Re: [Jmol-users] Please test (2)
Yes, it's related to the fact that BondSet is an inner class of Bond. Something is as happening out of order. Utlimately, Bond.BondSet is created just fine. Very curious! On Tue, Nov 26, 2013 at 12:02 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet continues working. You may see error reports with Firebug. This might come from lines like this one in Bond.js and other files: J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []); The call to superConstructor assumes that J, modelset and Bond are directories, while BondSet is a file with the ‘.js’ extension. Jaim On Nov 26, 2013, at 12:02 AM, Robert Hanson hans...@stolaf.edu wrote: The Bond/BondSet.js message is certainly curious, but it's not a show stopper. This appears even on web-site access via Safari. The message just after that is the killer, having to do with not being able to load core.z.js. Safari (like Chrome or Firefox without special settings) will not allow access to local files. The yellow box should be gone now for Safari hosted access to Jmol. The problem was that apparently Safari is no longer accepting the object tag. The applet tag is required so that you can click on the windows and accept the website for the applet. Must be a bug, but I have switched JSmol to the applet tag when it detects Safari. There is still a problem with local file reading. It looks to me as though Safari is not recognizing local JNLP applications within the browser. Or there is some setting we are missing. Firefox is working fine for Safari local file access, so I concur with Phil and suggest we just write off Safari for now. Bob On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays pb...@saintmarys.edu wrote: I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.eduwrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now.
Re: [Jmol-users] Please test (2)
On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, it's related to the fact that BondSet is an inner class of Bond. Something is as happening out of order. Utlimately, Bond.BondSet is created just fine. Very curious! Found in your code a few other calls to Clazz.superConstructor( that would generate a non-existing file path, like it happens with J.modelset.Bond.BondSet Are these working Ok? If this is the case, then why? J.jvxl.calc.MarchingSquares.ContourVertex J.jvxl.readers.Dsn6BinaryReader JSV.source.JSVXmlReader.DataBuffer JZ.Inflate.Return Jaim -- 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] Please test (2)
Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.edu wrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.edu wrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
The Bond/BondSet.js message is certainly curious, but it's not a show stopper. This appears even on web-site access via Safari. The message just after that is the killer, having to do with not being able to load core.z.js. Safari (like Chrome or Firefox without special settings) will not allow access to local files. The yellow box should be gone now for Safari hosted access to Jmol. The problem was that apparently Safari is no longer accepting the object tag. The applet tag is required so that you can click on the windows and accept the website for the applet. Must be a bug, but I have switched JSmol to the applet tag when it detects Safari. There is still a problem with local file reading. It looks to me as though Safari is not recognizing local JNLP applications within the browser. Or there is some setting we are missing. Firefox is working fine for Safari local file access, so I concur with Phil and suggest we just write off Safari for now. Bob On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays pb...@saintmarys.edu wrote: I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.edu wrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile
Re: [Jmol-users] Please test (2)
The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet continues working. You may see error reports with Firebug. This might come from lines like this one in Bond.js and other files: J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []); The call to superConstructor assumes that J, modelset and Bond are directories, while BondSet is a file with the ‘.js’ extension. Jaim On Nov 26, 2013, at 12:02 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: The Bond/BondSet.js message is certainly curious, but it's not a show stopper. This appears even on web-site access via Safari. The message just after that is the killer, having to do with not being able to load core.z.js. Safari (like Chrome or Firefox without special settings) will not allow access to local files. The yellow box should be gone now for Safari hosted access to Jmol. The problem was that apparently Safari is no longer accepting the object tag. The applet tag is required so that you can click on the windows and accept the website for the applet. Must be a bug, but I have switched JSmol to the applet tag when it detects Safari. There is still a problem with local file reading. It looks to me as though Safari is not recognizing local JNLP applications within the browser. Or there is some setting we are missing. Firefox is working fine for Safari local file access, so I concur with Phil and suggest we just write off Safari for now. Bob On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote: I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edumailto:pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto: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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edumailto:pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users
Re: [Jmol-users] Please test (2)
Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 Unable to convince Safari 7.0 to run a local applet. Also tried with a Proteopedia exported page and (again FFox on Mac) it works great!! Jaim On Nov 24, 2013, at 8:47 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. And, of course, to try your own pages. Bob On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukmailto:h.rz...@imperial.ac.uk wrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto: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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R)
Re: [Jmol-users] Please test (2)
On 24 Nov 2013, at 08:58, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 Unable to convince Safari 7.0 to run a local applet. I can run Safari 7.0 as a local applet, merely not the Certificate signed one! signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Mac OSX 10.9, Java 7 update 45 (latest) Runs fine in Firefox. Safari is a no-go. I get the yellow error that Java is not enables in the browser, even though it is and the certificates are set properly. In fact, none of the applet options in test2 work. (signed, unsigned, HTML5) It appears that Safari does not read its own preferences, or the Java Panel settings. I cannot find the Java cache in the current Java panel so I have not cleared it. Phil On Nov 24, 2013, at 1:47 AM, Robert Hanson hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. And, of course, to try your own pages. Bob On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson hans...@stolaf.edu wrote: Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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
Re: [Jmol-users] Please test (2)
On 24 Nov 2013, at 14:19, Philip Bays pb...@saintmarys.edu wrote: Mac OSX 10.9, Java 7 update 45 (latest) Runs fine in Firefox. Safari is a no-go. I get the yellow error that Java is not enables in the browser, even though it is and the certificates are set properly. In fact, none of the applet options in test2 work. (signed, unsigned, HTML5) It appears that Safari does not read its own preferences, or the Java Panel settings. I cannot find the Java cache in the current Java panel so I have not cleared it. I find nothing works well unless the Java cache is indeed purged. But you can only do that if you set Developer mode in Safari when “empty caches” is then enabled (I forget how I set the developer mode). Indeed, just to be sure, purge the cache, then restart Safari as the most reliable method. signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
On 24 Nov 2013, at 06:47, Robert Hanson hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. I have found that on OS X Mavericks at least, local mode give “found unsigned entry in resource file://Users … /Java/JmolAppletsigned.jar” But separately I have found that if one specifies the full path length for a file (relative to the users home directory) it loads the file and displays it (the full path may have to be quoted) but if only a relative path is given it does not load. This behaviour (not honouring relative paths) is new? Is it OS specific? I got this by the way not with Bob’s new signed applet, but the standard production one. To get that far by the way one has to allow local documents in unsafe mode from Safari preferences. signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Using Safari on Mac Mavericks Disabling local file restrictions in the Develop menu indeed allows JSmol to run locally. But I still get an error with the Java links telling me that Java is not enabled. Clearing caches from the developers menu, and even disabling cache totally, does not resolve the issue. There used to be a Java cache purging option in the Java console, but I no longer find it there. Back to JSMol: When I have the developers error console open, the loading of the js applet is much slower and in fact throws an error twice. In both cases it is looking for the file BondSet.js. I do not find it manually anywhere in the download, nor do I find the directory Bond in which it is supposed to be located. ……...jmol-13.3.9_2013.11.23b/jsmol/j2s/J/modelset/Bond/BondSet.js Phil On Nov 24, 2013, at 10:59 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 24 Nov 2013, at 06:47, Robert Hanson hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. I have found that on OS X Mavericks at least, local mode give “found unsigned entry in resource file://Users … /Java/JmolAppletsigned.jar” But separately I have found that if one specifies the full path length for a file (relative to the users home directory) it loads the file and displays it (the full path may have to be quoted) but if only a relative path is given it does not load. This behaviour (not honouring relative paths) is new? Is it OS specific? I got this by the way not with Bob’s new signed applet, but the standard production one. To get that far by the way one has to allow local documents in unsafe mode from Safari preferences. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Phil, could you send me the error report? On Sun, Nov 24, 2013 at 11:31 AM, Philip Bays pb...@saintmarys.edu wrote: Using Safari on Mac Mavericks Disabling local file restrictions in the Develop menu indeed allows JSmol to run locally. But I still get an error with the Java links telling me that Java is not enabled. Clearing caches from the developers menu, and even disabling cache totally, does not resolve the issue. There used to be a Java cache purging option in the Java console, but I no longer find it there. Back to JSMol: When I have the developers error console open, the loading of the js applet is much slower and in fact throws an error twice. In both cases it is looking for the file BondSet.js. I do not find it manually anywhere in the download, nor do I find the directory Bond in which it is supposed to be located. ……...jmol-13.3.9_2013.11.23b/jsmol/j2s/J/modelset/Bond/BondSet.js Phil On Nov 24, 2013, at 10:59 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 24 Nov 2013, at 06:47, Robert Hanson hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. I have found that on OS X Mavericks at least, local mode give “found unsigned entry in resource file://Users … /Java/JmolAppletsigned.jar” But separately I have found that if one specifies the full path length for a file (relative to the users home directory) it loads the file and displays it (the full path may have to be quoted) but if only a relative path is given it does not load. This behaviour (not honouring relative paths) is new? Is it OS specific? I got this by the way not with Bob’s new signed applet, but the standard production one. To get that far by the way one has to allow local documents in unsafe mode from Safari preferences. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
[Error] Failed to load resource: The requested URL was not found on this server. (BondSet.js, line 0) [Error] Failed to load resource: The requested URL was not found on this server. (BondSet.js, line 0) On Nov 24, 2013, at 12:40 PM, Robert Hanson hans...@stolaf.edu wrote: Phil, could you send me the error report? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
And this is what appears in the console (not the browser error console) 11/24/13 3:24:28.561 PM com.apple.WebKit.WebContent[3733]: Could not create a sandbox extension for '/Users/pbays/Desktop/jmol-13.3.9_2013.11.23b/jsmol/j2s/J/modelset/Bond/BondSet.js' On Nov 24, 2013, at 12:40 PM, Robert Hanson hans...@stolaf.edu wrote: Phil, could you send me the error report? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Jaim, could you please try http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.24.zip with the PyMOL reading test at http://ispcsrv.weizmann.ac.il/a2jmolb/browseand report back how it went? I'm not having any problem with the files that are listed as failed on this end, so whatever that is, I'm thinking it might be fixed. Bob On Sun, Nov 24, 2013 at 2:58 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 Unable to convince Safari 7.0 to run a local applet. Also tried with a Proteopedia exported page and (again FFox on Mac) it works great!! Jaim On Nov 24, 2013, at 8:47 AM, Robert Hanson hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. And, of course, to try your own pages. Bob On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson hans...@stolaf.edu wrote: Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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
Re: [Jmol-users] Please test (2)
I'm pretty confused. What I see is this: *Back to JSMol: When I have the developers error console open, the loading of the js applet is much slower and in fact throws an error twice. In both cases it is looking for the file BondSet.js. I do not find it manually anywhere in the download, nor do I find the directory Bond in which it is supposed to be located.* I think it's probably some strange bug in the developer console. We found an enormous bug in the Mac/Firefox developer console a couple of weeks ago. There is no BondSet.js; The BondSet class is a subclass of Bond class, in J/modelset/Bond.js. But there are lots of such subclasses. This only occurs with the dev console open? Maybe others with Macs can pinpoint where the problem is. Could be just because you have some sort of profiling going on or some other default activity (checking for breakpoints, variable value changes, etc.) that is slowing it way down. There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Can I ask for a test for local files to be included? Loading Jmol + data from a local directory has always behaved rather differently, and Oracle might be changing the rules here as well (Previously, using Nico’s signed Jmol it loaded fine from a server but refused to load at all locally. Conversely, it loaded fine locally if NOT signed with a certificate. Go figure!) (PS Local files are not a problem for JSmol of course). (PPS I care since I use Jmol instead of Powerpoint) (PPPS I will no doubt test local use if I can find Bob’s signed Jmol to download). signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Here i have java 1.7.045. Everything works fine, with just one message displaying the author. When reloading i receive no new warning message. Just one question: if i swithc to JSmol, it doesn't load any molecule nor it loads a molecul with direct call to database or any search Pino -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Hi, My results under Win 7, Chrome, Java 7u45. On Sat, Nov 23, 2013 at 12:59 AM, Robert Hanson hans...@stolaf.edu wrote: Ho, ho! Looks like the Oracle guidelines are changing every day. This one in our favor. I have added the following line to the manifests inside the Jar files: Caller-Allowable-Codebase: * and I do believe that gets rid of the warning messages. Interesting, I was already doing this on my other Java project. Test of trusted-signed certificate for the full Jmol build http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Q: Did you get a warning message at all? Q: How many warning dialogs do you get? Of what nature? First, Chrome message at the top of the window Java needs your permission to run - Always run on this site Nothing more, but I probably trusted your certificate before. Q: If you reload the page does it still ask you to approve? Same number of times? No message Q: If you close your browser and reopen it and go to the page, any differences there? (Back to asking all the questions, or no questions, or fewer?) No message Q: If you *go to another browser *do you get that message? Or is it completely gone now? IE 10: No message FF 25: No message Nico -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
I have registered a question at the Oracle Technology Network forum. Not that it's a solution, but you can reference http://.. in Info.jarPath and then run that (remote) applet from a page that is file:// based. On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
OS X 10.6.8, Java1.6.0_65, Chrome latest 31.0.1650.57 On 23 November 2013 10:59, Robert Hanson hans...@stolaf.edu wrote: Ho, ho! Looks like the Oracle guidelines are changing every day. This one in our favor. I have added the following line to the manifests inside the Jar files: Caller-Allowable-Codebase: * and I do believe that gets rid of the warning messages. Test of trusted-signed certificate for the full Jmol build http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Q: Did you get a warning message at all? No Q: How many warning dialogs do you get? Of what nature? None. Q: If you reload the page does it still ask you to approve? Same number of times? No warnings. Q: If you close your browser and reopen it and go to the page, any differences there? (Back to asking all the questions, or no questions, or fewer?) No warnings. Q: If you *go to another browser *do you get that message? Or is it completely gone now? Safari 5.1.10 - one dialog The website “chemapps.stolaf.edu” contains a Java applet. Do you want to allow the applet to load? Does not reappear on page reload, or restart of Safari, unless Safari completely reset. Firefox 25.0.1 - loads with no messages at all. Reloads with no messages. 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. And, of course, to try your own pages. Bob On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson hans...@stolaf.edu wrote: Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Please test (2)
Ho, ho! Looks like the Oracle guidelines are changing every day. This one in our favor. I have added the following line to the manifests inside the Jar files: Caller-Allowable-Codebase: * and I do believe that gets rid of the warning messages. Test of trusted-signed certificate for the full Jmol build http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Q: Did you get a warning message at all? Q: How many warning dialogs do you get? Of what nature? Q: If you reload the page does it still ask you to approve? Same number of times? Q: If you close your browser and reopen it and go to the page, any differences there? (Back to asking all the questions, or no questions, or fewer?) Q: If you *go to another browser *do you get that message? Or is it completely gone now? 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED On Fri, Nov 22, 2013 at 5:59 PM, Robert Hanson hans...@stolaf.edu wrote: Ho, ho! Looks like the Oracle guidelines are changing every day. This one in our favor. I have added the following line to the manifests inside the Jar files: Caller-Allowable-Codebase: * and I do believe that gets rid of the warning messages. Test of trusted-signed certificate for the full Jmol build http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Q: Did you get a warning message at all? Q: How many warning dialogs do you get? Of what nature? Q: If you reload the page does it still ask you to approve? Same number of times? Q: If you close your browser and reopen it and go to the page, any differences there? (Back to asking all the questions, or no questions, or fewer?) Q: If you *go to another browser *do you get that message? Or is it completely gone now? 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 -- 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
On 22 Nov 2013, at 23:59, Robert Hanson hans...@stolaf.edu wrote: Ho, ho! Looks like the Oracle guidelines are changing every day. This one in our favor. I have added the following line to the manifests inside the Jar files: Caller-Allowable-Codebase: * and I do believe that gets rid of the warning messages. Test of trusted-signed certificate for the full Jmol build http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED Q: Did you get a warning message at all? Q: How many warning dialogs do you get? Of what nature? Q: If you reload the page does it still ask you to approve? Same number of times? Q: If you close your browser and reopen it and go to the page, any differences there? (Back to asking all the questions, or no questions, or fewer?) Q: If you go to another browser do you get that message? Or is it completely gone now? Following an emptying of caches and reloading, no error/information message at all on initial load or refresh. Never seen such an absence before! Great. I have set Safari/OS X 10.9 to always trust chemapps.stolaf.edu signature.asc Description: Message signed with OpenPGP using GPGMail -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
