[LON-CAPA-admin] JSmol and /adm/ folder location

[Stuart Raeburn]

Bob,

> I've coded up a problem using JSmol and it does work.  The only
> documentation I found was in this post:
>
> http://install.lon-capa.org/bugzilla/long_list.cgi?buglist=4729

My specific comment relevant to jsmol is comment #13 of that bug:
http://bugs.loncapa.org/show_bug.cgi?id=4729#c13

> There is another example invocation following this one in the post which
> shows many options being set.

This style of calling jmol:

<script src="/adm/jmol/Jmol.js" type="text/javascript"></script>
<script type="text/javascript">jmolInitialize("/adm/jmol"); jmolApplet(250,
"load /res/sfu/somepath/somefile.pdb");
</script>

has the advantage that it will work on LON-CAPA instances which only  
support jmol (i.e., those running 2.11.0 and older) as well as on  
LON-CAPA instances which support jsmol, (i.e., those running 2.11.1),  
where, by default, jsmol/HTML5 will be used.

The other style of calling jmol, which uses a Jmol object, and is  
described at: http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
will not display on LON-CAPA 2.11.0 and older.

You will also find documentation for jmol at http://wiki.jmol.org
and for jsmol at: http://wiki.jmol.org/index.php/JSmol

> The one I used worked for the Chrome and Firefox browsers but not for
> Safari and Internet Explorer.  This might be solved with the second
> invocation and setting the proper variable but I have no idea which
> combination(s) might fix it.

I have just replied to this question separately via the lon-capa-users  
list, (where you originally posted about this at the end of October).  
See:
http://mail.lon-capa.org/pipermail/lon-capa-users/2015-November/004981.html


Stuart Raeburn
LON-CAPA Academic Consortium

Quoting Bob Gonzales <rgonzal at binghamton.edu>:

> Lee,
>
> I've coded up a problem using JSmol and it does work.  The only
> documentation I found was in this post:
>
> http://install.lon-capa.org/bugzilla/long_list.cgi?buglist=4729
>
> I used this invocation, as mentioned in the post:
>
> <script src="/adm/jmol/Jmol.js" type="text/javascript"></script>
> <script type="text/javascript">jmolInitialize("/adm/jmol"); jmolApplet(250,
> "load /res/sfu/somepath/somefile.pdb");
> </script>
>
> There is another example invocation following this one in the post which
> shows many options being set.
>
> The one I used worked for the Chrome and Firefox browsers but not for
> Safari and Internet Explorer.  This might be solved with the second
> invocation and setting the proper variable but I have no idea which
> combination(s) might fix it.
>
> Bob Gonzales
> Binghamton University
> Chemistry Dept
>
>
>
> On Mon, Nov 9, 2015 at 1:36 PM, Bynum, Lee Hamilton <leebynum at illinois.edu>
> wrote:
>
>> Hello,
>>
>> I've been asked to confirm that 2.11.1 includes JSmol.  Looking at the
>> documentation, it appears that it should.  However, I've looked into the
>> /home/httpd/html/adm/ folder and have not found JSmol or updated versions
>> of jmol.  I suspect I am either looking in the wrong location or that the
>> javascript modules didn't update with the updater.  The former is much more
>> likely.
>>
>> Can someone point me to where these modules live on the server?
>>
>> Thanks,
>>
>> Lee
>> _______________________________________________
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