[LON-CAPA-users] {Disarmed} Re: Jsmol with Internet Explorer and Safari

Bob Gonzales rgonzal at binghamton.edu
Tue Nov 10 12:38:52 EST 2015


Stuart,

I did see the comments in the wiki about extra server side processing for
binary files but because I was using .mol files I didn't think that was the
issue.  I will try the binary file fix.

Thank you for the help.
Bob

On Mon, Nov 9, 2015 at 10:26 PM, Stuart Raeburn <raeburn at msu.edu> wrote:

> 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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>>
>
>
>
> Stuart Raeburn, Ph.D.          LON-CAPA (cell) +1 517 881-3308
> Dept. Physics & Astronomy      Other (cell) +1 734 277-2795
> Michigan State University      raeburn at msu.edu
> MI 48824 USA
>
>
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