Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/01/2013 09:42 PM, Robert Hanson wrote: On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. I think your server is not set up to deliver gzipped files automatically. Perhaps? The problem whith this is here that the file content is served by a CGI script instead of a static file. As far as I could find out the Apache web server configuration options don't seem to be usable in this case. And switching to direct file serving is not really an option for me. I am working on a way to mimic it by the CGI script but it doesn't work yet. There might be an additional more general way (not only for standard compressed binary files) to avoid sending the data three times involving a PHP script. A CGI script could serve the binary data directly encoded as base64 without the need for an additional PHP script and two additional data transfers. I think there would be needed two configurable options for this: 1) A special CGI binary mode indicator in the file URL (like the '.bin' file extension). In my case this could be for example cgi-bin/idb_send.pl. 2) A special parameter attached to the CGI URL, e.g. ENCODING=base64 by JSmol. Option 2) would prevent that base64 encoding would have to be done also with Java although it wouldn't be necessary there. Since the actual 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if Java or HTML5 will be chosen by the client it would be better to add the 'ENCODING' parameter only if necessary on the client side by JSmol. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Rolf, Maybe the way I work on Proteopedia might help you. I have a CGI script that sends the content of the structure files to Jmol/JSmol: getlateststructure The script gets as a parameter the name of the file to return or the PDB id for that file, and looks for the ending “.gz” on that parameter. This “.gz” ending gets removed from the actual name of the requested data and kept as a flag of the type of data required. No additional CGI parameter is required. If the “.gz” flag is present then the script will do whatever its necessary to get the data and send it gzipped. Otherwise it will send it uncompressed. This is, depending on the request, the script will uncompress compressed files before sending, or will compress plain data, to keep the receiving applet happy. Jaim On Dec 2, 2013, at 2:20 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 12/01/2013 09:42 PM, Robert Hanson wrote: On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. I think your server is not set up to deliver gzipped files automatically. Perhaps? The problem whith this is here that the file content is served by a CGI script instead of a static file. As far as I could find out the Apache web server configuration options don't seem to be usable in this case. And switching to direct file serving is not really an option for me. I am working on a way to mimic it by the CGI script but it doesn't work yet. There might be an additional more general way (not only for standard compressed binary files) to avoid sending the data three times involving a PHP script. A CGI script could serve the binary data directly encoded as base64 without the need for an additional PHP script and two additional data transfers. I think there would be needed two configurable options for this: 1) A special CGI binary mode indicator in the file URL (like the '.bin' file extension). In my case this could be for example cgi-bin/idb_send.pl. 2) A special parameter attached to the CGI URL, e.g. ENCODING=base64 by JSmol. Option 2) would prevent that base64 encoding would have to be done also with Java although it wouldn't be necessary there. Since the actual 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if Java or HTML5 will be chosen by the client it would be better to add the 'ENCODING' parameter only if necessary on the client side by JSmol. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/02/2013 02:13 PM, Jaime Prilusky wrote: Rolf, Maybe the way I work on Proteopedia might help you. I have a CGI script that sends the content of the structure files to Jmol/JSmol: getlateststructure The script gets as a parameter the name of the file to return or the PDB id for that file, and looks for the ending “.gz” on that parameter. This “.gz” ending gets removed from the actual name of the requested data and kept as a flag of the type of data required. No additional CGI parameter is required. If the “.gz” flag is present then the script will do whatever its necessary to get the data and send it gzipped. Otherwise it will send it uncompressed. This is, depending on the request, the script will uncompress compressed files before sending, or will compress plain data, to keep the receiving applet happy. Jaim, thanks for the hint. This sounds similar to what my CGI script does since the beginning of the 'Jena3D Viewer'. The downside is sending the data uncompressed. That's why I am working on using the 'Content-encoding' response header parameter to get compressed CGI data to a browser which has sent 'gzip' in the 'Accept-encoding' request header parameter. This would mimic what Paul and Bob have suggested by changing the Apache web server configuration. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 12/02/2013 02:29 PM, Rolf Huehne wrote: Jaim, thanks for the hint. This sounds similar to what my CGI script does since the beginning of the 'Jena3D Viewer'. The downside is sending the data uncompressed. That's why I am working on using the 'Content-encoding' response header parameter to get compressed CGI data to a browser which has sent 'gzip' in the 'Accept-encoding' request header parameter. This would mimic what Paul and Bob have suggested by changing the Apache web server configuration. It works now. The only drawback compared to the 'jsmol.php' solution will be, that for browsers that don't accept compressed content it will be several times slower, based on my experience with uncommpressed PDB files. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: On 11/28/2013 06:15 PM, Robert Hanson wrote: The files are loading, so Jmol is recognizing them as binary. I'll add Jmol._alertNoBinary that you can set false. But, really, you're doing a double send -- once to the relay host in binary, then again in BASE64 to JSmol, then a decoding back into binary. So think about if there is a way to avoid that. They are just PDB or mmCIF files, right? Yes, for usage with Jmol they are currently gzip-compressed PDB files. If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. Sending them uncompressed instead is not really an option. Especially the biological unit files can get very large, even compressed. Before I figured out how to activate the binary file loading in JSmol it was done this way. But it took very long to load a file with a compressed size of ~2 megabyte on a 2 MBit/s connection. Even with the double send it was several times faster with activated binary file loading of the compressed file. I think your server is not set up to deliver gzipped files automatically. Perhaps? Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
If you have access to your server’s feature, you can also enable gzip compression (on Apache it’s the mo_deflate program) for the associated plain text format. Then the server and the browser will do the job ! Paul Le 28 nov. 2013 à 13:12, Rolf Huehne rhue...@fli-leibniz.de a écrit : On 11/28/2013 06:15 PM, Robert Hanson wrote: The files are loading, so Jmol is recognizing them as binary. I'll add Jmol._alertNoBinary that you can set false. But, really, you're doing a double send -- once to the relay host in binary, then again in BASE64 to JSmol, then a decoding back into binary. So think about if there is a way to avoid that. They are just PDB or mmCIF files, right? Yes, for usage with Jmol they are currently gzip-compressed PDB files. If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. Sending them uncompressed instead is not really an option. Especially the biological unit files can get very large, even compressed. Before I figured out how to activate the binary file loading in JSmol it was done this way. But it took very long to load a file with a compressed size of ~2 megabyte on a 2 MBit/s connection. Even with the double send it was several times faster with activated binary file loading of the compressed file. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/28/2013 09:40 PM, Paul Pillot wrote: If you have access to your server’s feature, you can also enable gzip compression (on Apache it’s the mo_deflate program) for the associated plain text format. Then the server and the browser will do the job ! The problem with 'mod_deflate' is, that it would require to uncompress the already compressed PDB files first and then let the module compress the data from the CGI script again. I would like to avoid that, especially with larger biological unit PDB files. I digged a bit deeper into this and might be able to achieve the same as 'mod_deflate' directly with the CGI script bei reading and writing the corresponding response headers of the browser request. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Happy Thanksgiving!! Mac OSX 9 (Mavericks), Safari 7.0 Firefox works both locally and from Bob’s site using the three links below. The only issue is that test2 running locally gives an access control exception with the unsigned applet. Safari 7.0 is the issue with the HTML5 code. The hosted the applet will not load unless the error console is on. I posted the error thrown last night. Locally, test.htm and test2.htm load fine. jsmol.htm will not load hosted without the error console This morning I have looked at three files: simplej.htm, simpleOpt.htm, and supersimple.htm. All three purport to do the same thing. I have not looked at the code to see what is different. simplej.htm is fine both locally and hosted without the error console, albeit slowly. The other two, both locally and hosted, require the error console to be open to load the applet. If the console is closed, the code thrown is the same as I posted last evening. As I indicated last evening On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/28/2013 12:55 AM, Robert Hanson wrote: OK, here we go... Thank you all for the testing. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27d.zip Should fix the Bond/BondSet issue. Should fix the mouse wheeling issues. Mousewheel works now in Chromium 30 on Linux the same with Java and HTML5: zooming with the mousewheel after first click into the applet That's ok for me. Firefox 25 on Linux works as before (no initial click needed for zooming with the mousewheel). Should fix the menu language issue. (should start up in your language) At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm; language switching works (both with HTML5 and Java, in Firefox 25 and Chromium 30 on Linux). And the check marks in the menu are now set correctly Within the development 'Jena3D Viewer' language switching works with Java but not (always) with HTML5. In Firefox 25 there is no error message at all but in Chromium 30 there is the following error message: -- Failed to load resource: the server responded with a status of 404 (Not Found) http://jenalib.fli-leibniz.de/cgi-bin//ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po -- If I set 'Info.j2sPath' to an absolute URL (http://jenalib.fli-leibniz.de/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/j2s;) instead of a server absolute URL (/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/j2s) language switching works (menu and console). But Firefox still displays this Javascript error message: -- Timestamp: 11/28/2013 04:26:16 PM Error: not well-formed Source File: http://jenalib.fli-leibniz.de/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po Line: 1, Column: 2 Source Code: # German translation of the Jmol applet -- Additionally, in Chromium 30 on Linux with HTML5 and the development 'Jena3D Viewer' an alert box is opened: JmolCore.js: synchronous binary file transfer is requested but not available After clicking ok the structure file is loaded anyway. There is also the following Javascript error message: -- XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S) requests made from the window context. -- Is the alert box just a warning or was there really a problem? If it is just a warning, can it be deactivated for productive use? Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
How does one get Safari 7? I just upgraded my MacOS then additionally immediately upgraded Safari to 6.1. Where's Safari 7 ??? On Thu, Nov 28, 2013 at 6:36 AM, Philip Bays pb...@saintmarys.edu wrote: Happy Thanksgiving!! Mac OSX 9 (Mavericks), Safari 7.0 Firefox works both locally and from Bob’s site using the three links below. The only issue is that test2 running locally gives an access control exception with the unsigned applet. Safari 7.0 is the issue with the HTML5 code. The hosted the applet will not load unless the error console is on. I posted the error thrown last night. Locally, test.htm and test2.htm load fine. jsmol.htm will not load hosted without the error console This morning I have looked at three files: simplej.htm, simpleOpt.htm, and supersimple.htm. All three purport to do the same thing. I have not looked at the code to see what is different. simplej.htm is fine both locally and hosted without the error console, albeit slowly. The other two, both locally and hosted, require the error console to be open to load the applet. If the console is closed, the code thrown is the same as I posted last evening. As I indicated last evening On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Now that's interesting. When I upgraded to Mavericks, the upgrade to Safari was automatic - no choice that I could see. Did Apple finally decide that they have a disaster on their hands? JSmol was not the only problem with this version of Safari. I actually switched to Chrome for routine work because of crashing at other sites. Otis On Thu, Nov 28, 2013 at 10:54 AM, Robert Hanson hans...@stolaf.edu wrote: How does one get Safari 7? I just upgraded my MacOS then additionally immediately upgraded Safari to 6.1. Where's Safari 7 ??? On Thu, Nov 28, 2013 at 6:36 AM, Philip Bays pb...@saintmarys.edu wrote: Happy Thanksgiving!! Mac OSX 9 (Mavericks), Safari 7.0 Firefox works both locally and from Bob’s site using the three links below. The only issue is that test2 running locally gives an access control exception with the unsigned applet. Safari 7.0 is the issue with the HTML5 code. The hosted the applet will not load unless the error console is on. I posted the error thrown last night. Locally, test.htm and test2.htm load fine. jsmol.htm will not load hosted without the error console This morning I have looked at three files: simplej.htm, simpleOpt.htm, and supersimple.htm. All three purport to do the same thing. I have not looked at the code to see what is different. simplej.htm is fine both locally and hosted without the error console, albeit slowly. The other two, both locally and hosted, require the error console to be open to load the applet. If the console is closed, the code thrown is the same as I posted last evening. As I indicated last evening On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Good to hear... On Thu, Nov 28, 2013 at 9:54 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 11/28/2013 12:55 AM, Robert Hanson wrote: OK, here we go... Thank you all for the testing. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27d.zip Should fix the Bond/BondSet issue. Should fix the mouse wheeling issues. Mousewheel works now in Chromium 30 on Linux the same with Java and HTML5: zooming with the mousewheel after first click into the applet That's ok for me. Firefox 25 on Linux works as before (no initial click needed for zooming with the mousewheel). Excellent. Should fix the menu language issue. (should start up in your language) At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm; language switching works (both with HTML5 and Java, in Firefox 25 and Chromium 30 on Linux). And the check marks in the menu are now set correctly great. Within the development 'Jena3D Viewer' language switching works with Java but not (always) with HTML5. In Firefox 25 there is no error message at all but in Chromium 30 there is the following error message: -- Failed to load resource: the server responded with a status of 404 (Not Found) http://jenalib.fli-leibniz.de/cgi-bin//ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po -- Right, I guess you didn't upload the idioma subdirectory. It's certainly in the zip file. The file is not there. Nor is anything at http://jenalib.fli-leibniz.de/cgi-bin/ImgLibPDB If I set 'Info.j2sPath' to an absolute URL (http://jenalib.fli-leibniz.de/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/j2s;) instead of a server absolute URL (/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/j2s) language switching works (menu and console). But Firefox still displays this Javascript error message: -- Timestamp: 11/28/2013 04:26:16 PM Error: not well-formed Source File: http://jenalib.fli-leibniz.de/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po Line: 1, Column: 2 Source Code: # German translation of the Jmol applet -- I think that's some sort of standard message that browsers give. For some reason they always try to parse these as XML with AJAX. Don't know why. Additionally, in Chromium 30 on Linux with HTML5 and the development 'Jena3D Viewer' an alert box is opened: JmolCore.js: synchronous binary file transfer is requested but not available After clicking ok the structure file is loaded anyway. There is also the following Javascript error message: -- XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S) requests made from the window context. -- Is the alert box just a warning or was there really a problem? If it is just a warning, can it be deactivated for productive use? This first is the test that JSmol uses to check for availability of synchronous binary file loading. The message is saying that a relay is being used because this browser can't read binary data that way (Chrome and Safari and MSIE). It's tell you (the developer) that a binary file has been requested (probably GZIP? Certainly no longer necessary to do that --- servers will automatically convert to gz, and browsers will automatically unzip them.) Whatever you are using for Info.serverUrl is being used to encode the data as base64 on the server side and decode it back on the page by JSmol. Any chance you can just avoid binary? Feel free to remove the message. I could add something that you could turn off. Thanks much -- glad this is all working properly for you. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Safari seems to be changing every day. On Thu, Nov 28, 2013 at 10:07 AM, Otis Rothenberger osrot...@chemagic.comwrote: Now that's interesting. When I upgraded to Mavericks, the upgrade to Safari was automatic - no choice that I could see. Did Apple finally decide that they have a disaster on their hands? JSmol was not the only problem with this version of Safari. I actually switched to Chrome for routine work because of crashing at other sites. Otis On Thu, Nov 28, 2013 at 10:54 AM, Robert Hanson hans...@stolaf.eduwrote: How does one get Safari 7? I just upgraded my MacOS then additionally immediately upgraded Safari to 6.1. Where's Safari 7 ??? On Thu, Nov 28, 2013 at 6:36 AM, Philip Bays pb...@saintmarys.eduwrote: Happy Thanksgiving!! Mac OSX 9 (Mavericks), Safari 7.0 Firefox works both locally and from Bob’s site using the three links below. The only issue is that test2 running locally gives an access control exception with the unsigned applet. Safari 7.0 is the issue with the HTML5 code. The hosted the applet will not load unless the error console is on. I posted the error thrown last night. Locally, test.htm and test2.htm load fine. jsmol.htm will not load hosted without the error console This morning I have looked at three files: simplej.htm, simpleOpt.htm, and supersimple.htm. All three purport to do the same thing. I have not looked at the code to see what is different. simplej.htm is fine both locally and hosted without the error console, albeit slowly. The other two, both locally and hosted, require the error console to be open to load the applet. If the console is closed, the code thrown is the same as I posted last evening. As I indicated last evening On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/28/2013 05:11 PM, Robert Hanson wrote: On Thu, Nov 28, 2013 at 9:54 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Within the development 'Jena3D Viewer' language switching works with Java but not (always) with HTML5. In Firefox 25 there is no error message at all but in Chromium 30 there is the following error message: -- Failed to load resource: the server responded with a status of 404 (Not Found) http://jenalib.fli-leibniz.de/cgi-bin//ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po -- Right, I guess you didn't upload the idioma subdirectory. It's certainly in the zip file. The file is not there. Nor is anything at http://jenalib.fli-leibniz.de/cgi-bin/ImgLibPDB No, the idioma subdirectory is at the proper place. But apparantly the server absolute path (indicated by the '/' at the beginning) provided as 'Info.j2sPath' is mistaken as a relative path. Since the page is build from a CGI script the base URL for the page is http://jenalib.fli-leibniz.de/cgi-bin/;. Now the major part of the 'j2sPath' seems to be appended to the base URL resulting in the wrong URL http://jenalib.fli-leibniz.de/cgi-bin//ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po;. Instead it should have been appended to the server root path http://jenalib.fli-leibniz.de/; to build the correct URL http://jenalib.fli-leibniz.de/ImgLibPDB/jmol/jmol-13.3.9d/jsmol/idioma/de.po;. Additionally, in Chromium 30 on Linux with HTML5 and the development 'Jena3D Viewer' an alert box is opened: JmolCore.js: synchronous binary file transfer is requested but not available After clicking ok the structure file is loaded anyway. There is also the following Javascript error message: -- XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S) requests made from the window context. -- Is the alert box just a warning or was there really a problem? If it is just a warning, can it be deactivated for productive use? This first is the test that JSmol uses to check for availability of synchronous binary file loading. The message is saying that a relay is being used because this browser can't read binary data that way (Chrome and Safari and MSIE). It's tell you (the developer) that a binary file has been requested (probably GZIP? Certainly no longer necessary to do that --- servers will automatically convert to gz, and browsers will automatically unzip them.) Whatever you are using for Info.serverUrl is being used to encode the data as base64 on the server side and decode it back on the page by JSmol. Any chance you can just avoid binary? I can't really avoid it. On the server all PDB Files are deposited as '.gz' files. But they are provided by a CGI script that sometimes needs to manipulate them before they are send to the browser or JSmol or switch to a different directory. I wouldn't want to loose the flexibility that is enabled by this. Fortunately the binary file indicator can be anywhere in the URL so that I could just add .bin to the existing flexible 'MODE' parameter of the CGI script. Feel free to remove the message. I could add something that you could turn off. I would prefer an option to turn it off. The larger the list of local adaptations grows the more difficult and time consuming updates to bug fix or new releases will become, also for other page developers. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/28/2013 06:15 PM, Robert Hanson wrote: The files are loading, so Jmol is recognizing them as binary. I'll add Jmol._alertNoBinary that you can set false. But, really, you're doing a double send -- once to the relay host in binary, then again in BASE64 to JSmol, then a decoding back into binary. So think about if there is a way to avoid that. They are just PDB or mmCIF files, right? Yes, for usage with Jmol they are currently gzip-compressed PDB files. If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. Sending them uncompressed instead is not really an option. Especially the biological unit files can get very large, even compressed. Before I figured out how to activate the binary file loading in JSmol it was done this way. But it took very long to load a file with a compressed size of ~2 megabyte on a 2 MBit/s connection. Even with the double send it was several times faster with activated binary file loading of the compressed file. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] local testing ready iteration 1,203,304,440
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip is ready for local-applet testing. Please do! hosted site testing can be done using http://chemapps.stolaf.edu/jmol/jsmol http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=HTML5 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED Thanks. I still have not worked on a number of issues, but this at least should solve the Bond/BondSet issue and a number of other errors I made yesterday. Maybe even the infinite-loop issue. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/27/2013 06:13 PM, Robert Hanson wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip is ready for local-applet testing. Please do! hosted site testing can be done using http://chemapps.stolaf.edu/jmol/jsmol http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=HTML5 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED There is no mousewheel support (zooming) with Chromium 30 on Linux with HTML5 but it works with Java. With Firefox 25 the mousewheel works with both HTML5 and Java. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/27/2013 07:20 PM, Robert Hanson wrote: Rolf, please: 1) Open a Jmol console or otherwise enter the command set debug When I do this with HTML5 I get the following error message: - script ERROR: RangeError: Maximum call stack size exceeded - In Firefox I get a different one: - script ERROR: InternalError: too much recursion - Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
That's what I'm trying to solve now... On Wed, Nov 27, 2013 at 12:29 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: On 11/27/2013 07:20 PM, Robert Hanson wrote: Rolf, please: 1) Open a Jmol console or otherwise enter the command set debug When I do this with HTML5 I get the following error message: - script ERROR: RangeError: Maximum call stack size exceeded - In Firefox I get a different one: - script ERROR: InternalError: too much recursion - Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
better: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=108lAPPLET=unsignedJMOLJAR=http://chemapps.stolaf.edu/jmol/jsmol/java/JmolAppletSigned.jar 1) Enter set loglevel 6 in your command box. 2) run the mouse and wheel 3) check the Java console. It should report something like: mouse action: LEFT+down LEFT+down mouse action: LEFT+drag mouse action: LEFT+drag mouse action: LEFT+drag mouse action: LEFT+drag mouse action: LEFT+up LEFT+up mouse action: MIDDLE+down MIDDLE+down mouse action: MIDDLE+drag mouse action: MIDDLE+drag mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: WHEEL mouse action: MIDDLE+up MIDDLE+up On Wed, Nov 27, 2013 at 12:20 PM, Robert Hanson hans...@stolaf.edu wrote: Rolf, please: 1) Open a Jmol console or otherwise enter the command set debug 2) run your mouse, wheel, etc. 3) report back what the Java console says. Should be something like: MIDDLE+down MIDDLE+up MIDDLE+down MIDDLE+up MIDDLE+click MIDDLE+double+down MIDDLE+double+up MIDDLE+double+click (I guess the drags don't get reported, but that will at least let us know if the wheel is getting picked up.) On Wed, Nov 27, 2013 at 12:07 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: On 11/27/2013 06:13 PM, Robert Hanson wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip is ready for local-applet testing. Please do! hosted site testing can be done using http://chemapps.stolaf.edu/jmol/jsmol http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=HTML5 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED There is no mousewheel support (zooming) with Chromium 30 on Linux with HTML5 but it works with Java. With Firefox 25 the mousewheel works with both HTML5 and Java. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
On 11/27/2013 07:37 PM, Robert Hanson wrote: better: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=108lAPPLET=unsignedJMOLJAR=http://chemapps.stolaf.edu/jmol/jsmol/java/JmolAppletSigned.jar 1) Enter set loglevel 6 in your command box. 2) run the mouse and wheel 3) check the Java console. It should report something like: I can't do that because the IcedTea Java plugin doesn't provide a Java console. (I guess you have noticed: with Java the mousewheel works with Chromium.) Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Restart your browser and try that again -- this time open the Jmol console and issue set loglevel 6 from there. On Wed, Nov 27, 2013 at 12:48 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: On 11/27/2013 07:37 PM, Robert Hanson wrote: better: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=108lAPPLET=unsignedJMOLJAR=http://chemapps.stolaf.edu/jmol/jsmol/java/JmolAppletSigned.jar 1) Enter set loglevel 6 in your command box. 2) run the mouse and wheel 3) check the Java console. It should report something like: I can't do that because the IcedTea Java plugin doesn't provide a Java console. (I guess you have noticed: with Java the mousewheel works with Chromium.) Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Am 27.11.2013 21:10, schrieb Robert Hanson: Restart your browser and try that again -- this time open the Jmol console and issue set loglevel 6 from there. The output looks like this: - mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 4 16 LEFT+down mouse action: 5 16 LEFT+up mouse action: 2 16 LEFT+click mouse action: 4 4 RIGHT+down mouse action: 5 4 RIGHT+up mouse action: 2 4 RIGHT+click mouse action: 4 16 LEFT+down mouse action: 5 16 LEFT+up mouse action: 2 16 LEFT+click mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL --- When the second set of mouse wheel events were reported suddenly zooming with the wheel worked. So I reloaded the page and a single left-click was sufficient to activate zooming with the mousewheel. But now I am working with Chrome on Win7 at home. I'm quite sure that I mixed my zooming attempts with rotations at work so I should have noticed this. I will check tomorrow. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
could be. Might have to leave it that way. HTML5 works OK? or not? On Wed, Nov 27, 2013 at 2:32 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: Am 27.11.2013 21:10, schrieb Robert Hanson: Restart your browser and try that again -- this time open the Jmol console and issue set loglevel 6 from there. The output looks like this: - mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 4 16 LEFT+down mouse action: 5 16 LEFT+up mouse action: 2 16 LEFT+click mouse action: 4 4 RIGHT+down mouse action: 5 4 RIGHT+up mouse action: 2 4 RIGHT+click mouse action: 4 16 LEFT+down mouse action: 5 16 LEFT+up mouse action: 2 16 LEFT+click mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL mouse action: 3 32 WHEEL --- When the second set of mouse wheel events were reported suddenly zooming with the wheel worked. So I reloaded the page and a single left-click was sufficient to activate zooming with the mousewheel. But now I am working with Chrome on Win7 at home. I'm quite sure that I mixed my zooming attempts with rotations at work so I should have noticed this. I will check tomorrow. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Am 27.11.2013 21:50, schrieb Robert Hanson: could be. Might have to leave it that way. HTML5 works OK? or not? Sorry, I mixed up the Java and HTML5 versions here. The Click-activation of zooming with the mousewheel works only with Java and not with HTML5. So also on Win7 there is no mousewheel zooming with Chrome 31. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
I see. OK, well, in this next update that messaging is still in, so you can check Java or HTML5. On Wed, Nov 27, 2013 at 4:04 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: Am 27.11.2013 21:50, schrieb Robert Hanson: could be. Might have to leave it that way. HTML5 works OK? or not? Sorry, I mixed up the Java and HTML5 versions here. The Click-activation of zooming with the mousewheel works only with Java and not with HTML5. So also on Win7 there is no mousewheel zooming with Chrome 31. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
OK, here we go... Thank you all for the testing. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27d.zip Should fix the Bond/BondSet issue. Should fix the mouse wheeling issues. Should fix the menu language issue. (should start up in your language) I have no idea about the infinite loop problem. (optimistic) browser expectations : file:// ?_USE=HTML5 file:// ?_USE=JAVA file:// ?_USE=SIGNED http://?_USE=HTML5 http:// ?_USE=JAVA http:// ?_USE=SIGNED FF ok sandboxed ok ok ok ok Safari no (no AJAX) sandboxed ok ok(slow) ok ok Chrome no (no AJAX) sandboxed ok ok ok ok tests: for local downloading: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob On Wed, Nov 27, 2013 at 4:36 PM, Robert Hanson hans...@stolaf.edu wrote: I see. OK, well, in this next update that messaging is still in, so you can check Java or HTML5. On Wed, Nov 27, 2013 at 4:04 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: Am 27.11.2013 21:50, schrieb Robert Hanson: could be. Might have to leave it that way. HTML5 works OK? or not? Sorry, I mixed up the Java and HTML5 versions here. The Click-activation of zooming with the mousewheel works only with Java and not with HTML5. So also on Win7 there is no mousewheel zooming with Chrome 31. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Can't believe I did that. Hang on On Wed, Nov 27, 2013 at 5:55 PM, Robert Hanson hans...@stolaf.edu wrote: OK, here we go... Thank you all for the testing. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27d.zip Should fix the Bond/BondSet issue. Should fix the mouse wheeling issues. Should fix the menu language issue. (should start up in your language) I have no idea about the infinite loop problem. (optimistic) browser expectations : file:// ?_USE=HTML5 file:// ?_USE=JAVA file:// ?_USE=SIGNED http://?_USE=HTML5 http:// ?_USE=JAVA http:// ?_USE=SIGNED FF ok sandboxed ok ok ok ok Safari no (no AJAX) sandboxed ok ok(slow) ok ok Chrome no (no AJAX) sandboxed ok ok ok ok tests: for local downloading: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob On Wed, Nov 27, 2013 at 4:36 PM, Robert Hanson hans...@stolaf.edu wrote: I see. OK, well, in this next update that messaging is still in, so you can check Java or HTML5. On Wed, Nov 27, 2013 at 4:04 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: Am 27.11.2013 21:50, schrieb Robert Hanson: could be. Might have to leave it that way. HTML5 works OK? or not? Sorry, I mixed up the Java and HTML5 versions here. The Click-activation of zooming with the mousewheel works only with Java and not with HTML5. So also on Win7 there is no mousewheel zooming with Chrome 31. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
OK --- that's ready. On Wed, Nov 27, 2013 at 6:00 PM, Robert Hanson hans...@stolaf.edu wrote: Can't believe I did that. Hang on On Wed, Nov 27, 2013 at 5:55 PM, Robert Hanson hans...@stolaf.edu wrote: OK, here we go... Thank you all for the testing. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27d.zip Should fix the Bond/BondSet issue. Should fix the mouse wheeling issues. Should fix the menu language issue. (should start up in your language) I have no idea about the infinite loop problem. (optimistic) browser expectations : file:// ?_USE=HTML5 file:// ?_USE=JAVA file:// ?_USE=SIGNED http://?_USE=HTML5 http:// ?_USE=JAVA http:// ?_USE=SIGNED FF ok sandboxed ok ok ok ok Safari no (no AJAX) sandboxed ok ok(slow) ok ok Chrome no (no AJAX) sandboxed ok ok ok ok tests: for local downloading: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob On Wed, Nov 27, 2013 at 4:36 PM, Robert Hanson hans...@stolaf.eduwrote: I see. OK, well, in this next update that messaging is still in, so you can check Java or HTML5. On Wed, Nov 27, 2013 at 4:04 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: Am 27.11.2013 21:50, schrieb Robert Hanson: could be. Might have to leave it that way. HTML5 works OK? or not? Sorry, I mixed up the Java and HTML5 versions here. The Click-activation of zooming with the mousewheel works only with Java and not with HTML5. So also on Win7 there is no mousewheel zooming with Chrome 31. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
I have just had time to see if the applets load from your site. Java and signed load fine. HTML5 only loads if the error console is open. Error comments are as follows: [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2236) (anonymous function) (core.z.js, line 2228) (anonymous function) (core.z.js, line 2205) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 2204) (anonymous function) (core.z.js, line 2253) (anonymous function) (core.z.js, line 937) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 505) (anonymous function) (core.z.js, line 503) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 258) __nextExecution (JSmol.min.js, line 263) On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: OK --- that's ready. tests: for local downloading: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
