<div dir="ltr"><div><div><div>Stuart,<br><br></div>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. <br></div><br>Thank you for the help.<br></div>Bob<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 9, 2015 at 10:26 PM, Stuart Raeburn <span dir="ltr"><<a href="mailto:raeburn@msu.edu" target="_blank">raeburn@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Bob,<span class=""><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The file name does not contain the extension .bin, but if the URL was<br>
being examined instead of the file name, then the string ".bin" does<br>
appear (in .binghamton).<br>
</blockquote>
<br></span>
If I use the IP address for loncapa7.chem,<a href="http://binghamton.edu" rel="noreferrer" target="_blank">binghamton.edu</a> instead of the hostname, i.e., <a href="http://128.226.130.234/res/msu/raeburn/testing/jmol/jsmolwebpage.html" rel="noreferrer" target="_blank"><font color="red"><b>MailScanner warning: numerical links are often malicious:</b></font> http://128.226.130.234/res/msu/raeburn/testing/jmol/jsmolwebpage.html</a><br>
<br>
then Safari will display the molecule in jsmol without error.<br>
<br>
That supports my idea that the string: .bin within <a href="http://chem.binghamton.edu" rel="noreferrer" target="_blank">chem.binghamton.edu</a> is causing jsmol to consider that the "load caffeine.mol" call in jmolApplet() is a request for a binary file.<span class=""><br>
<br>
Stuart Raeburn<br>
LON-CAPA Academic Consortium<br>
<br>
<br></span><div><div class="h5">
Quoting Stuart Raeburn <<a href="mailto:raeburn@msu.edu" target="_blank">raeburn@msu.edu</a>>:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Bob,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've coded up my first problem with Jsmol and it works fine on the latest<br>
Chrome and Firefox. But it doesn't work on Internet Explorer 11 or Safari<br>
(latest).<br>
</blockquote>
<br>
This issue appears to be specific to the binghamton servers. I am able<br>
to display an example web page of mine (published public) which uses<br>
jmol/jsmol:<br>
<br>
/res/msu/raeburn/testing/jmol/jsmolwebpage.html<br>
<br>
successfully in Safari on a number of LON-CAPA servers in the network,<br>
apart from the ones in your domain. (I am also able to display that<br>
resource from servers in your domain if I use Firefox or Chrome).<br>
<br>
When I attempt to use Safari to display that page on:<br>
<a href="http://loncapaN.chem.binghamton.edu" rel="noreferrer" target="_blank">loncapaN.chem.binghamton.edu</a> (N = 2, 3, 5, 6, or 7) two errors are displayed:<br>
<br>
(a) A dialog box with the message: "JSmolCore.js: synchronous binary<br>
file transfer is requested but not available"<br>
and then (if I click "OK") some seconds later:<br>
<br>
(b) A dialog box with the message:<br>
<br>
Error connecting to server:<br>
<a href="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" rel="noreferrer" target="_blank">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</a><br>
<br>
Looking at the jsmol documentation:<br>
<a href="http://wiki.jmol.org/index.php/Jmol_JavaScript_Object" rel="noreferrer" target="_blank">http://wiki.jmol.org/index.php/Jmol_JavaScript_Object</a><br>
<br>
(see: "Reading binary files" section)<br>
<br>
I find that jsmol.php will be called if a binary format file (gz, zip,<br>
pse, etc.) is requested from Safari, Chrome, or MSIE, and a jsmol.php<br>
file needs to be used to convert the binary data to BASE64 format. The<br>
documentation states jsmol.php is a "A server-side PHP utility that<br>
allows a number of functions that can increase the platform and browser<br>
compatibility of JSmol".<br>
<br>
By default <a href="http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php" rel="noreferrer" target="_blank">http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php</a> will be used.<br>
However, if you modify /home/httpd/html/jmol/Jmol.js by modifying this line:<br>
<br>
serverURL: "<a href="http://your.server.here/jsmol.php" rel="noreferrer" target="_blank">http://your.server.here/jsmol.php</a>", // required for binary<br>
file loading (.bin .gz .zip .jpg .png .jmol .smol .spartan .mrc or .pse<br>
files).<br>
<br>
and replace <a href="http://your.server.here/jsmol.php" rel="noreferrer" target="_blank">http://your.server.here/jsmol.php</a> with the hostname of your<br>
server (and an appropriate path) you could use a local jsmol.php file,<br>
and thereby override the default behavior of jmolInitialize().<br>
<br>
You would need to obtain jsmol.php from the jmol binary (from<br>
<a href="http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/Jmol-14.2.13_2015.03.23-binary.zip/download" rel="noreferrer" target="_blank">http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.13/Jmol-14.2.13_2015.03.23-binary.zip/download</a> ) because the jmol-loncapa.zip file included in the LON-CAPA 2.11.1 tarball does not include<br>
it.<br>
<br>
What is odd about this is that the caffeine.mol file (MIME:<br>
chemical/x-mdl-molfile) is not a binary file, and I am able to download<br>
this text file directly via:<br>
<a href="http://loncapa7.chem.binghamton.edu/res/msu/raeburn/testing/jmol/caffeine.mol" rel="noreferrer" target="_blank">http://loncapa7.chem.binghamton.edu/res/msu/raeburn/testing/jmol/caffeine.mol</a><br>
<br>
The documentation does say:<br>
<br>
'These "extensions" can appear anywhere in a file name to trigger the<br>
binary access mode. So, for example, if you rename any file to include<br>
.bin anywhere in its name, that will instruct JSmol to read it as a<br>
binary file'.<br>
<br>
The file name does not contain the extension .bin, but if the URL was<br>
being examined instead of the file name, then the string ".bin" does<br>
appear (in .binghamton).<br>
<br>
<br>
Stuart Raeburn<br>
LON-CAPA Academic Consortium<br>
<br>
Quoting Bob Gonzales <<a href="mailto:rgonzal@binghamton.edu" target="_blank">rgonzal@binghamton.edu</a>>:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I've coded up my first problem with Jsmol and it works fine on the latest<br>
Chrome and Firefox. But it doesn't work on Internet Explorer 11 or Safari<br>
(latest). The both complain about the file format. IE says 'unrecognized<br>
file format for file xxx' and Safari says it doesn't know how to open the<br>
binary file.<br>
<br>
I'm using .mol files.<br>
<br>
I'm invoking the viewer with the following code:<br>
<br>
<script src="/adm/jmol/Jmol.js" type="text/javascript"></script><br>
<script type="text/javascript">jmolInitialize("/adm/jmol");</script><br>
<script type="text/javascript">jmolApplet(150,"background [xFFFFCC]; load<br>
../Graphics/type04/$correctMolecularGeometry.mol");</script><br>
<br>
It would be great to get this to work on IE since that is what is available<br>
on our instructional computers.<br>
<br>
Thanks,<br>
Bob Gonzales<br>
</blockquote>
<br>
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</blockquote>
<br>
<br>
<br></div></div>
Stuart Raeburn, Ph.D. LON-CAPA (cell) <a href="tel:%2B1%20517%20881-3308" value="+15178813308" target="_blank">+1 517 881-3308</a><br>
Dept. Physics & Astronomy Other (cell) <a href="tel:%2B1%20734%20277-2795" value="+17342772795" target="_blank">+1 734 277-2795</a><br>
Michigan State University <a href="mailto:raeburn@msu.edu" target="_blank">raeburn@msu.edu</a><br>
MI 48824 USA<div class="HOEnZb"><div class="h5"><br>
<br>
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</div></div></blockquote></div><br></div>