This is very helpful to a novice. I think I figured out to select multiple atoms and hence muck around with bond fatness.
Phil
On Jan 28, 2004, at 5:36 PM, Miguel Howard wrote:
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
------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
