Re: [Jmol-users] Old File

OK, so perhaps it goes back as far as Firefox 3.6.0 or 3.6.2. Hopefully someone at Mozilla will take this on. It's not going to be just Jmol On Sun, Jul 25, 2010 at 5:45 PM, Philip Bays wrote: > Here is a link to one of the stereochemistry files. If you truncate the > link through the Stere

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

That's coming from Jmol.js. It's confused because you are using Safari with mozilla. I didn't know you could do that. On Sun, Jul 25, 2010 at 7:14 PM, Philip Bays wrote: > Hmmm. The attached image made my message too large so I will type it: > > I opened the NT1 page in Safari and then, using

Re: [Jmol-users] Modelkit Mode Question

I've added the hoverEnabled check to bond hover. On Sun, Jul 25, 2010 at 9:18 PM, Otis Rothenberger wrote: > Bob, > > For our isu/chemagic modelkit application, I have been controlling the > model kit (on, off, and kit functions) by page links and callback > functions. I wrote to you a while bac

[Jmol-users] Modelkit Mode Question

Bob, For our isu/chemagic modelkit application, I have been controlling the model kit (on, off, and kit functions) by page links and callback functions. I wrote to you a while back on this subject, and I have been using the hooks in the page you suggested: http://jmol.svn.sourceforge.net/viewv

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Hmmm. The attached image made my message too large so I will type it: I opened the NT1 page in Safari and then, using the develop menu, selected as user agent Firefox 3.63 (latest edition choice) and the chlorophyll load gave an error alert. Your web browser is not fully com

[Jmol-users] Old File

Here is a link to one of the stereochemistry files. If you truncate the link through the Stereochemistry, of it you use the menu button on this page, you will have other examples. But this is the only one that is running the unsigned applet. The others are signed. I have changed it for th

Re: [Jmol-users] History

Hmm. Still, we are seeing it now only with Firefox 3.6.7/3.6.8. Send us a link to one of those pages if you can. I still think this could be two issues. On Sun, Jul 25, 2010 at 5:25 PM, Philip Bays wrote: > No. I am saying the issue (java exception) was happening in May for me on > pages that

Re: [Jmol-users] History

No. I am saying the issue (java exception) was happening in May for me on pages that had previously worked. And the symptoms were the same -- only in Mozilla browsers. And I as not using jmol.js. They files were composed over 5 years ago. Phil On Jul 25, 2010, at 5:56 PM, Robert Hanson

Re: [Jmol-users] History

Right July 20, 2010: Firefox 3.6.7 was a security and stability update that fixed several issues.[19] July 23, 2010: Firefox 3.6.8 is a security and stability update that was released a mere 3 days after 3.6.7, to fix yet another

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Well, I figured out on my Mac how to go back to Java 1.4 using Java Preferences App, but oddly enough on my machine I can't get it to use Java 1.6 even though it is at the top of the preferences list (Jmol still reports Java 1.4 or 1.5) so I can't get this problem on my own machine. Also, oddly eno

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Sorry I could not find Firefox 3.5.7 to try. But for what is worth Firefox 4.0 beta, java 1.6 on an intel mac with 10.6.4 works fine. Jay On 7/25/10 4:01 PM, "Robert Hanson" wrote: We need someone to try this one last combination: Java 1.5 Firefox 3.5.7/Mac -- GOOD (Bob) Java 1.5 Firefox

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

We need someone to try this one last combination: Java 1.5 Firefox 3.5.7/Mac -- GOOD (Bob) Java 1.5 Firefox 3.6.8/Mac -- GOOD (Bob) Java 1.6 Firefox 3.5.7/Mac -- Java 1.6 Firefox 3.6.8/Mac -- BAD (Phil, Jay, Nick, Jeff) Looks like that will do it. I can't seem to update Java on my Ma

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

on a g4 for 10.4 and java 1.5.0_16 and fresh firefox everything worked well on an intel mac with 10.6.4, java 1.6.0 and fresh firefox, first time through everything worked well after closing and re-opening I got java.security.AccessControlException when trying to load chlorophyll. I hope that

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Bob: I have not responded to Bugzilla. Waiting to hear what you think we should say. I am off to a neighborhood picnic for a while. You need to take some time off too!! FYI: I have downloaded a fresh version of Firefox, to no avail. Phil On Jul 25, 2010, at 2:28 PM, Robert Hanson wrote:

[Jmol-users] History

For what it worth: Java update 2 (1.6.0_20) was posted on May 18, 2010. Mac OS 10.6.4 was released on June 15, 2010 There is an interesting history of Firefox 3.6 at: http://en.wikipedia.org/wiki/Mozilla_Firefox_3.6 J. Philip Bays Professor of Chemistry Department of Chemistry and

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Well, I've earned something today. I was unaware of the Java Preferences app in Mac OS X. I was unaware of the files that it had been caching for years! I tried this Mac users -- we need you to try this on Firefox 3.6.8: 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html 2. clic

[Jmol-users] java exception

Bob: I have searched back through my posts to the list. On June 7, I began a thread entitled Java Exception. In it I reported this problem, occurring with programs that had previously been running. Students had used them in the spring semester, though, I must confess, I had not checked them

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Furthermore, if after you have loaded the structure from the console, you can repeatedly reload the page and it runs correctly. On Jul 25, 2010, at 2:28 PM, Robert Hanson wrote: > OK, So now we have (on the Mac): > > Phil: unsigned applet is requiring useCommandThread, then it works -- 3.6.8

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Bob: As I recall, 3.6.8 was just released in the past week or so. The issue was also present in 3.6.7 for me. In fact, it has been an issue since the spring for my stereochemistry pages, which is why I moved to the signed applet for them at that time. (And this was about the time Firefox invo

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

OK, So now we have (on the Mac): Phil: unsigned applet is requiring useCommandThread, then it works -- 3.6.8 and Java 1.6.0_20 (I think) Bob: works fine, with fresh Firefox 3.6.8 and Java 1.5.0_16 Jay: works, fine with fresh Firefox 3.6.8 and Java [what??] Jeff: doesn't work with Firefox 3.6.8 an

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Go to Application/Utilities/Java Preferences.ap. Once open go to the network tab. Toward the bottom there is a button to view cache files. If you select them all, and there may be many, click the X at the top to delete them. Or, if you really want to demonstrate the issue, only remove the one

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Sorry, not sure where to find that. I cleared them from the Firefox Tools menu. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

I can confirm the same behavior. I clicked the link for NT3 and it worked fine. I reloaded NT1 (in another tab) and it worked fine. After restarting Firefox and loading NT1, it did not work again until NT3 was loaded and I reloaded the NT1 page. *

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Did you clear the Java cache from the java preferences panel? That seems to be the key. On Jul 25, 2010, at 1:15 PM, Jeff Hansen wrote: > Under no circumstances am I now able to get the chlorophyll model to load. I > cleared the cache and restarted Firefox and it didn't load chlorophyll. > >

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Under no circumstances am I now able to get the chlorophyll model to load. I cleared the cache and restarted Firefox and it didn't load chlorophyll. Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8 Java 1.6.0_20 **

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Bob: Several answers and a comment. The signed applet always works fine. In fact, once it is run, the unsigned page works fine, IF you do not close down firefox, and it correctly loads the unsigned applet.. The first structure always loads fine. I have not done your tests yet. However, let

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

I had no problems on a g4 with 10.4.11 and a fresh Firefox (3.6.8). On 7/25/10 10:24 AM, "Robert Hanson" wrote: OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8. No such problem. Phil, it looks to me like it might be a bad early version of 3.6.8. Mac users -- we need y

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Correction to my previous message, at successive attempts I had the following error : FileManager opening http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/Structures/chlorophyll.pdb eval ERROR: java.security.AccessControlException: access denied (java.util.PropertyPermission http.agent read)

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Le 25 juil. 2010 à 17:24, Robert Hanson a écrit : > > > Mac users -- we need you to try this on Firefox 3.6.8: > > 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html OK > 2. click on the link under the applet to display chlorophyl OK > 3. close the browser > 4. open the browser

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

OK, I've tested this on my Mac with a freshly downloaded Firefox 3.6.8. No such problem. Phil, it looks to me like it might be a bad early version of 3.6.8. Mac users -- we need you to try this on Firefox 3.6.8: 1. load http://www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html 2. click on the

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Phil, I went ahead and added a comment to that bug report to see what they say. I'll try to dig up Firefox 3.6.8 on a Mac around here to get additional specifics. Bob On Sun, Jul 25, 2010 at 8:30 AM, Robert Hanson wrote: > Phil, wait, there are a couple more issues before you go back to them. >

Re: [Jmol-users] Molecular graphics on ipad/iPhone

Or is it just that the iPad is not up to speed yet? On Sun, Jul 25, 2010 at 5:04 AM, Rzepa, Henry wrote: > >fun! > > > >On Sat, Jul 24, 2010 at 3:10 PM, Thomas Stout < thomasjst...@gmail.com>thomasjst...@gmail.com> wrote: > > > >Just an "FYI"... I ran across this today: > >

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Phil, wait, there are a couple more issues before you go back to them. 1) Did you say in that bug report that the signed applet has the same problem? That would be a BIG and different issue. 2) The first structure always loads, right? That indicates that Java can access its cache appropriately.

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

You should be able to get any version of Firefox, and in fact, if you search your Mac applications directory you will probably find it. Just start it. OK, I have run a little test: 1. Monitor the Java Cache before and after starting the browser and loading http://chemapps.stolaf.edu/jmol/docs/exa

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Not to get too technical, but if it a java bug, why does it show up only with Mozilla based browsers. I have a lot of other browsers, some of them very obscure they all work -- except the Mozilla based ones. Is there a source for getting a pre-3.6 version of Firefox? I would just like to try

Re: [Jmol-users] Appending with inline data not working in 12.0

Thanks for the clarification on append versus set appendNew - I was just looking for a reason that the data wasn't being appended. Seems to work now. Dean On Sun, Jul 25, 2010 at 1:05 AM, Robert Hanson wrote: > By the way, DATA is now merged with LOAD. You basically just use the load > command

Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Right - that does make sense -- submit a Java bug report, then. Make sure you have the latest Java available. On Sun, Jul 25, 2010 at 6:27 AM, Philip Bays wrote: > Does this response make sense to anyone? If Firefox does not look at java > cache, how can adjusting the cache (removing a file, tu

[Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly

Does this response make sense to anyone? If Firefox does not look at java cache, how can adjusting the cache (removing a file, turning it on or off) have any affect? Because it is a bug in java that does not affect non-mozilla browsers??? Phil Begin forwarded message: > From: bugzilla-dae..

Re: [Jmol-users] Molecular graphics on ipad/iPhone

>fun! > >On Sat, Jul 24, 2010 at 3:10 PM, Thomas Stout ><thomasjst...@gmail.com> wrote: > >Just an "FYI"... I ran across this today: >http://www.molsoft.com/ipad.html > I note with interest that whilst the iPad can receive (by emai