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 <raeb...@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 <raeb...@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 <rgon...@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 >>> >> >> _______________________________________________ >> LON-CAPA-users mailing list >> LON-CAPA-users@mail.lon-capa.org >> http://mail.lon-capa.org/mailman/listinfo/lon-capa-users >> > > > > Stuart Raeburn, Ph.D. LON-CAPA (cell) +1 517 881-3308 > Dept. Physics & Astronomy Other (cell) +1 734 277-2795 > Michigan State University raeb...@msu.edu > MI 48824 USA > > > _______________________________________________ > LON-CAPA-users mailing list > LON-CAPA-users@mail.lon-capa.org > http://mail.lon-capa.org/mailman/listinfo/lon-capa-users >
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