posted some things about a simple web page using the
JmolApplet. I thought it would be a good idea to use it as an example to
describe the parameters to the JmolApplet. I have replace the angle
brackets with square brackets to make sure this gets through email filters
...
[html]
[head]
[title]Structure 457[/title]
[/head]
[body bgcolor="#FFF6C4" text="#0000FF"]
[h3]Structure 457[/h3]
[applet code ="JmolApplet"
archive="JmolApplet.jar"
codebase="./jmol"
width = "400" height = "400"]
[param name="bgcolor" value ="#CCFFFF"]
[param name="load" value = "cell457b.pdb"]
[param name="script" value="
select all;cpk on;cpk 0.40;wireframe on;
wireframe 0.15;select oxygen;
cpk 0.1; wireframe 0.1"]
[/applet]
[/body]
[/html]
code="JmolApplet"
-----------------
Name of the class to run
always required
always *exactly* the same
archive="JmolApplet.jar"
------------------------
Name of the .jar (java archive) file that holds the classes
always required
always *exactly* the same (unless you rename the file :-)
codebase="./jmol"
-----------------
This is the name of the directory where JmolApplet.jar is pulled from
the codebase attribute is optional
In the sample above, it is being pulled from a subdirectory named
'jmol' which is below the directory where the .html page is located
If not specified, then JmolApplet.jar is pulled from the
same directory as the .html page.
If specified, the JmolApplet.jar is pulled from the specified
directory.
a subdirectory:
codebase="someSubdirectory/"
a sibling directory:
codebase="../jmol"
an absolute path:
codebase="/jmolAppletDirectory"
You should NEVER have a hostname in this parameter
codebase="http://some.web.server/some/directory"; <<<< WRONG!
not even
codebase="http://my.web.server/jmol"; <<<< BAD!
If you get this parameter wrong, the applet will *not* be loaded
and you will see a red X.
param name="load" value="cell457b.pdb"
--------------------------------------
The name of the molecular model to load
optional - but if you don't have one then you better
have a script someplace to load molecular models :-)
In the sample above, it is being pulled from the same
directory as the .html page
Could be in a subdirectory:
value="models/cell457b.pdb"
or a sibling directory:
value="../models/cell457b.pdb"
or an absolute directory:
value="/allTheModels/cell457b.pdb"
or even a cgi that does a database lookup:
value="/cgi-bin/loadMolecule.cgi?format=pdb&id=1crn
This should also NOT be a fully qualified URL that contains
a hostname
value="http://some.web.server/models/cell457b.pdb"; <<<< WRONG!
nor
value="http://my.web.server/models"; <<<< BAD!
If you get this wrong, your model will not be loaded and you will
see a blank JmolApplet ... white, black, or the bgcolor you chose
If things are not working, open up your Java Console and see what
kinds of messages are printed out there.
Good Luck!
Miguel
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