Re: [Jmol-users] Super Simple JSMol
I don't think it has anything to do with that, but I won't have time to check on that until late next week, unfortunately. On Sat, Nov 9, 2013 at 6:01 AM, Otis Rothenberger wrote: > Bob, > > I assume this is the same problem I'm seeing in a number of situations, > primarily with callbacks, bindings, and partial charge calculation. I may > also see it with minimization. I'm not sure. The problems are all random. > > I don't see the problems when I use modelkitmode from the Jmol > modelkitmode menus, which is an option for me. Is there away to pop up that > modelkitmode menu with a command - i.e. like the menu command for the Jmol > menu. > > Otis > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > On Nov 8, 2013, at 11:20 PM, Robert Hanson wrote: > > Understand that that is just a "slow-mode" test that will revert to not > working before the weekend is over when I take out those comments. We do > not have a solution to this. I might be able to report it, but I think we > just have to hope that this gets fixed in the next Safari release. I cannot > imagine a small example that reproduces it. We tried this on three > different Macs, and only one had the problem (and two had the same 7.0 > Safari). I think we just have to write off that particular version of > Safari. > > > > > > > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. > Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and > register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Bob, I assume this is the same problem I'm seeing in a number of situations, primarily with callbacks, bindings, and partial charge calculation. I may also see it with minimization. I'm not sure. The problems are all random. I don't see the problems when I use modelkitmode from the Jmol modelkitmode menus, which is an option for me. Is there away to pop up that modelkitmode menu with a command - i.e. like the menu command for the Jmol menu. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 8, 2013, at 11:20 PM, Robert Hanson wrote: > Understand that that is just a "slow-mode" test that will revert to not > working before the weekend is over when I take out those comments. We do not > have a solution to this. I might be able to report it, but I think we just > have to hope that this gets fixed in the next Safari release. I cannot > imagine a small example that reproduces it. We tried this on three different > Macs, and only one had the problem (and two had the same 7.0 Safari). I think > we just have to write off that particular version of Safari. > > > > -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Understand that that is just a "slow-mode" test that will revert to not working before the weekend is over when I take out those comments. We do not have a solution to this. I might be able to report it, but I think we just have to hope that this gets fixed in the next Safari release. I cannot imagine a small example that reproduces it. We tried this on three different Macs, and only one had the problem (and two had the same 7.0 Safari). I think we just have to write off that particular version of Safari. On Fri, Nov 8, 2013 at 6:19 PM, Philip Bays wrote: > Right. It now works:-) > > > On Nov 8, 2013, at 7:56 PM, Robert Hanson wrote: > > > Well, good news and bad news. The good news is that I can identify the > situation that causes this bug. The bad news is that it is (specifically, I > think) a Safari 7.0 bug totally out of our control. Something VERY odd is > happening in this system that does depend upon timing. So, for example, > just adding console debugging messages to the process prevents the problem. > Here are two runs on the same Mac with two different comment sets, tracking > when variables are defined: > > > > setb setting testflag3 to false 0.27491440204903483 > > setb setting testflag4 to undefined 0.27491440204903483 > > setb setting tracealpha to undefined 0.27491440204903483 > > setb setting translucent to undefined 0.27491440204903483 > > setb setting twistedsheets to undefined 0.27491440204903483 > > setb setting usearcball to undefined 0.27491440204903483 > > setb setting useminimizationthread to undefined 0.27491440204903483 > > > > > > > > setb OK > > setb setting testflag3 to false 0.11562557681463659 > > setb OK > > setb setting testflag4 to false 0.11562557681463659 > > setb OK > > setb setting tracealpha to true 0.11562557681463659 > > setb OK > > setb setting translucent to true 0.11562557681463659 > > setb OK > > setb setting twistedsheets to false 0.11562557681463659 > > setb OK > > setb setting usearcball to undefined 0.11562557681463659 > > setb OK > > setb setting useminimizationthread to undefined 0.11562557681463659 > > setb OK > > > > Notice that the "undefined" start at different points. And if there are > no comments, the undefined start earlier. > > > > Amazingly, what is between the "undefined" and the OK lines is a call > that REQUIRES the variable to be defined -- thus the original error, BUT > these are not throwing that error now! Huh? you say? Impossible? Right. One > would think that. > > > > So this is about all I'm going to do on this now. No real solution and > no work-around. I don't know what the solution is. But I bet this page > works now that the comments are in. Right, Nick? > > > > > -- > > November Webinars for C, C++, Fortran Developers > > Accelerate application performance with scalable programming models. > Explore > > techniques for threading, error checking, porting, and tuning. Get the > most > > from the latest Intel processors and coprocessors. See abstracts and > register > > > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/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 > > > > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. > Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and > register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Right. It now works:-) On Nov 8, 2013, at 7:56 PM, Robert Hanson wrote: > Well, good news and bad news. The good news is that I can identify the > situation that causes this bug. The bad news is that it is (specifically, I > think) a Safari 7.0 bug totally out of our control. Something VERY odd is > happening in this system that does depend upon timing. So, for example, just > adding console debugging messages to the process prevents the problem. Here > are two runs on the same Mac with two different comment sets, tracking when > variables are defined: > > setb setting testflag3 to false 0.27491440204903483 > setb setting testflag4 to undefined 0.27491440204903483 > setb setting tracealpha to undefined 0.27491440204903483 > setb setting translucent to undefined 0.27491440204903483 > setb setting twistedsheets to undefined 0.27491440204903483 > setb setting usearcball to undefined 0.27491440204903483 > setb setting useminimizationthread to undefined 0.27491440204903483 > > > > setb OK > setb setting testflag3 to false 0.11562557681463659 > setb OK > setb setting testflag4 to false 0.11562557681463659 > setb OK > setb setting tracealpha to true 0.11562557681463659 > setb OK > setb setting translucent to true 0.11562557681463659 > setb OK > setb setting twistedsheets to false 0.11562557681463659 > setb OK > setb setting usearcball to undefined 0.11562557681463659 > setb OK > setb setting useminimizationthread to undefined 0.11562557681463659 > setb OK > > Notice that the "undefined" start at different points. And if there are no > comments, the undefined start earlier. > > Amazingly, what is between the "undefined" and the OK lines is a call that > REQUIRES the variable to be defined -- thus the original error, BUT these are > not throwing that error now! Huh? you say? Impossible? Right. One would think > that. > > So this is about all I'm going to do on this now. No real solution and no > work-around. I don't know what the solution is. But I bet this page works now > that the comments are in. Right, Nick? > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Well, good news and bad news. The good news is that I can identify the situation that causes this bug. The bad news is that it is (specifically, I think) a Safari 7.0 bug totally out of our control. Something VERY odd is happening in this system that does depend upon timing. So, for example, just adding console debugging messages to the process prevents the problem. Here are two runs on the same Mac with two different comment sets, tracking when variables are defined: setb setting testflag3 to false 0.27491440204903483 setb setting testflag4 to undefined 0.27491440204903483 setb setting tracealpha to undefined 0.27491440204903483 setb setting translucent to undefined 0.27491440204903483 setb setting twistedsheets to undefined 0.27491440204903483 setb setting usearcball to undefined 0.27491440204903483 setb setting useminimizationthread to undefined 0.27491440204903483 setb OK setb setting testflag3 to false 0.11562557681463659 setb OK setb setting testflag4 to false 0.11562557681463659 setb OK setb setting tracealpha to true 0.11562557681463659 setb OK setb setting translucent to true 0.11562557681463659 setb OK setb setting twistedsheets to false 0.11562557681463659 setb OK setb setting usearcball to undefined 0.11562557681463659 setb OK setb setting useminimizationthread to undefined 0.11562557681463659 setb OK Notice that the "undefined" start at different points. And if there are no comments, the undefined start earlier. Amazingly, what is between the "undefined" and the OK lines is a call that REQUIRES the variable to be defined -- thus the original error, BUT these are not throwing that error now! Huh? you say? Impossible? Right. One would think that. So this is about all I'm going to do on this now. No real solution and no work-around. I don't know what the solution is. But I bet this page works now that the comments are in. Right, Nick? -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Sorry that just got to you today. I sent it several days ago and it was held up by the administrator, probably because of the included error messages. Phil On Nov 8, 2013, at 10:40 AM, Robert Hanson wrote: > planning on getting to this today > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
planning on getting to this today -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
When you try to open the link without the console on, nothing happens. if you
then open the error console, you see the following:
[Error] Failed to load resource: the server responded with a status of 503
(Service Unavailable) (get-js, line 0)
[Error] java.lang.NullPointerException
(anonymous function) (core.z.js, line 398)
(anonymous function) (core.z.js, line 2258)
(anonymous function) (core.z.js, line 2250)
(anonymous function) (core.z.js, line 2227)
instantialize (JSmol.min.js, line 343)
(anonymous function) (core.z.js, line 2225)
innerTypeInstance (JSmol.min.js, line 358)
(anonymous function) (core.z.js, line 2194)
(anonymous function) (core.z.js, line 938)
(anonymous function) (core.z.js, line 926)
(anonymous function) (core.z.js, line 917)
instantialize (JSmol.min.js, line 343)
(anonymous function) (core.z.js, line 913)
(anonymous function) (core.z.js, line 506)
(anonymous function) (core.z.js, line 506)
(anonymous function) (core.z.js, line 504)
instantialize (JSmol.min.js, line 343)
(anonymous function) (core.z.js, line 503)
__startAppletJS (JSmol.min.js, line 257)
__nextExecution (JSmol.min.js, line 262)
If you now reload the page, you see the same error messages, but the applet
loads.
On Nov 6, 2013, at 11:25 AM, Robert Hanson wrote:
> But straight-up fresh-start Maverick Safari just never shows the JSapp at
> all?
>
> And, when the console is opened, there are no reports there?
>
>
>
>
> On Wed, Nov 6, 2013 at 8:21 AM, Philip Bays wrote:
> Once the applet is loaded (with the error console on) things seem to work,
> though rather clunky.
>
>
> On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
>
>> Other links work just fine, though, right? Just the center ones I listed are
>> problematic? Or the applet does not work at all?
>>
>>
>> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
>> I observe the same by turning on the “Show Error Console” . The page then
>> loads.
>>
>>
>> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger wrote:
>>
>>> Dang!
>>>
>>> When I put the JavaScript console up, it loads on Maverick Safari.
>>>
>>> Timing...
>>>
>>> Otis
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
>>> wrote:
>>>
Bob,
OK, you've been right on this point in the past (100% right!), but
remember these are Mavericks Safari problems - not Chrome and FF. I'm not
sure about MSIE.
To work on this, I've been bouncing around versions of JSmol. Right now
the version that you put up yesterday does not load on Mavericks Safari.
See:
http://chemagic.com/JSmolVMK.htm
on Mavericks Safari vs Chrome.
I need to decide what version to use to scope out problems. I've jumped
back to 13.3.3 before I installed the version you posted yesterday. I'll
leave this broken version in place for you to take a look.
If there are any Mac Mavericks users, I'd be interested if you see what
I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
this page?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
> Otis, don't try to solve this problem yourself. I have access to plenty
> of Macs. Point me to the simplest pages you can conjure up that cause the
> problem and let me fix it. No rogue hacks, please!
>
> This one sounds like a bug in the asynchronous scripting components of
> Jmol within the Java-derived code.
>
> Bob
>
>
>
> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
> wrote:
> Bob and Phil,
>
> It does not work for me either in Safari for Mavericks, but know this:
> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
> rewriting our whole virtual model kit to deal with the quirks. I don't
> think these are JSmol problems or bugs. This version of Safari is just
> not behaving normally. Callbacks are a problem. Things that I do
> sequentially, no longer work. For example, if I want to do a partial
> charge calculation in script, I must play a game with two JavaScript
> functions:
>
> function chargeStuff1() {
> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
> }
>
> function chargeStuff2() {
> THE REST OS THE Jmolscript STUFF
> }
>
> I never had to do this before, and now I only have to do it for Mavericks
> Safari. Currently, I'm looking for ways to avoid call backs.
>
> Maybe this is about Safari bugs, b
Re: [Jmol-users] Super Simple JSMol
just hang on on this one; you won't figure it out
On Wed, Nov 6, 2013 at 8:48 AM, Philip Bays wrote:
> On looking at the console more closely, the item that is colored red in
> the console seems to be “get-js” which shows a status of 503. Not sure
> what that means. However, repeated loading of the page shows the timing
> on that item varying from 55 ms to over 2 sec.
>
>
> On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
>
> Other links work just fine, though, right? Just the center ones I listed
> are problematic? Or the applet does not work at all?
>
>
> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
>
>> I observe the same by turning on the “Show Error Console” . The page
>> then loads.
>>
>>
>> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger
>> wrote:
>>
>> Dang!
>>
>> When I put the JavaScript console up, it loads on Maverick Safari.
>>
>> Timing...
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
>> wrote:
>>
>> Bob,
>>
>> OK, you've been right on this point in the past (100% right!), but
>> remember these are Mavericks Safari problems - not Chrome and FF. I'm not
>> sure about MSIE.
>>
>> To work on this, I've been bouncing around versions of JSmol. Right now
>> the version that you put up yesterday does not load on Mavericks Safari.
>> See:
>>
>> http://chemagic.com/JSmolVMK.htm
>>
>> on Mavericks Safari vs Chrome.
>>
>> I need to decide what version to use to scope out problems. I've jumped
>> back to 13.3.3 before I installed the version you posted yesterday. I'll
>> leave this broken version in place for you to take a look.
>>
>> If there are any Mac Mavericks users, I'd be interested if you see what
>> I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
>> this page?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>
>> Otis, don't try to solve this problem yourself. I have access to plenty
>> of Macs. Point me to the simplest pages you can conjure up that cause the
>> problem and let me fix it. No rogue hacks, please!
>>
>> This one sounds like a bug in the asynchronous scripting components of
>> Jmol within the Java-derived code.
>>
>> Bob
>>
>>
>>
>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>> wrote:
>>
>>> Bob and Phil,
>>>
>>> It does not work for me either in Safari for Mavericks, but know this:
>>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>>> rewriting our whole virtual model kit to deal with the quirks. I don't
>>> think these are JSmol problems or bugs. This version of Safari is just not
>>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>>> no longer work. For example, if I want to do a partial charge calculation
>>> in script, I must play a game with two JavaScript functions:
>>>
>>> function chargeStuff1() {
>>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>>> }
>>>
>>> function chargeStuff2() {
>>> THE REST OS THE Jmolscript STUFF
>>> }
>>>
>>> I never had to do this before, and now I only have to do it for
>>> Mavericks Safari. Currently, I'm looking for ways to avoid call backs.
>>>
>>> Maybe this is about Safari bugs, but I have the feeling that Apple is
>>> just doing things differently. I mentioned in a previous note that they
>>> purposely degraded the functionality of Pages and Numbers just to make this
>>> office duo compatible with hand held devices.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>>
>>> still a problem? I just tested it with my 1st-gen iPad with Safari and
>>> it was fine.
>>>
>>>
>>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>>
I have been out of the loop for a while taking care of my wife who has
a broken and repaired knee cap. I knew we ought to pay off those gambling
debts:-)
I have been looking today at the Super Simple JSmol page (
http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
However, the HTML5 link does not work in Safari. A new page is launched
with the search bar, but the applet (or whatever we are now calling it)
does not load even after waiting for 10 minutes.
On the other hand, if I simply open the “Show Error Console” in the
developers menu in Safari, the HTML5 loads fine. It is not clear to why
simply having the console open allows jsmol to load. Is it a timing
thing??
I see the following error messages in the console for the incident when
jsmol did not load:
[Error] Failed to load resource: the server responded with a status of
503 (Service Unavailable
Re: [Jmol-users] Super Simple JSMol
Bob,
I put 13.3.9_2013.11.06 on:
http://chemistry.illinoisstate.edu/osrothen/JSmolVMK.htm
To reiterate, if you get it loaded by using the Safari Error Console trick,
then the following problem can be observed:
You can see one of the problems, again on Mavericks Safari. Click the Edit
button and do an H click replacement with C. It replaces the H with C, then
freezes. It's choking on a message call back that does some housekeeping:
if ((z.indexOf("assign atom") > -1 || z.indexOf("assign connect") > -1 ||
z.indexOf("assign bond") > -1) && menuNum == 6) {
if (aIN < 50) { Jmol.script(jmolApplet0, 'minimize
steps 2;'); }
Jmol.script(jmolApplet0, 'select *; wireframe 0.15;
spacefill 23%; boundbox {*};centerat boundbox; {*}.partialcharge=0.0; color
label pink;label ""; select formalCharge <> 0;label %C;');
}
While the variables may be obscure, I'm basically checking number of atoms and
doing a really crude minimize if this number is less than 50. This is followed
by some display housekeeping.
On clicking the edit button, the Jmol console reports:
bondPicking = false
atomPicking = false
modelkitMode = false
Click an atom to convert it to C, or click-drag|away from an atom to add a new
atom.
bondPicking = false
atomPicking = true
Now that I have the consoles open (Jmol and Safari per Phils note), it works
properly. Jmol console reporting:
Initial MMFF E = 49.879 kJ criterion = 0.004187 max steps = 2
MMFF Step 2E = 10.372609dE = -0.820101
18 atoms selected
0 atoms selected
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 11:14 AM, Robert Hanson wrote:
> Just for reference, I would like comments specifically based on
>
> http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.06.zip
>
> Anything older than that will just confuse the issue. Obviously something
> broke
>
> Bob
>
>
--
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Re: [Jmol-users] Super Simple JSMol
First check -- this has nothing to do with the console. It's a null
pointer exception within Jmol.
On Wed, Nov 6, 2013 at 8:48 AM, Philip Bays wrote:
> On looking at the console more closely, the item that is colored red in
> the console seems to be “get-js” which shows a status of 503. Not sure
> what that means. However, repeated loading of the page shows the timing
> on that item varying from 55 ms to over 2 sec.
>
>
> On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
>
> Other links work just fine, though, right? Just the center ones I listed
> are problematic? Or the applet does not work at all?
>
>
> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
>
>> I observe the same by turning on the “Show Error Console” . The page
>> then loads.
>>
>>
>> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger
>> wrote:
>>
>> Dang!
>>
>> When I put the JavaScript console up, it loads on Maverick Safari.
>>
>> Timing...
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
>> wrote:
>>
>> Bob,
>>
>> OK, you've been right on this point in the past (100% right!), but
>> remember these are Mavericks Safari problems - not Chrome and FF. I'm not
>> sure about MSIE.
>>
>> To work on this, I've been bouncing around versions of JSmol. Right now
>> the version that you put up yesterday does not load on Mavericks Safari.
>> See:
>>
>> http://chemagic.com/JSmolVMK.htm
>>
>> on Mavericks Safari vs Chrome.
>>
>> I need to decide what version to use to scope out problems. I've jumped
>> back to 13.3.3 before I installed the version you posted yesterday. I'll
>> leave this broken version in place for you to take a look.
>>
>> If there are any Mac Mavericks users, I'd be interested if you see what
>> I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
>> this page?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>
>> Otis, don't try to solve this problem yourself. I have access to plenty
>> of Macs. Point me to the simplest pages you can conjure up that cause the
>> problem and let me fix it. No rogue hacks, please!
>>
>> This one sounds like a bug in the asynchronous scripting components of
>> Jmol within the Java-derived code.
>>
>> Bob
>>
>>
>>
>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>> wrote:
>>
>>> Bob and Phil,
>>>
>>> It does not work for me either in Safari for Mavericks, but know this:
>>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>>> rewriting our whole virtual model kit to deal with the quirks. I don't
>>> think these are JSmol problems or bugs. This version of Safari is just not
>>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>>> no longer work. For example, if I want to do a partial charge calculation
>>> in script, I must play a game with two JavaScript functions:
>>>
>>> function chargeStuff1() {
>>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>>> }
>>>
>>> function chargeStuff2() {
>>> THE REST OS THE Jmolscript STUFF
>>> }
>>>
>>> I never had to do this before, and now I only have to do it for
>>> Mavericks Safari. Currently, I'm looking for ways to avoid call backs.
>>>
>>> Maybe this is about Safari bugs, but I have the feeling that Apple is
>>> just doing things differently. I mentioned in a previous note that they
>>> purposely degraded the functionality of Pages and Numbers just to make this
>>> office duo compatible with hand held devices.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>>
>>> still a problem? I just tested it with my 1st-gen iPad with Safari and
>>> it was fine.
>>>
>>>
>>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>>
I have been out of the loop for a while taking care of my wife who has
a broken and repaired knee cap. I knew we ought to pay off those gambling
debts:-)
I have been looking today at the Super Simple JSmol page (
http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
However, the HTML5 link does not work in Safari. A new page is launched
with the search bar, but the applet (or whatever we are now calling it)
does not load even after waiting for 10 minutes.
On the other hand, if I simply open the “Show Error Console” in the
developers menu in Safari, the HTML5 loads fine. It is not clear to why
simply having the console open allows jsmol to load. Is it a timing
thing??
I see the following error messages in the console for the incident when
jsmol did not load:
[Error] Failed to load resource: the server responded wi
Re: [Jmol-users] Super Simple JSMol
Bob,
I'm running 2013.11.05. I'll change it after I send this.
Currently, you can see one of the problems, again on Mavericks Safari. Click
the Edit button and do an H click replacement with C. It replaces the H with C,
then freezes. It's choking on a message call back that does some housekeeping:
if ((z.indexOf("assign atom") > -1 || z.indexOf("assign connect") > -1 ||
z.indexOf("assign bond") > -1) && menuNum == 6) {
if (aIN < 50) { Jmol.script(jmolApplet0, 'minimize
steps 2;'); }
Jmol.script(jmolApplet0, 'select *; wireframe 0.15;
spacefill 23%; boundbox {*};centerat boundbox; {*}.partialcharge=0.0; color
label pink;label ""; select formalCharge <> 0;label %C;');
}
While the variables may be obscure, I'm basically checking number of atoms and
doing a really crude minimize if this number is less than 50. This is followed
by some display housekeeping.
On clicking the edit button, the Jmol console reports:
bondPicking = false
atomPicking = false
modelkitMode = false
Click an atom to convert it to C, or click-drag|away from an atom to add a new
atom.
bondPicking = false
atomPicking = true
Now that I have the consoles open (Jmol and Safari per Phils note), it works
properly. Jmol console reporting:
Initial MMFF E = 49.879 kJ criterion = 0.004187 max steps = 2
MMFF Step 2E = 10.372609dE = -0.820101
18 atoms selected
0 atoms selected
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 11:14 AM, Robert Hanson wrote:
> Just for reference, I would like comments specifically based on
>
> http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.06.zip
>
> Anything older than that will just confuse the issue. Obviously something
> broke
>
> Bob
>
>
>
> On Wed, Nov 6, 2013 at 8:08 AM, Otis Rothenberger
> wrote:
> Dang!
>
> When I put the JavaScript console up, it loads on Maverick Safari.
>
> Timing...
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger wrote:
>
>> Bob,
>>
>> OK, you've been right on this point in the past (100% right!), but remember
>> these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
>> MSIE.
>>
>> To work on this, I've been bouncing around versions of JSmol. Right now the
>> version that you put up yesterday does not load on Mavericks Safari. See:
>>
>> http://chemagic.com/JSmolVMK.htm
>>
>> on Mavericks Safari vs Chrome.
>>
>> I need to decide what version to use to scope out problems. I've jumped back
>> to 13.3.3 before I installed the version you posted yesterday. I'll leave
>> this broken version in place for you to take a look.
>>
>> If there are any Mac Mavericks users, I'd be interested if you see what I'm
>> seeing on the page above. Also, I wonder what Lion Safari is doing on this
>> page?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>
>>> Otis, don't try to solve this problem yourself. I have access to plenty of
>>> Macs. Point me to the simplest pages you can conjure up that cause the
>>> problem and let me fix it. No rogue hacks, please!
>>>
>>> This one sounds like a bug in the asynchronous scripting components of Jmol
>>> within the Java-derived code.
>>>
>>> Bob
>>>
>>>
>>>
>>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>>> wrote:
>>> Bob and Phil,
>>>
>>> It does not work for me either in Safari for Mavericks, but know this:
>>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>>> rewriting our whole virtual model kit to deal with the quirks. I don't
>>> think these are JSmol problems or bugs. This version of Safari is just not
>>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>>> no longer work. For example, if I want to do a partial charge calculation
>>> in script, I must play a game with two JavaScript functions:
>>>
>>> function chargeStuff1() {
>>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>>> }
>>>
>>> function chargeStuff2() {
>>> THE REST OS THE Jmolscript STUFF
>>> }
>>>
>>> I never had to do this before, and now I only have to do it for Mavericks
>>> Safari. Currently, I'm looking for ways to avoid call backs.
>>>
>>> Maybe this is about Safari bugs, but I have the feeling that Apple is just
>>> doing things differently. I mentioned in a previous note that they
>>> purposely degraded the functionality of Pages and Numbers just to make this
>>> office duo compatible with hand held devices.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>>
still a problem? I just tested it with my 1st-gen
Re: [Jmol-users] Super Simple JSMol
On looking at the console more closely, the item that is colored red in the
console seems to be “get-js” which shows a status of 503. Not sure what that
means. However, repeated loading of the page shows the timing on that item
varying from 55 ms to over 2 sec.
On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
> Other links work just fine, though, right? Just the center ones I listed are
> problematic? Or the applet does not work at all?
>
>
> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
> I observe the same by turning on the “Show Error Console” . The page then
> loads.
>
>
> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger wrote:
>
>> Dang!
>>
>> When I put the JavaScript console up, it loads on Maverick Safari.
>>
>> Timing...
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger wrote:
>>
>>> Bob,
>>>
>>> OK, you've been right on this point in the past (100% right!), but remember
>>> these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
>>> MSIE.
>>>
>>> To work on this, I've been bouncing around versions of JSmol. Right now the
>>> version that you put up yesterday does not load on Mavericks Safari. See:
>>>
>>> http://chemagic.com/JSmolVMK.htm
>>>
>>> on Mavericks Safari vs Chrome.
>>>
>>> I need to decide what version to use to scope out problems. I've jumped
>>> back to 13.3.3 before I installed the version you posted yesterday. I'll
>>> leave this broken version in place for you to take a look.
>>>
>>> If there are any Mac Mavericks users, I'd be interested if you see what I'm
>>> seeing on the page above. Also, I wonder what Lion Safari is doing on this
>>> page?
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>>
Otis, don't try to solve this problem yourself. I have access to plenty of
Macs. Point me to the simplest pages you can conjure up that cause the
problem and let me fix it. No rogue hacks, please!
This one sounds like a bug in the asynchronous scripting components of
Jmol within the Java-derived code.
Bob
On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
wrote:
Bob and Phil,
It does not work for me either in Safari for Mavericks, but know this:
Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
rewriting our whole virtual model kit to deal with the quirks. I don't
think these are JSmol problems or bugs. This version of Safari is just not
behaving normally. Callbacks are a problem. Things that I do sequentially,
no longer work. For example, if I want to do a partial charge calculation
in script, I must play a game with two JavaScript functions:
function chargeStuff1() {
Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
}
function chargeStuff2() {
THE REST OS THE Jmolscript STUFF
}
I never had to do this before, and now I only have to do it for Mavericks
Safari. Currently, I'm looking for ways to avoid call backs.
Maybe this is about Safari bugs, but I have the feeling that Apple is just
doing things differently. I mentioned in a previous note that they
purposely degraded the functionality of Pages and Numbers just to make
this office duo compatible with hand held devices.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
> still a problem? I just tested it with my 1st-gen iPad with Safari and it
> was fine.
>
>
> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
> I have been out of the loop for a while taking care of my wife who has a
> broken and repaired knee cap. I knew we ought to pay off those gambling
> debts:-)
>
> I have been looking today at the Super Simple JSmol page
> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>
> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
> However, the HTML5 link does not work in Safari. A new page is launched
> with the search bar, but the applet (or whatever we are now calling it)
> does not load even after waiting for 10 minutes.
>
> On the other hand, if I simply open the “Show Error Console” in the
> developers menu in Safari, the HTML5 loads fine. It is not clear to why
> simply having the console open allows jsmol to load. Is it a timing
> thing??
>
> I see the following error messages in the console for the incident when
> jsmol did not load:
>
> [Error] Failed to load
Re: [Jmol-users] Super Simple JSMol
Other links work just fine, though, right? Just the center ones I listed
are problematic? Or the applet does not work at all?
On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
> I observe the same by turning on the “Show Error Console” . The page then
> loads.
>
>
> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger
> wrote:
>
> Dang!
>
> When I put the JavaScript console up, it loads on Maverick Safari.
>
> Timing...
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
> wrote:
>
> Bob,
>
> OK, you've been right on this point in the past (100% right!), but
> remember these are Mavericks Safari problems - not Chrome and FF. I'm not
> sure about MSIE.
>
> To work on this, I've been bouncing around versions of JSmol. Right now
> the version that you put up yesterday does not load on Mavericks Safari.
> See:
>
> http://chemagic.com/JSmolVMK.htm
>
> on Mavericks Safari vs Chrome.
>
> I need to decide what version to use to scope out problems. I've jumped
> back to 13.3.3 before I installed the version you posted yesterday. I'll
> leave this broken version in place for you to take a look.
>
> If there are any Mac Mavericks users, I'd be interested if you see what
> I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
> this page?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>
> Otis, don't try to solve this problem yourself. I have access to plenty of
> Macs. Point me to the simplest pages you can conjure up that cause the
> problem and let me fix it. No rogue hacks, please!
>
> This one sounds like a bug in the asynchronous scripting components of
> Jmol within the Java-derived code.
>
> Bob
>
>
>
> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
> wrote:
>
>> Bob and Phil,
>>
>> It does not work for me either in Safari for Mavericks, but know this:
>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>> rewriting our whole virtual model kit to deal with the quirks. I don't
>> think these are JSmol problems or bugs. This version of Safari is just not
>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>> no longer work. For example, if I want to do a partial charge calculation
>> in script, I must play a game with two JavaScript functions:
>>
>> function chargeStuff1() {
>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>> }
>>
>> function chargeStuff2() {
>> THE REST OS THE Jmolscript STUFF
>> }
>>
>> I never had to do this before, and now I only have to do it for Mavericks
>> Safari. Currently, I'm looking for ways to avoid call backs.
>>
>> Maybe this is about Safari bugs, but I have the feeling that Apple is
>> just doing things differently. I mentioned in a previous note that they
>> purposely degraded the functionality of Pages and Numbers just to make this
>> office duo compatible with hand held devices.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>
>> still a problem? I just tested it with my 1st-gen iPad with Safari and it
>> was fine.
>>
>>
>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>
>>> I have been out of the loop for a while taking care of my wife who has a
>>> broken and repaired knee cap. I knew we ought to pay off those gambling
>>> debts:-)
>>>
>>> I have been looking today at the Super Simple JSmol page (
>>> http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>>>
>>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
>>> However, the HTML5 link does not work in Safari. A new page is launched
>>> with the search bar, but the applet (or whatever we are now calling it)
>>> does not load even after waiting for 10 minutes.
>>>
>>> On the other hand, if I simply open the “Show Error Console” in the
>>> developers menu in Safari, the HTML5 loads fine. It is not clear to why
>>> simply having the console open allows jsmol to load. Is it a timing thing??
>>>
>>> I see the following error messages in the console for the incident when
>>> jsmol did not load:
>>>
>>> [Error] Failed to load resource: the server responded with a status of
>>> 503 (Service Unavailable) (get-js, line 0)
>>> [Error] java.lang.NullPointerException
>>> (anonymous function) (core.z.js, line 398)
>>> (anonymous function) (core.z.js, line 2256)
>>> (anonymous function) (core.z.js, line 2248)
>>> (anonymous function) (core.z.js, line 2225)
>>> instantialize (JSmol.min.js, line 343)
>>> (anonymous function) (core.z.js, line 2223)
>>> innerTypeInstance (JSmol.min.js, line 358)
>>> (anonymous function) (core.z.js, line 2192)
>>> (anonymous function) (core.z.js, line 938)
>>> (anonymous function) (core.
Re: [Jmol-users] Super Simple JSMol
But straight-up fresh-start Maverick Safari just never shows the JSapp at
all?
And, when the console is opened, there are no reports there?
On Wed, Nov 6, 2013 at 8:21 AM, Philip Bays wrote:
> Once the applet is loaded (with the error console on) things seem to work,
> though rather clunky.
>
>
> On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
>
> Other links work just fine, though, right? Just the center ones I listed
> are problematic? Or the applet does not work at all?
>
>
> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
>
>> I observe the same by turning on the “Show Error Console” . The page
>> then loads.
>>
>>
>> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger
>> wrote:
>>
>> Dang!
>>
>> When I put the JavaScript console up, it loads on Maverick Safari.
>>
>> Timing...
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
>> wrote:
>>
>> Bob,
>>
>> OK, you've been right on this point in the past (100% right!), but
>> remember these are Mavericks Safari problems - not Chrome and FF. I'm not
>> sure about MSIE.
>>
>> To work on this, I've been bouncing around versions of JSmol. Right now
>> the version that you put up yesterday does not load on Mavericks Safari.
>> See:
>>
>> http://chemagic.com/JSmolVMK.htm
>>
>> on Mavericks Safari vs Chrome.
>>
>> I need to decide what version to use to scope out problems. I've jumped
>> back to 13.3.3 before I installed the version you posted yesterday. I'll
>> leave this broken version in place for you to take a look.
>>
>> If there are any Mac Mavericks users, I'd be interested if you see what
>> I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
>> this page?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>
>> Otis, don't try to solve this problem yourself. I have access to plenty
>> of Macs. Point me to the simplest pages you can conjure up that cause the
>> problem and let me fix it. No rogue hacks, please!
>>
>> This one sounds like a bug in the asynchronous scripting components of
>> Jmol within the Java-derived code.
>>
>> Bob
>>
>>
>>
>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>> wrote:
>>
>>> Bob and Phil,
>>>
>>> It does not work for me either in Safari for Mavericks, but know this:
>>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>>> rewriting our whole virtual model kit to deal with the quirks. I don't
>>> think these are JSmol problems or bugs. This version of Safari is just not
>>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>>> no longer work. For example, if I want to do a partial charge calculation
>>> in script, I must play a game with two JavaScript functions:
>>>
>>> function chargeStuff1() {
>>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>>> }
>>>
>>> function chargeStuff2() {
>>> THE REST OS THE Jmolscript STUFF
>>> }
>>>
>>> I never had to do this before, and now I only have to do it for
>>> Mavericks Safari. Currently, I'm looking for ways to avoid call backs.
>>>
>>> Maybe this is about Safari bugs, but I have the feeling that Apple is
>>> just doing things differently. I mentioned in a previous note that they
>>> purposely degraded the functionality of Pages and Numbers just to make this
>>> office duo compatible with hand held devices.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>>
>>> still a problem? I just tested it with my 1st-gen iPad with Safari and
>>> it was fine.
>>>
>>>
>>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>>
I have been out of the loop for a while taking care of my wife who has
a broken and repaired knee cap. I knew we ought to pay off those gambling
debts:-)
I have been looking today at the Super Simple JSmol page (
http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
However, the HTML5 link does not work in Safari. A new page is launched
with the search bar, but the applet (or whatever we are now calling it)
does not load even after waiting for 10 minutes.
On the other hand, if I simply open the “Show Error Console” in the
developers menu in Safari, the HTML5 loads fine. It is not clear to why
simply having the console open allows jsmol to load. Is it a timing
thing??
I see the following error messages in the console for the incident when
jsmol did not load:
[Error] Failed to load resource: the server responded with a status of
503 (Service Unavailable) (get-js, line 0)
[Error] java.lang.NullPointerException
(anonymou
Re: [Jmol-users] Super Simple JSMol
Once the applet is loaded (with the error console on) things seem to work,
though rather clunky.
On Nov 6, 2013, at 11:20 AM, Robert Hanson wrote:
> Other links work just fine, though, right? Just the center ones I listed are
> problematic? Or the applet does not work at all?
>
>
> On Wed, Nov 6, 2013 at 8:18 AM, Philip Bays wrote:
> I observe the same by turning on the “Show Error Console” . The page then
> loads.
>
>
> On Nov 6, 2013, at 11:08 AM, Otis Rothenberger wrote:
>
>> Dang!
>>
>> When I put the JavaScript console up, it loads on Maverick Safari.
>>
>> Timing...
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger wrote:
>>
>>> Bob,
>>>
>>> OK, you've been right on this point in the past (100% right!), but remember
>>> these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
>>> MSIE.
>>>
>>> To work on this, I've been bouncing around versions of JSmol. Right now the
>>> version that you put up yesterday does not load on Mavericks Safari. See:
>>>
>>> http://chemagic.com/JSmolVMK.htm
>>>
>>> on Mavericks Safari vs Chrome.
>>>
>>> I need to decide what version to use to scope out problems. I've jumped
>>> back to 13.3.3 before I installed the version you posted yesterday. I'll
>>> leave this broken version in place for you to take a look.
>>>
>>> If there are any Mac Mavericks users, I'd be interested if you see what I'm
>>> seeing on the page above. Also, I wonder what Lion Safari is doing on this
>>> page?
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>>
Otis, don't try to solve this problem yourself. I have access to plenty of
Macs. Point me to the simplest pages you can conjure up that cause the
problem and let me fix it. No rogue hacks, please!
This one sounds like a bug in the asynchronous scripting components of
Jmol within the Java-derived code.
Bob
On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
wrote:
Bob and Phil,
It does not work for me either in Safari for Mavericks, but know this:
Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
rewriting our whole virtual model kit to deal with the quirks. I don't
think these are JSmol problems or bugs. This version of Safari is just not
behaving normally. Callbacks are a problem. Things that I do sequentially,
no longer work. For example, if I want to do a partial charge calculation
in script, I must play a game with two JavaScript functions:
function chargeStuff1() {
Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
}
function chargeStuff2() {
THE REST OS THE Jmolscript STUFF
}
I never had to do this before, and now I only have to do it for Mavericks
Safari. Currently, I'm looking for ways to avoid call backs.
Maybe this is about Safari bugs, but I have the feeling that Apple is just
doing things differently. I mentioned in a previous note that they
purposely degraded the functionality of Pages and Numbers just to make
this office duo compatible with hand held devices.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
> still a problem? I just tested it with my 1st-gen iPad with Safari and it
> was fine.
>
>
> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
> I have been out of the loop for a while taking care of my wife who has a
> broken and repaired knee cap. I knew we ought to pay off those gambling
> debts:-)
>
> I have been looking today at the Super Simple JSmol page
> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>
> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
> However, the HTML5 link does not work in Safari. A new page is launched
> with the search bar, but the applet (or whatever we are now calling it)
> does not load even after waiting for 10 minutes.
>
> On the other hand, if I simply open the “Show Error Console” in the
> developers menu in Safari, the HTML5 loads fine. It is not clear to why
> simply having the console open allows jsmol to load. Is it a timing
> thing??
>
> I see the following error messages in the console for the incident when
> jsmol did not load:
>
> [Error] Failed to load resource: the server responded with a status of
> 503 (Service Unavailable) (get-js, line 0)
> [Error] java.lang.NullPointerException
> (anonymous fun
Re: [Jmol-users] Super Simple JSMol
How inconvenient! A bug that requires that bug reporting is off! On Wed, Nov 6, 2013 at 8:17 AM, Philip Bays wrote: > In the Safari develop menu item (across the top) which you need to turn on > in preferences, there is an item called "Show Error Console”. > > > On Nov 6, 2013, at 11:14 AM, Robert Hanson wrote: > > When you say "error console", what are you talking about exactly? > > > On Wed, Nov 6, 2013 at 8:12 AM, Philip Bays wrote: > >> Bob: >> On both of these links, the jmol window does not open unless I have the >> error console turned on. When it is on, the center column links seem to >> work. >> >> >> On Nov 6, 2013, at 10:44 AM, Robert Hanson wrote: >> >> There is one and only one thread. However, there are several tricks that >> I use now to "fake" threads -- script interruptions that save their exact >> state and restart when a thread is complete. There are several tests at my >> site that use "threads". I would like you to try and report back on them. >> These are at >> >> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (minified) >> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (developer-friendly) >> >> center column: >> >> minimize (watch the minimization) >> drag-minimize (drag an atom) >> thread test (background changes colors with delays; OK prompt occurs; >> more background color changes, ending with black) >> moveto (rotation, then background changes) >> delay/hover (messages, selectionhalos, and hover working) >> animation >> spin/vibration >> >> Mac feedback critical. >> >> Bob >> >> >> >> >> >> On Wed, Nov 6, 2013 at 6:50 AM, Otis Rothenberger >> wrote: >> >>> Phil, >>> >>> I noticed this console behavior with several of my scripting problems. >>> With the console open, the problems got better. This sounds like timing >>> issues - i.e. the console feed is letting things catch up. >>> >>> Bob, does calculate partialCharge run in a separate thread? >>> >>> Otis >>> >>> >>> -- >>> Otis Rothenberger >>> o...@chemagic.com >>> http://chemagic.com >>> >>> >>> >>> >>> On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: >>> >>> Bob: >>> Sorry that my first message is not clear. Safari on iOS devices works >>> fine. it is Safari on my laptop and desktop that has the problem. But it >>> is consistently solved by opening, and keeping open, the error console?? >>> >>> >>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: >>> >>> still a problem? I just tested it with my 1st-gen iPad with Safari and >>> it was fine. >>> >>> >>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: >>> I have been out of the loop for a while taking care of my wife who has a broken and repaired knee cap. I knew we ought to pay off those gambling debts:-) I have been looking today at the Super Simple JSmol page ( http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). However, the HTML5 link does not work in Safari. A new page is launched with the search bar, but the applet (or whatever we are now calling it) does not load even after waiting for 10 minutes. On the other hand, if I simply open the “Show Error Console” in the developers menu in Safari, the HTML5 loads fine. It is not clear to why simply having the console open allows jsmol to load. Is it a timing thing?? I see the following error messages in the console for the incident when jsmol did not load: [Error] Failed to load resource: the server responded with a status of 503 (Service Unavailable) (get-js, line 0) [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2256) (anonymous function) (core.z.js, line 2248) (anonymous function) (core.z.js, line 2225) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 2223) innerTypeInstance (JSmol.min.js, line 358) (anonymous function) (core.z.js, line 2192) (anonymous function) (core.z.js, line 938) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 504) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 256) __nextExecution (JSmol.min.js, line 261) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu ---
Re: [Jmol-users] Super Simple JSMol
I observe the same by turning on the “Show Error Console” . The page then
loads.
On Nov 6, 2013, at 11:08 AM, Otis Rothenberger wrote:
> Dang!
>
> When I put the JavaScript console up, it loads on Maverick Safari.
>
> Timing...
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger wrote:
>
>> Bob,
>>
>> OK, you've been right on this point in the past (100% right!), but remember
>> these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
>> MSIE.
>>
>> To work on this, I've been bouncing around versions of JSmol. Right now the
>> version that you put up yesterday does not load on Mavericks Safari. See:
>>
>> http://chemagic.com/JSmolVMK.htm
>>
>> on Mavericks Safari vs Chrome.
>>
>> I need to decide what version to use to scope out problems. I've jumped back
>> to 13.3.3 before I installed the version you posted yesterday. I'll leave
>> this broken version in place for you to take a look.
>>
>> If there are any Mac Mavericks users, I'd be interested if you see what I'm
>> seeing on the page above. Also, I wonder what Lion Safari is doing on this
>> page?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>>
>>> Otis, don't try to solve this problem yourself. I have access to plenty of
>>> Macs. Point me to the simplest pages you can conjure up that cause the
>>> problem and let me fix it. No rogue hacks, please!
>>>
>>> This one sounds like a bug in the asynchronous scripting components of Jmol
>>> within the Java-derived code.
>>>
>>> Bob
>>>
>>>
>>>
>>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>>> wrote:
>>> Bob and Phil,
>>>
>>> It does not work for me either in Safari for Mavericks, but know this:
>>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>>> rewriting our whole virtual model kit to deal with the quirks. I don't
>>> think these are JSmol problems or bugs. This version of Safari is just not
>>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>>> no longer work. For example, if I want to do a partial charge calculation
>>> in script, I must play a game with two JavaScript functions:
>>>
>>> function chargeStuff1() {
>>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>>> }
>>>
>>> function chargeStuff2() {
>>> THE REST OS THE Jmolscript STUFF
>>> }
>>>
>>> I never had to do this before, and now I only have to do it for Mavericks
>>> Safari. Currently, I'm looking for ways to avoid call backs.
>>>
>>> Maybe this is about Safari bugs, but I have the feeling that Apple is just
>>> doing things differently. I mentioned in a previous note that they
>>> purposely degraded the functionality of Pages and Numbers just to make this
>>> office duo compatible with hand held devices.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>>
still a problem? I just tested it with my 1st-gen iPad with Safari and it
was fine.
On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
I have been out of the loop for a while taking care of my wife who has a
broken and repaired knee cap. I knew we ought to pay off those gambling
debts:-)
I have been looking today at the Super Simple JSmol page
(http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
However, the HTML5 link does not work in Safari. A new page is launched
with the search bar, but the applet (or whatever we are now calling it)
does not load even after waiting for 10 minutes.
On the other hand, if I simply open the “Show Error Console” in the
developers menu in Safari, the HTML5 loads fine. It is not clear to why
simply having the console open allows jsmol to load. Is it a timing
thing??
I see the following error messages in the console for the incident when
jsmol did not load:
[Error] Failed to load resource: the server responded with a status of 503
(Service Unavailable) (get-js, line 0)
[Error] java.lang.NullPointerException
(anonymous function) (core.z.js, line 398)
(anonymous function) (core.z.js, line 2256)
(anonymous function) (core.z.js, line 2248)
(anonymous function) (core.z.js, line 2225)
instantialize (JSmol.min.js, line 343)
(anonymous function) (core.z.js, line 2223)
innerTypeInstance (JSmol.min.js, line 358)
(anonymous function) (core.z.js, line 2192)
(anonymous function) (core.z.js, line 938)
Re: [Jmol-users] Super Simple JSMol
In the Safari develop menu item (across the top) which you need to turn on in preferences, there is an item called "Show Error Console”. On Nov 6, 2013, at 11:14 AM, Robert Hanson wrote: > When you say "error console", what are you talking about exactly? > > > On Wed, Nov 6, 2013 at 8:12 AM, Philip Bays wrote: > Bob: > On both of these links, the jmol window does not open unless I have the error > console turned on. When it is on, the center column links seem to work. > > > On Nov 6, 2013, at 10:44 AM, Robert Hanson wrote: > >> There is one and only one thread. However, there are several tricks that I >> use now to "fake" threads -- script interruptions that save their exact >> state and restart when a thread is complete. There are several tests at my >> site that use "threads". I would like you to try and report back on them. >> These are at >> >> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (minified) >> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (developer-friendly) >> >> center column: >> >> minimize (watch the minimization) >> drag-minimize (drag an atom) >> thread test (background changes colors with delays; OK prompt occurs; more >> background color changes, ending with black) >> moveto (rotation, then background changes) >> delay/hover (messages, selectionhalos, and hover working) >> animation >> spin/vibration >> >> Mac feedback critical. >> >> Bob >> >> >> >> >> >> On Wed, Nov 6, 2013 at 6:50 AM, Otis Rothenberger >> wrote: >> Phil, >> >> I noticed this console behavior with several of my scripting problems. With >> the console open, the problems got better. This sounds like timing issues - >> i.e. the console feed is letting things catch up. >> >> Bob, does calculate partialCharge run in a separate thread? >> >> Otis >> >> >> -- >> Otis Rothenberger >> o...@chemagic.com >> http://chemagic.com >> >> >> >> >> On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: >> >>> Bob: >>> Sorry that my first message is not clear. Safari on iOS devices works >>> fine. it is Safari on my laptop and desktop that has the problem. But it >>> is consistently solved by opening, and keeping open, the error console?? >>> >>> >>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: >>> still a problem? I just tested it with my 1st-gen iPad with Safari and it was fine. On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: I have been out of the loop for a while taking care of my wife who has a broken and repaired knee cap. I knew we ought to pay off those gambling debts:-) I have been looking today at the Super Simple JSmol page (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). However, the HTML5 link does not work in Safari. A new page is launched with the search bar, but the applet (or whatever we are now calling it) does not load even after waiting for 10 minutes. On the other hand, if I simply open the “Show Error Console” in the developers menu in Safari, the HTML5 loads fine. It is not clear to why simply having the console open allows jsmol to load. Is it a timing thing?? I see the following error messages in the console for the incident when jsmol did not load: [Error] Failed to load resource: the server responded with a status of 503 (Service Unavailable) (get-js, line 0) [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2256) (anonymous function) (core.z.js, line 2248) (anonymous function) (core.z.js, line 2225) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 2223) innerTypeInstance (JSmol.min.js, line 358) (anonymous function) (core.z.js, line 2192) (anonymous function) (core.z.js, line 938) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 504) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 256) __nextExecution (JSmol.min.js, line 261) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Android is increasing in popularity, but the open development platform that >>
Re: [Jmol-users] Super Simple JSMol
When you say "error console", what are you talking about exactly? On Wed, Nov 6, 2013 at 8:12 AM, Philip Bays wrote: > Bob: > On both of these links, the jmol window does not open unless I have the > error console turned on. When it is on, the center column links seem to > work. > > > On Nov 6, 2013, at 10:44 AM, Robert Hanson wrote: > > There is one and only one thread. However, there are several tricks that I > use now to "fake" threads -- script interruptions that save their exact > state and restart when a thread is complete. There are several tests at my > site that use "threads". I would like you to try and report back on them. > These are at > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (minified) > http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (developer-friendly) > > center column: > > minimize (watch the minimization) > drag-minimize (drag an atom) > thread test (background changes colors with delays; OK prompt occurs; more > background color changes, ending with black) > moveto (rotation, then background changes) > delay/hover (messages, selectionhalos, and hover working) > animation > spin/vibration > > Mac feedback critical. > > Bob > > > > > > On Wed, Nov 6, 2013 at 6:50 AM, Otis Rothenberger > wrote: > >> Phil, >> >> I noticed this console behavior with several of my scripting problems. >> With the console open, the problems got better. This sounds like timing >> issues - i.e. the console feed is letting things catch up. >> >> Bob, does calculate partialCharge run in a separate thread? >> >> Otis >> >> >> -- >> Otis Rothenberger >> o...@chemagic.com >> http://chemagic.com >> >> >> >> >> On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: >> >> Bob: >> Sorry that my first message is not clear. Safari on iOS devices works >> fine. it is Safari on my laptop and desktop that has the problem. But it >> is consistently solved by opening, and keeping open, the error console?? >> >> >> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: >> >> still a problem? I just tested it with my 1st-gen iPad with Safari and it >> was fine. >> >> >> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: >> >>> I have been out of the loop for a while taking care of my wife who has a >>> broken and repaired knee cap. I knew we ought to pay off those gambling >>> debts:-) >>> >>> I have been looking today at the Super Simple JSmol page ( >>> http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). >>> >>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). >>> However, the HTML5 link does not work in Safari. A new page is launched >>> with the search bar, but the applet (or whatever we are now calling it) >>> does not load even after waiting for 10 minutes. >>> >>> On the other hand, if I simply open the “Show Error Console” in the >>> developers menu in Safari, the HTML5 loads fine. It is not clear to why >>> simply having the console open allows jsmol to load. Is it a timing thing?? >>> >>> I see the following error messages in the console for the incident when >>> jsmol did not load: >>> >>> [Error] Failed to load resource: the server responded with a status of >>> 503 (Service Unavailable) (get-js, line 0) >>> [Error] java.lang.NullPointerException >>> (anonymous function) (core.z.js, line 398) >>> (anonymous function) (core.z.js, line 2256) >>> (anonymous function) (core.z.js, line 2248) >>> (anonymous function) (core.z.js, line 2225) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 2223) >>> innerTypeInstance (JSmol.min.js, line 358) >>> (anonymous function) (core.z.js, line 2192) >>> (anonymous function) (core.z.js, line 938) >>> (anonymous function) (core.z.js, line 926) >>> (anonymous function) (core.z.js, line 917) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 913) >>> (anonymous function) (core.z.js, line 506) >>> (anonymous function) (core.z.js, line 506) >>> (anonymous function) (core.z.js, line 504) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 503) >>> __startAppletJS (JSmol.min.js, line 256) >>> __nextExecution (JSmol.min.js, line 261) >>> >>> >>> Philip Bays >>> Emeritus Professor of Chemistry >>> Saint Mary's College >>> Notre Dame, IN 46556 >>> pb...@saintmarys.edu >>> >>> >>> >>> >>> -- >>> Android is increasing in popularity, but the open development platform >>> that >>> developers love is also attractive to malware creators. Download this >>> white >>> paper to learn more about secure code signing practices that can help >>> keep >>> Android apps secure. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk >>> ___ >>> Jmol-users mailing list >
Re: [Jmol-users] Super Simple JSMol
Just for reference, I would like comments specifically based on
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.06.zip
Anything older than that will just confuse the issue. Obviously something
broke
Bob
On Wed, Nov 6, 2013 at 8:08 AM, Otis Rothenberger wrote:
> Dang!
>
> When I put the JavaScript console up, it loads on Maverick Safari.
>
> Timing...
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 11:00 AM, Otis Rothenberger
> wrote:
>
> Bob,
>
> OK, you've been right on this point in the past (100% right!), but
> remember these are Mavericks Safari problems - not Chrome and FF. I'm not
> sure about MSIE.
>
> To work on this, I've been bouncing around versions of JSmol. Right now
> the version that you put up yesterday does not load on Mavericks Safari.
> See:
>
> http://chemagic.com/JSmolVMK.htm
>
> on Mavericks Safari vs Chrome.
>
> I need to decide what version to use to scope out problems. I've jumped
> back to 13.3.3 before I installed the version you posted yesterday. I'll
> leave this broken version in place for you to take a look.
>
> If there are any Mac Mavericks users, I'd be interested if you see what
> I'm seeing on the page above. Also, I wonder what Lion Safari is doing on
> this page?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>
> Otis, don't try to solve this problem yourself. I have access to plenty of
> Macs. Point me to the simplest pages you can conjure up that cause the
> problem and let me fix it. No rogue hacks, please!
>
> This one sounds like a bug in the asynchronous scripting components of
> Jmol within the Java-derived code.
>
> Bob
>
>
>
> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
> wrote:
>
>> Bob and Phil,
>>
>> It does not work for me either in Safari for Mavericks, but know this:
>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>> rewriting our whole virtual model kit to deal with the quirks. I don't
>> think these are JSmol problems or bugs. This version of Safari is just not
>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>> no longer work. For example, if I want to do a partial charge calculation
>> in script, I must play a game with two JavaScript functions:
>>
>> function chargeStuff1() {
>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>> }
>>
>> function chargeStuff2() {
>> THE REST OS THE Jmolscript STUFF
>> }
>>
>> I never had to do this before, and now I only have to do it for Mavericks
>> Safari. Currently, I'm looking for ways to avoid call backs.
>>
>> Maybe this is about Safari bugs, but I have the feeling that Apple is
>> just doing things differently. I mentioned in a previous note that they
>> purposely degraded the functionality of Pages and Numbers just to make this
>> office duo compatible with hand held devices.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>
>> still a problem? I just tested it with my 1st-gen iPad with Safari and it
>> was fine.
>>
>>
>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>
>>> I have been out of the loop for a while taking care of my wife who has a
>>> broken and repaired knee cap. I knew we ought to pay off those gambling
>>> debts:-)
>>>
>>> I have been looking today at the Super Simple JSmol page (
>>> http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>>>
>>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
>>> However, the HTML5 link does not work in Safari. A new page is launched
>>> with the search bar, but the applet (or whatever we are now calling it)
>>> does not load even after waiting for 10 minutes.
>>>
>>> On the other hand, if I simply open the “Show Error Console” in the
>>> developers menu in Safari, the HTML5 loads fine. It is not clear to why
>>> simply having the console open allows jsmol to load. Is it a timing thing??
>>>
>>> I see the following error messages in the console for the incident when
>>> jsmol did not load:
>>>
>>> [Error] Failed to load resource: the server responded with a status of
>>> 503 (Service Unavailable) (get-js, line 0)
>>> [Error] java.lang.NullPointerException
>>> (anonymous function) (core.z.js, line 398)
>>> (anonymous function) (core.z.js, line 2256)
>>> (anonymous function) (core.z.js, line 2248)
>>> (anonymous function) (core.z.js, line 2225)
>>> instantialize (JSmol.min.js, line 343)
>>> (anonymous function) (core.z.js, line 2223)
>>> innerTypeInstance (JSmol.min.js, line 358)
>>> (anonymous function) (core.z.js, line 2192)
>>> (anonymous function) (core.z.js, line 938)
>>> (anonymous function) (core.z.js, line 926)
>>> (anonymous function) (cor
Re: [Jmol-users] Super Simple JSMol
Bob: On both of these links, the jmol window does not open unless I have the error console turned on. When it is on, the center column links seem to work. On Nov 6, 2013, at 10:44 AM, Robert Hanson wrote: > There is one and only one thread. However, there are several tricks that I > use now to "fake" threads -- script interruptions that save their exact state > and restart when a thread is complete. There are several tests at my site > that use "threads". I would like you to try and report back on them. These > are at > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (minified) > http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (developer-friendly) > > center column: > > minimize (watch the minimization) > drag-minimize (drag an atom) > thread test (background changes colors with delays; OK prompt occurs; more > background color changes, ending with black) > moveto (rotation, then background changes) > delay/hover (messages, selectionhalos, and hover working) > animation > spin/vibration > > Mac feedback critical. > > Bob > > > > > > On Wed, Nov 6, 2013 at 6:50 AM, Otis Rothenberger > wrote: > Phil, > > I noticed this console behavior with several of my scripting problems. With > the console open, the problems got better. This sounds like timing issues - > i.e. the console feed is letting things catch up. > > Bob, does calculate partialCharge run in a separate thread? > > Otis > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: > >> Bob: >> Sorry that my first message is not clear. Safari on iOS devices works fine. >> it is Safari on my laptop and desktop that has the problem. But it is >> consistently solved by opening, and keeping open, the error console?? >> >> >> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: >> >>> still a problem? I just tested it with my 1st-gen iPad with Safari and it >>> was fine. >>> >>> >>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: >>> I have been out of the loop for a while taking care of my wife who has a >>> broken and repaired knee cap. I knew we ought to pay off those gambling >>> debts:-) >>> >>> I have been looking today at the Super Simple JSmol page >>> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). >>> >>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). >>> However, the HTML5 link does not work in Safari. A new page is launched >>> with the search bar, but the applet (or whatever we are now calling it) >>> does not load even after waiting for 10 minutes. >>> >>> On the other hand, if I simply open the “Show Error Console” in the >>> developers menu in Safari, the HTML5 loads fine. It is not clear to why >>> simply having the console open allows jsmol to load. Is it a timing thing?? >>> >>> I see the following error messages in the console for the incident when >>> jsmol did not load: >>> >>> [Error] Failed to load resource: the server responded with a status of 503 >>> (Service Unavailable) (get-js, line 0) >>> [Error] java.lang.NullPointerException >>> (anonymous function) (core.z.js, line 398) >>> (anonymous function) (core.z.js, line 2256) >>> (anonymous function) (core.z.js, line 2248) >>> (anonymous function) (core.z.js, line 2225) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 2223) >>> innerTypeInstance (JSmol.min.js, line 358) >>> (anonymous function) (core.z.js, line 2192) >>> (anonymous function) (core.z.js, line 938) >>> (anonymous function) (core.z.js, line 926) >>> (anonymous function) (core.z.js, line 917) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 913) >>> (anonymous function) (core.z.js, line 506) >>> (anonymous function) (core.z.js, line 506) >>> (anonymous function) (core.z.js, line 504) >>> instantialize (JSmol.min.js, line 343) >>> (anonymous function) (core.z.js, line 503) >>> __startAppletJS (JSmol.min.js, line 256) >>> __nextExecution (JSmol.min.js, line 261) >>> >>> >>> Philip Bays >>> Emeritus Professor of Chemistry >>> Saint Mary's College >>> Notre Dame, IN 46556 >>> pb...@saintmarys.edu >>> >>> >>> >>> -- >>> Android is increasing in popularity, but the open development platform that >>> developers love is also attractive to malware creators. Download this white >>> paper to learn more about secure code signing practices that can help keep >>> Android apps secure. >>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>>
Re: [Jmol-users] Super Simple JSMol
Dang!
When I put the JavaScript console up, it loads on Maverick Safari.
Timing...
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 11:00 AM, Otis Rothenberger wrote:
> Bob,
>
> OK, you've been right on this point in the past (100% right!), but remember
> these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
> MSIE.
>
> To work on this, I've been bouncing around versions of JSmol. Right now the
> version that you put up yesterday does not load on Mavericks Safari. See:
>
> http://chemagic.com/JSmolVMK.htm
>
> on Mavericks Safari vs Chrome.
>
> I need to decide what version to use to scope out problems. I've jumped back
> to 13.3.3 before I installed the version you posted yesterday. I'll leave
> this broken version in place for you to take a look.
>
> If there are any Mac Mavericks users, I'd be interested if you see what I'm
> seeing on the page above. Also, I wonder what Lion Safari is doing on this
> page?
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
>
>> Otis, don't try to solve this problem yourself. I have access to plenty of
>> Macs. Point me to the simplest pages you can conjure up that cause the
>> problem and let me fix it. No rogue hacks, please!
>>
>> This one sounds like a bug in the asynchronous scripting components of Jmol
>> within the Java-derived code.
>>
>> Bob
>>
>>
>>
>> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
>> wrote:
>> Bob and Phil,
>>
>> It does not work for me either in Safari for Mavericks, but know this:
>> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
>> rewriting our whole virtual model kit to deal with the quirks. I don't think
>> these are JSmol problems or bugs. This version of Safari is just not
>> behaving normally. Callbacks are a problem. Things that I do sequentially,
>> no longer work. For example, if I want to do a partial charge calculation in
>> script, I must play a game with two JavaScript functions:
>>
>> function chargeStuff1() {
>> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
>> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
>> }
>>
>> function chargeStuff2() {
>> THE REST OS THE Jmolscript STUFF
>> }
>>
>> I never had to do this before, and now I only have to do it for Mavericks
>> Safari. Currently, I'm looking for ways to avoid call backs.
>>
>> Maybe this is about Safari bugs, but I have the feeling that Apple is just
>> doing things differently. I mentioned in a previous note that they purposely
>> degraded the functionality of Pages and Numbers just to make this office duo
>> compatible with hand held devices.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>>
>>> still a problem? I just tested it with my 1st-gen iPad with Safari and it
>>> was fine.
>>>
>>>
>>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>>> I have been out of the loop for a while taking care of my wife who has a
>>> broken and repaired knee cap. I knew we ought to pay off those gambling
>>> debts:-)
>>>
>>> I have been looking today at the Super Simple JSmol page
>>> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>>>
>>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
>>> However, the HTML5 link does not work in Safari. A new page is launched
>>> with the search bar, but the applet (or whatever we are now calling it)
>>> does not load even after waiting for 10 minutes.
>>>
>>> On the other hand, if I simply open the “Show Error Console” in the
>>> developers menu in Safari, the HTML5 loads fine. It is not clear to why
>>> simply having the console open allows jsmol to load. Is it a timing thing??
>>>
>>> I see the following error messages in the console for the incident when
>>> jsmol did not load:
>>>
>>> [Error] Failed to load resource: the server responded with a status of 503
>>> (Service Unavailable) (get-js, line 0)
>>> [Error] java.lang.NullPointerException
>>> (anonymous function) (core.z.js, line 398)
>>> (anonymous function) (core.z.js, line 2256)
>>> (anonymous function) (core.z.js, line 2248)
>>> (anonymous function) (core.z.js, line 2225)
>>> instantialize (JSmol.min.js, line 343)
>>> (anonymous function) (core.z.js, line 2223)
>>> innerTypeInstance (JSmol.min.js, line 358)
>>> (anonymous function) (core.z.js, line 2192)
>>> (anonymous function) (core.z.js, line 938)
>>> (anonymous function) (core.z.js, line 926)
>>> (anonymous function) (core.z.js, line 917)
>>> instantialize (JSmol.min.js, line 343)
>>> (anonymous function) (core.z.js, line 913)
>>> (anonymous function) (core.z.js, line 506)
>>> (anonymous function) (c
Re: [Jmol-users] Super Simple JSMol
Bob,
OK, you've been right on this point in the past (100% right!), but remember
these are Mavericks Safari problems - not Chrome and FF. I'm not sure about
MSIE.
To work on this, I've been bouncing around versions of JSmol. Right now the
version that you put up yesterday does not load on Mavericks Safari. See:
http://chemagic.com/JSmolVMK.htm
on Mavericks Safari vs Chrome.
I need to decide what version to use to scope out problems. I've jumped back to
13.3.3 before I installed the version you posted yesterday. I'll leave this
broken version in place for you to take a look.
If there are any Mac Mavericks users, I'd be interested if you see what I'm
seeing on the page above. Also, I wonder what Lion Safari is doing on this page?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 10:35 AM, Robert Hanson wrote:
> Otis, don't try to solve this problem yourself. I have access to plenty of
> Macs. Point me to the simplest pages you can conjure up that cause the
> problem and let me fix it. No rogue hacks, please!
>
> This one sounds like a bug in the asynchronous scripting components of Jmol
> within the Java-derived code.
>
> Bob
>
>
>
> On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger
> wrote:
> Bob and Phil,
>
> It does not work for me either in Safari for Mavericks, but know this: Safari
> for Mavericks (iPad aside) is a JSmol disaster. I'm literally rewriting our
> whole virtual model kit to deal with the quirks. I don't think these are
> JSmol problems or bugs. This version of Safari is just not behaving normally.
> Callbacks are a problem. Things that I do sequentially, no longer work. For
> example, if I want to do a partial charge calculation in script, I must play
> a game with two JavaScript functions:
>
> function chargeStuff1() {
> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
> }
>
> function chargeStuff2() {
> THE REST OS THE Jmolscript STUFF
> }
>
> I never had to do this before, and now I only have to do it for Mavericks
> Safari. Currently, I'm looking for ways to avoid call backs.
>
> Maybe this is about Safari bugs, but I have the feeling that Apple is just
> doing things differently. I mentioned in a previous note that they purposely
> degraded the functionality of Pages and Numbers just to make this office duo
> compatible with hand held devices.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>
>> still a problem? I just tested it with my 1st-gen iPad with Safari and it
>> was fine.
>>
>>
>> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>> I have been out of the loop for a while taking care of my wife who has a
>> broken and repaired knee cap. I knew we ought to pay off those gambling
>> debts:-)
>>
>> I have been looking today at the Super Simple JSmol page
>> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>>
>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
>> However, the HTML5 link does not work in Safari. A new page is launched
>> with the search bar, but the applet (or whatever we are now calling it) does
>> not load even after waiting for 10 minutes.
>>
>> On the other hand, if I simply open the “Show Error Console” in the
>> developers menu in Safari, the HTML5 loads fine. It is not clear to why
>> simply having the console open allows jsmol to load. Is it a timing thing??
>>
>> I see the following error messages in the console for the incident when
>> jsmol did not load:
>>
>> [Error] Failed to load resource: the server responded with a status of 503
>> (Service Unavailable) (get-js, line 0)
>> [Error] java.lang.NullPointerException
>> (anonymous function) (core.z.js, line 398)
>> (anonymous function) (core.z.js, line 2256)
>> (anonymous function) (core.z.js, line 2248)
>> (anonymous function) (core.z.js, line 2225)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 2223)
>> innerTypeInstance (JSmol.min.js, line 358)
>> (anonymous function) (core.z.js, line 2192)
>> (anonymous function) (core.z.js, line 938)
>> (anonymous function) (core.z.js, line 926)
>> (anonymous function) (core.z.js, line 917)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 913)
>> (anonymous function) (core.z.js, line 506)
>> (anonymous function) (core.z.js, line 506)
>> (anonymous function) (core.z.js, line 504)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 503)
>> __startAppletJS (JSmol.min.js, line 256)
>> __nextExecution (JSmol.min.js, line 261)
>>
>>
>> Philip Bays
>> Emeritus Professor of Chemistry
>> Saint Mary's College
>> No
Re: [Jmol-users] Super Simple JSMol
There is one and only one thread. However, there are several tricks that I use now to "fake" threads -- script interruptions that save their exact state and restart when a thread is complete. There are several tests at my site that use "threads". I would like you to try and report back on them. These are at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (minified) http://chemapps.stolaf.edu/jmol/jsmol/test2.htm (developer-friendly) center column: minimize (watch the minimization) drag-minimize (drag an atom) thread test (background changes colors with delays; OK prompt occurs; more background color changes, ending with black) moveto (rotation, then background changes) delay/hover (messages, selectionhalos, and hover working) animation spin/vibration Mac feedback critical. Bob On Wed, Nov 6, 2013 at 6:50 AM, Otis Rothenberger wrote: > Phil, > > I noticed this console behavior with several of my scripting problems. > With the console open, the problems got better. This sounds like timing > issues - i.e. the console feed is letting things catch up. > > Bob, does calculate partialCharge run in a separate thread? > > Otis > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: > > Bob: > Sorry that my first message is not clear. Safari on iOS devices works > fine. it is Safari on my laptop and desktop that has the problem. But it > is consistently solved by opening, and keeping open, the error console?? > > > On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: > > still a problem? I just tested it with my 1st-gen iPad with Safari and it > was fine. > > > On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: > >> I have been out of the loop for a while taking care of my wife who has a >> broken and repaired knee cap. I knew we ought to pay off those gambling >> debts:-) >> >> I have been looking today at the Super Simple JSmol page ( >> http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). >> >> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). >> However, the HTML5 link does not work in Safari. A new page is launched >> with the search bar, but the applet (or whatever we are now calling it) >> does not load even after waiting for 10 minutes. >> >> On the other hand, if I simply open the “Show Error Console” in the >> developers menu in Safari, the HTML5 loads fine. It is not clear to why >> simply having the console open allows jsmol to load. Is it a timing thing?? >> >> I see the following error messages in the console for the incident when >> jsmol did not load: >> >> [Error] Failed to load resource: the server responded with a status of >> 503 (Service Unavailable) (get-js, line 0) >> [Error] java.lang.NullPointerException >> (anonymous function) (core.z.js, line 398) >> (anonymous function) (core.z.js, line 2256) >> (anonymous function) (core.z.js, line 2248) >> (anonymous function) (core.z.js, line 2225) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 2223) >> innerTypeInstance (JSmol.min.js, line 358) >> (anonymous function) (core.z.js, line 2192) >> (anonymous function) (core.z.js, line 938) >> (anonymous function) (core.z.js, line 926) >> (anonymous function) (core.z.js, line 917) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 913) >> (anonymous function) (core.z.js, line 506) >> (anonymous function) (core.z.js, line 506) >> (anonymous function) (core.z.js, line 504) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 503) >> __startAppletJS (JSmol.min.js, line 256) >> __nextExecution (JSmol.min.js, line 261) >> >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> >> -- >> Android is increasing in popularity, but the open development platform >> that >> developers love is also attractive to malware creators. Download this >> white >> paper to learn more about secure code signing practices that can help keep >> Android apps secure. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 > > -- > November
Re: [Jmol-users] Super Simple JSMol
Otis, don't try to solve this problem yourself. I have access to plenty of
Macs. Point me to the simplest pages you can conjure up that cause the
problem and let me fix it. No rogue hacks, please!
This one sounds like a bug in the asynchronous scripting components of Jmol
within the Java-derived code.
Bob
On Wed, Nov 6, 2013 at 6:45 AM, Otis Rothenberger wrote:
> Bob and Phil,
>
> It does not work for me either in Safari for Mavericks, but know this:
> Safari for Mavericks (iPad aside) is a JSmol disaster. I'm literally
> rewriting our whole virtual model kit to deal with the quirks. I don't
> think these are JSmol problems or bugs. This version of Safari is just not
> behaving normally. Callbacks are a problem. Things that I do sequentially,
> no longer work. For example, if I want to do a partial charge calculation
> in script, I must play a game with two JavaScript functions:
>
> function chargeStuff1() {
> Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
> END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
> }
>
> function chargeStuff2() {
> THE REST OS THE Jmolscript STUFF
> }
>
> I never had to do this before, and now I only have to do it for Mavericks
> Safari. Currently, I'm looking for ways to avoid call backs.
>
> Maybe this is about Safari bugs, but I have the feeling that Apple is just
> doing things differently. I mentioned in a previous note that they
> purposely degraded the functionality of Pages and Numbers just to make this
> office duo compatible with hand held devices.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
>
> still a problem? I just tested it with my 1st-gen iPad with Safari and it
> was fine.
>
>
> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
>
>> I have been out of the loop for a while taking care of my wife who has a
>> broken and repaired knee cap. I knew we ought to pay off those gambling
>> debts:-)
>>
>> I have been looking today at the Super Simple JSmol page (
>> http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>>
>> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
>> However, the HTML5 link does not work in Safari. A new page is launched
>> with the search bar, but the applet (or whatever we are now calling it)
>> does not load even after waiting for 10 minutes.
>>
>> On the other hand, if I simply open the “Show Error Console” in the
>> developers menu in Safari, the HTML5 loads fine. It is not clear to why
>> simply having the console open allows jsmol to load. Is it a timing thing??
>>
>> I see the following error messages in the console for the incident when
>> jsmol did not load:
>>
>> [Error] Failed to load resource: the server responded with a status of
>> 503 (Service Unavailable) (get-js, line 0)
>> [Error] java.lang.NullPointerException
>> (anonymous function) (core.z.js, line 398)
>> (anonymous function) (core.z.js, line 2256)
>> (anonymous function) (core.z.js, line 2248)
>> (anonymous function) (core.z.js, line 2225)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 2223)
>> innerTypeInstance (JSmol.min.js, line 358)
>> (anonymous function) (core.z.js, line 2192)
>> (anonymous function) (core.z.js, line 938)
>> (anonymous function) (core.z.js, line 926)
>> (anonymous function) (core.z.js, line 917)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 913)
>> (anonymous function) (core.z.js, line 506)
>> (anonymous function) (core.z.js, line 506)
>> (anonymous function) (core.z.js, line 504)
>> instantialize (JSmol.min.js, line 343)
>> (anonymous function) (core.z.js, line 503)
>> __startAppletJS (JSmol.min.js, line 256)
>> __nextExecution (JSmol.min.js, line 261)
>>
>>
>> Philip Bays
>> Emeritus Professor of Chemistry
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>> --
>> Android is increasing in popularity, but the open development platform
>> that
>> developers love is also attractive to malware creators. Download this
>> white
>> paper to learn more about secure code signing practices that can help keep
>> Android apps secure.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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
Re: [Jmol-users] Super Simple JSMol
It works on iOS devices, but not OS. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 Sent from my iPhone On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: still a problem? I just tested it with my 1st-gen iPad with Safari and it was fine. On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: > I have been out of the loop for a while taking care of my wife who has a > broken and repaired knee cap. I knew we ought to pay off those gambling > debts:-) > > I have been looking today at the Super Simple JSmol page ( > http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). > > It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). > However, the HTML5 link does not work in Safari. A new page is launched > with the search bar, but the applet (or whatever we are now calling it) > does not load even after waiting for 10 minutes. > > On the other hand, if I simply open the “Show Error Console” in the > developers menu in Safari, the HTML5 loads fine. It is not clear to why > simply having the console open allows jsmol to load. Is it a timing thing?? > > I see the following error messages in the console for the incident when > jsmol did not load: > > [Error] Failed to load resource: the server responded with a status of 503 > (Service Unavailable) (get-js, line 0) > [Error] java.lang.NullPointerException > (anonymous function) (core.z.js, line 398) > (anonymous function) (core.z.js, line 2256) > (anonymous function) (core.z.js, line 2248) > (anonymous function) (core.z.js, line 2225) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 2223) > innerTypeInstance (JSmol.min.js, line 358) > (anonymous function) (core.z.js, line 2192) > (anonymous function) (core.z.js, line 938) > (anonymous function) (core.z.js, line 926) > (anonymous function) (core.z.js, line 917) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 913) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 504) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 503) > __startAppletJS (JSmol.min.js, line 256) > __nextExecution (JSmol.min.js, line 261) > > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
Phil, I noticed this console behavior with several of my scripting problems. With the console open, the problems got better. This sounds like timing issues - i.e. the console feed is letting things catch up. Bob, does calculate partialCharge run in a separate thread? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 6, 2013, at 9:32 AM, Bays Philip wrote: > Bob: > Sorry that my first message is not clear. Safari on iOS devices works fine. > it is Safari on my laptop and desktop that has the problem. But it is > consistently solved by opening, and keeping open, the error console?? > > > On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: > >> still a problem? I just tested it with my 1st-gen iPad with Safari and it >> was fine. >> >> >> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: >> I have been out of the loop for a while taking care of my wife who has a >> broken and repaired knee cap. I knew we ought to pay off those gambling >> debts:-) >> >> I have been looking today at the Super Simple JSmol page >> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). >> >> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). >> However, the HTML5 link does not work in Safari. A new page is launched >> with the search bar, but the applet (or whatever we are now calling it) does >> not load even after waiting for 10 minutes. >> >> On the other hand, if I simply open the “Show Error Console” in the >> developers menu in Safari, the HTML5 loads fine. It is not clear to why >> simply having the console open allows jsmol to load. Is it a timing thing?? >> >> I see the following error messages in the console for the incident when >> jsmol did not load: >> >> [Error] Failed to load resource: the server responded with a status of 503 >> (Service Unavailable) (get-js, line 0) >> [Error] java.lang.NullPointerException >> (anonymous function) (core.z.js, line 398) >> (anonymous function) (core.z.js, line 2256) >> (anonymous function) (core.z.js, line 2248) >> (anonymous function) (core.z.js, line 2225) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 2223) >> innerTypeInstance (JSmol.min.js, line 358) >> (anonymous function) (core.z.js, line 2192) >> (anonymous function) (core.z.js, line 938) >> (anonymous function) (core.z.js, line 926) >> (anonymous function) (core.z.js, line 917) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 913) >> (anonymous function) (core.z.js, line 506) >> (anonymous function) (core.z.js, line 506) >> (anonymous function) (core.z.js, line 504) >> instantialize (JSmol.min.js, line 343) >> (anonymous function) (core.z.js, line 503) >> __startAppletJS (JSmol.min.js, line 256) >> __nextExecution (JSmol.min.js, line 261) >> >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> Android is increasing in popularity, but the open development platform that >> developers love is also attractive to malware creators. Download this white >> paper to learn more about secure code signing practices that can help keep >> Android apps secure. >> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 >> >> -- >> November Webinars for C, C++, Fortran Developers >> Accelerate application performance with scalable programming models. Explore >> techniques for threading, error checking, porting, and tuning. Get the most >> from the latest Intel processors and coprocessors. See abstracts and register >> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > J. Philip Bays > Emeritus Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > -- > November Webinars for C, C++, Fortran Developers > Accelerate applica
Re: [Jmol-users] Super Simple JSMol
Bob and Phil,
It does not work for me either in Safari for Mavericks, but know this: Safari
for Mavericks (iPad aside) is a JSmol disaster. I'm literally rewriting our
whole virtual model kit to deal with the quirks. I don't think these are JSmol
problems or bugs. This version of Safari is just not behaving normally.
Callbacks are a problem. Things that I do sequentially, no longer work. For
example, if I want to do a partial charge calculation in script, I must play a
game with two JavaScript functions:
function chargeStuff1() {
Jmol.script STUFF UP TO AND INCLUDING CHARGE CALCULATION
END ABOVE WITH Jmol.script javascript TO SECOND FUNCTION
}
function chargeStuff2() {
THE REST OS THE Jmolscript STUFF
}
I never had to do this before, and now I only have to do it for Mavericks
Safari. Currently, I'm looking for ways to avoid call backs.
Maybe this is about Safari bugs, but I have the feeling that Apple is just
doing things differently. I mentioned in a previous note that they purposely
degraded the functionality of Pages and Numbers just to make this office duo
compatible with hand held devices.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote:
> still a problem? I just tested it with my 1st-gen iPad with Safari and it was
> fine.
>
>
> On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote:
> I have been out of the loop for a while taking care of my wife who has a
> broken and repaired knee cap. I knew we ought to pay off those gambling
> debts:-)
>
> I have been looking today at the Super Simple JSmol page
> (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm).
>
> It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7).
> However, the HTML5 link does not work in Safari. A new page is launched with
> the search bar, but the applet (or whatever we are now calling it) does not
> load even after waiting for 10 minutes.
>
> On the other hand, if I simply open the “Show Error Console” in the
> developers menu in Safari, the HTML5 loads fine. It is not clear to why
> simply having the console open allows jsmol to load. Is it a timing thing??
>
> I see the following error messages in the console for the incident when jsmol
> did not load:
>
> [Error] Failed to load resource: the server responded with a status of 503
> (Service Unavailable) (get-js, line 0)
> [Error] java.lang.NullPointerException
> (anonymous function) (core.z.js, line 398)
> (anonymous function) (core.z.js, line 2256)
> (anonymous function) (core.z.js, line 2248)
> (anonymous function) (core.z.js, line 2225)
> instantialize (JSmol.min.js, line 343)
> (anonymous function) (core.z.js, line 2223)
> innerTypeInstance (JSmol.min.js, line 358)
> (anonymous function) (core.z.js, line 2192)
> (anonymous function) (core.z.js, line 938)
> (anonymous function) (core.z.js, line 926)
> (anonymous function) (core.z.js, line 917)
> instantialize (JSmol.min.js, line 343)
> (anonymous function) (core.z.js, line 913)
> (anonymous function) (core.z.js, line 506)
> (anonymous function) (core.z.js, line 506)
> (anonymous function) (core.z.js, line 504)
> instantialize (JSmol.min.js, line 343)
> (anonymous function) (core.z.js, line 503)
> __startAppletJS (JSmol.min.js, line 256)
> __nextExecution (JSmol.min.js, line 261)
>
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
> --
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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
>
> --
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktr
Re: [Jmol-users] Super Simple JSMol
Bob: Sorry that my first message is not clear. Safari on iOS devices works fine. it is Safari on my laptop and desktop that has the problem. But it is consistently solved by opening, and keeping open, the error console?? On Nov 6, 2013, at 9:07 AM, Robert Hanson wrote: > still a problem? I just tested it with my 1st-gen iPad with Safari and it was > fine. > > > On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: > I have been out of the loop for a while taking care of my wife who has a > broken and repaired knee cap. I knew we ought to pay off those gambling > debts:-) > > I have been looking today at the Super Simple JSmol page > (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). > > It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). > However, the HTML5 link does not work in Safari. A new page is launched with > the search bar, but the applet (or whatever we are now calling it) does not > load even after waiting for 10 minutes. > > On the other hand, if I simply open the “Show Error Console” in the > developers menu in Safari, the HTML5 loads fine. It is not clear to why > simply having the console open allows jsmol to load. Is it a timing thing?? > > I see the following error messages in the console for the incident when jsmol > did not load: > > [Error] Failed to load resource: the server responded with a status of 503 > (Service Unavailable) (get-js, line 0) > [Error] java.lang.NullPointerException > (anonymous function) (core.z.js, line 398) > (anonymous function) (core.z.js, line 2256) > (anonymous function) (core.z.js, line 2248) > (anonymous function) (core.z.js, line 2225) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 2223) > innerTypeInstance (JSmol.min.js, line 358) > (anonymous function) (core.z.js, line 2192) > (anonymous function) (core.z.js, line 938) > (anonymous function) (core.z.js, line 926) > (anonymous function) (core.z.js, line 917) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 913) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 504) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 503) > __startAppletJS (JSmol.min.js, line 256) > __nextExecution (JSmol.min.js, line 261) > > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Emeritus Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Super Simple JSMol
still a problem? I just tested it with my 1st-gen iPad with Safari and it was fine. On Mon, Nov 4, 2013 at 11:32 AM, Philip Bays wrote: > I have been out of the loop for a while taking care of my wife who has a > broken and repaired knee cap. I knew we ought to pay off those gambling > debts:-) > > I have been looking today at the Super Simple JSmol page ( > http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). > > It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). > However, the HTML5 link does not work in Safari. A new page is launched > with the search bar, but the applet (or whatever we are now calling it) > does not load even after waiting for 10 minutes. > > On the other hand, if I simply open the “Show Error Console” in the > developers menu in Safari, the HTML5 loads fine. It is not clear to why > simply having the console open allows jsmol to load. Is it a timing thing?? > > I see the following error messages in the console for the incident when > jsmol did not load: > > [Error] Failed to load resource: the server responded with a status of 503 > (Service Unavailable) (get-js, line 0) > [Error] java.lang.NullPointerException > (anonymous function) (core.z.js, line 398) > (anonymous function) (core.z.js, line 2256) > (anonymous function) (core.z.js, line 2248) > (anonymous function) (core.z.js, line 2225) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 2223) > innerTypeInstance (JSmol.min.js, line 358) > (anonymous function) (core.z.js, line 2192) > (anonymous function) (core.z.js, line 938) > (anonymous function) (core.z.js, line 926) > (anonymous function) (core.z.js, line 917) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 913) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 506) > (anonymous function) (core.z.js, line 504) > instantialize (JSmol.min.js, line 343) > (anonymous function) (core.z.js, line 503) > __startAppletJS (JSmol.min.js, line 256) > __nextExecution (JSmol.min.js, line 261) > > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Super Simple JSMol
I have been out of the loop for a while taking care of my wife who has a broken and repaired knee cap. I knew we ought to pay off those gambling debts:-) I have been looking today at the Super Simple JSmol page (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). However, the HTML5 link does not work in Safari. A new page is launched with the search bar, but the applet (or whatever we are now calling it) does not load even after waiting for 10 minutes. On the other hand, if I simply open the “Show Error Console” in the developers menu in Safari, the HTML5 loads fine. It is not clear to why simply having the console open allows jsmol to load. Is it a timing thing?? I see the following error messages in the console for the incident when jsmol did not load: [Error] Failed to load resource: the server responded with a status of 503 (Service Unavailable) (get-js, line 0) [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2256) (anonymous function) (core.z.js, line 2248) (anonymous function) (core.z.js, line 2225) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 2223) innerTypeInstance (JSmol.min.js, line 358) (anonymous function) (core.z.js, line 2192) (anonymous function) (core.z.js, line 938) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 504) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 256) __nextExecution (JSmol.min.js, line 261) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
