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 2 E = 10.372609 dE = -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 <hans...@stolaf.edu> 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 <osrot...@chemagic.com>
> 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 <osrot...@chemagic.com> 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 <hans...@stolaf.edu> 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 <osrot...@chemagic.com>
>>> 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 <hans...@stolaf.edu> 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 <pb...@saintmarys.edu> 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.
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>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>> --
>>>> 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
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>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
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>>> _______________________________________________
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>>>
>>>
>>>
>>>
>>> --
>>> 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
>
>
> ------------------------------------------------------------------------------
> 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
------------------------------------------------------------------------------
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
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