[LON-CAPA-users] Jsmol with Internet Explorer and Safari

[Stuart Raeburn]

Bob,

> The file name does not contain the extension .bin, but if the URL was
> being examined instead of the file name, then the string ".bin" does
> appear (in .binghamton).

If I use the IP address for loncapa7.chem,binghamton.edu instead of  
the hostname, i.e.,  
http://128.226.130.234/res/msu/raeburn/testing/jmol/jsmolwebpage.html

then Safari will display the molecule in jsmol without error.

That supports my idea that the string: .bin within chem.binghamton.edu  
is causing jsmol to consider that the "load caffeine.mol" call in  
jmolApplet() is a request for a binary file.

Stuart Raeburn
LON-CAPA Academic Consortium


Quoting Stuart Raeburn <raeburn at msu.edu>:

> Bob,
>
>> I've coded up my first problem with Jsmol and it works fine on the latest
>> Chrome and Firefox.  But it doesn't work on Internet Explorer 11 or Safari
>> (latest).
>
> This issue appears to be specific to the binghamton servers. I am able
> to display an example web page of mine (published public) which uses
> jmol/jsmol:
>
> /res/msu/raeburn/testing/jmol/jsmolwebpage.html
>
> successfully in Safari on a number of LON-CAPA servers in the network,
> apart from the ones in your domain. (I am also able to display that
> resource from servers in your domain if I use Firefox or Chrome).
>
> When I attempt to use Safari to display that page on:
> loncapaN.chem.binghamton.edu (N = 2, 3, 5, 6, or 7) two errors are displayed:
>
> (a) A dialog box with the message: "JSmolCore.js: synchronous binary
> file transfer is requested but not available"
> and then (if I click "OK") some seconds later:
>
> (b) A dialog box with the message:
>
> Error connecting to server:
> http://your.server.here/jsmol.php?call=getRawDataFromDatabase&database=_&query=http%3A%2F%2Floncapa7.chem.binghamton.edu%2Fres%2Fmsu%2Fraeburn%2Ftesting%2Fjmol%2Fcaffeine.mol&encoding=base64
>
> Looking at the jsmol documentation:
> http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
>
> (see: "Reading binary files" section)
>
> I find that jsmol.php will be called if a binary format file (gz, zip,
> pse, etc.) is requested from Safari, Chrome, or MSIE, and a jsmol.php
> file needs to be used to convert the binary data to BASE64 format. The
> documentation states jsmol.php is a "A server-side PHP utility that
> allows a number of functions that can increase the platform and browser
> compatibility of JSmol".
>
> By default http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php will be used.
> However, if you modify /home/httpd/html/jmol/Jmol.js by modifying this line:
>
> serverURL: "http://your.server.here/jsmol.php", // required for binary
> file loading (.bin .gz .zip .jpg .png .jmol .smol .spartan .mrc or .pse
> files).
>
> and replace http://your.server.here/jsmol.php with the hostname of your
> server (and an appropriate path) you could use a local jsmol.php file,
> and thereby override the default behavior of jmolInitialize().
>
> You would need to obtain jsmol.php from the jmol binary (from
> http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/Jmol-14.2.13_2015.03.23-binary.zip/download ) because the jmol-loncapa.zip file included in the LON-CAPA 2.11.1 tarball does not   
> include
> it.
>
> What is odd about this is that the caffeine.mol file (MIME:
> chemical/x-mdl-molfile) is not a binary file, and I am able to download
> this text file directly via:
> http://loncapa7.chem.binghamton.edu/res/msu/raeburn/testing/jmol/caffeine.mol
>
> The documentation does say:
>
> 'These "extensions" can appear anywhere in a file name to trigger the
> binary access mode. So, for example, if you rename any file to include
> .bin anywhere in its name, that will instruct JSmol to read it as a
> binary file'.
>
> The file name does not contain the extension .bin, but if the URL was
> being examined instead of the file name, then the string ".bin" does
> appear (in .binghamton).
>
>
> Stuart Raeburn
> LON-CAPA Academic Consortium
>
> Quoting Bob Gonzales <rgonzal at binghamton.edu>:
>
>> Hi,
>>
>> I've coded up my first problem with Jsmol and it works fine on the latest
>> Chrome and Firefox.  But it doesn't work on Internet Explorer 11 or Safari
>> (latest).  The both complain about the file format.  IE says 'unrecognized
>> file format for file xxx' and Safari says it doesn't know how to open the
>> binary file.
>>
>> I'm using .mol files.
>>
>> I'm invoking the viewer with the following code:
>>
>> <script src="/adm/jmol/Jmol.js" type="text/javascript"></script>
>> <script type="text/javascript">jmolInitialize("/adm/jmol");</script>
>> <script type="text/javascript">jmolApplet(150,"background [xFFFFCC]; load
>> ../Graphics/type04/$correctMolecularGeometry.mol");</script>
>>
>> It would be great to get this to work on IE since that is what is available
>> on our instructional computers.
>>
>> Thanks,
>> Bob Gonzales
>
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