Re: [Jmol-users] sample JmolApplet

[Philip B. <pb...@sa...>]

Thanks Miguel!

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
>
>
>
>
>
>
>
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