Hi Pino,
It looks like the j2s scripts aren't loading. I think I can remove the data
directory, which will make 0.8 much, much smaller and easier to install.
However, when I look at the page source of your page, something very odd is
going on. All the content added by the shortcode is being marked up with HTML.
Compare:
Your site:
> <p><script type="text/javascript"></p>
> <p>// 1/21/2013 10:54:15 PM -- adds image handling</p>
> <p>var jmolApplet0; // set up in HTML table, below</p>
> <p>// logic is set by indicating order of USE -- default is HTML5 for this
> test page, though
> var use = "HTML5" // JAVA HTML5 WEBGL IMAGE are all otions
> var s = document.location.search;</p>
> <p>// Developers: The _debugCode flag is checked in j2s/core/core.z.js,
> // and, if TRUE, skips loading the core methods, forcing those
> // to be read from their individual directories. Set this
> // true if you want to do some code debugging by inserting
> // System.out.println, document.title, or alert commands
> // anywhere in the Java or Jmol code.</p>
> <p>Jmol._debugCode = (s.indexOf("debugcode") >= 0);</p>
> <p>jmol_isReady = function(applet) {
> Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
> } </p>
> <p>var xxxx = document.location.search
> if (xxxx.indexOf("_USE=") > 0)xxxx = xxxx.substring(0, xxxx.indexOf("_USE=")
> - 1);
> if (xxxx.length == 5 || xxxx.length == 0) {
> xxxx = (xxxx + "?1crn").substring(1,5)
> script = 'h2oOn=true;set animframecallback "jmolscript:if
> (!selectionHalos) {select model=_modelNumber}";'
> +'set errorCallback "myCallback";'
> +'set defaultloadscript "isDssp = false;set defaultVDW
> babel;if(!h2oOn){display !water}";'
> +'set zoomlarge false;set echo top left;echo loading XXXX...;refresh;'
> +'load "http://www.rcsb.org/pdb/files/XXXX.pdb";set echo top
> center;echo XXXX;'
> +'spacefill off;wireframe off;cartoons on;color structure;spin off;'
> script = script.replace(/XXXX/g, xxxx)
> } else {
> script = unescape(xxxx.substring(1))
> }</p>
> ....
One of mine:
> <script type="text/javascript">
>
> // 1/21/2013 10:54:15 PM -- adds image handling
>
> var jmolApplet0; // set up in HTML table, below
>
> // logic is set by indicating order of USE -- default is HTML5 for this test
> page, though
> var use = "HTML5" // JAVA HTML5 WEBGL IMAGE are all otions
> var s = document.location.search;
>
>
> // Developers: The _debugCode flag is checked in j2s/core/core.z.js,
> // and, if TRUE, skips loading the core methods, forcing those
> // to be read from their individual directories. Set this
> // true if you want to do some code debugging by inserting
> // System.out.println, document.title, or alert commands
> // anywhere in the Java or Jmol code.
>
> Jmol._debugCode = (s.indexOf("debugcode") >= 0);
>
> jmol_isReady = function(applet) {
> Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
> }
>
> var xxxx = document.location.search
> if (xxxx.indexOf("_USE=") > 0){
> xxxx = xxxx.substring(0, xxxx.indexOf("_USE=") - 1);
> }else{
> xxxx = '';
> }
> if (xxxx.length >= 5 || xxxx.length == 0) {
> xxxx = (xxxx + "?cube").substring(1)
> script = 'h2oOn=true;set animframecallback "jmolscript:if
> (!selectionHalos) {select model=_modelNumber}";'
> +'set errorCallback "myCallback";'
> +'set defaultloadscript "isDssp = false;set defaultVDW
> babel;if(!h2oOn){display !water}";'
> +'set zoomlarge false;set echo top left;echo loading cube...;refresh;'
> +'isosurface OBJ "http://localhost/tmp/cube.obj";set echo top
> center;echo cube;'
> +'spacefill 23%;wireframe 0.15;color cpk;spin off;'
> script = script.replace(/cube/g, xxxx)
> } else {
> script = unescape(xxxx.substring(1))
> }
> ...
I don't know where all the <p></p> tags are coming from, but I imagine they are
killing the loader script. Do you have another plugin installed that does some
kind of markup processing? Can you try a different theme? I suspect it may be
this problem:
http://ipanelthemes.com/kb/misc/wordpress/fixing-themes-custom-wpautop-priority/
Hope this helps.
Jim
On Jun 11, 2014, at 3:55 PM, pino.stricc...@libero.it wrote:
> Jim, i uploaded the files and activated the plugin in wordpress installation.
> I
> wrote this post with this code [jsmol pdb='1crn' caption='caption' commands
> ='']
> But nothing happens .... http://molecolevive.altervista.org/blog/trial-for-
> jsmol-plugin/
> What have i done wrong?
> Pino
>
>> ----Messaggio originale----
>> Da: jim.hu.bio...@gmail.com
>> Data: 09/06/2014 19.26
>> A: <jmol-users@lists.sourceforge.net>
>> Ogg: [Jmol-users] JSmol2wp wordpress plugin ver 0.6 alpha
>>
>> Hi All,
>>
>> I just pushed a new version of JSmol2wp to GitHub. I've now included a full
> zip archive of this version to make it easier to download and install.
>>
>> https://github.com/jimhu-tamu/wordpress/tree/master/plugins
>>
>> I've tested this on my laptop (OSX Lion), on our departmental server (Ubuntu
> VM), and my own Wordpress blog on a shared GoDaddy host. It works on all of
> these. However, Henry Rzepa and I have been working offline to solve the
> problem of the plugin not working on his wordpress installations, so
> something
> still needs to be fixed for it to be reliably usable.
>>
>> The most recent version also adds the ability to add script commands and to
> put back the command line input box. The former should be useful for
> overriding
> the default configurations after the applet loads.
>>
>> Jim
>> =====================================
>> Jim Hu
>> Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>
>> ------------------------------------------------------------------------------
>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>> Find What Matters Most in Your Big Data with HPCC Systems
>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>> http://p.sf.net/sfu/hpccsystems
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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