[Jmol-users] molecule moving parts
Hello, I know it is possible to move an entire molecule in Jmol, but is it also possible to move only part of the molecule? For example, a student would like to show a protein binding to a molecule. Perhaps it would be possible by combining multiple PDB files? Thanks. -- Daniel Barich Barich Assistive Technology Gambier, OH 43022 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jsmol page buttons not working
Sorry for the blank message. I'm using the var keyword now and the buttons
still don't work. I tested using the Control + Shift + J console in
Chrome, and myJmol is created as a Canvas2D object.
On Fri, Jun 14, 2013 at 4:01 PM, Daniel Barich wrote:
>
>
>
> On Fri, Jun 14, 2013 at 3:33 PM, Otis Rothenberger
> wrote:
>
>> Daniel,
>>
>> Try a global declaration of myJmol - i.e.
>>
>> var myJmol;
>>
>> Otis
>>
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Jun 14, 2013, at 3:24 PM, Daniel Barich wrote:
>>
>> I added a DOCTYPE and an html tag at the top, but the buttons still don't
>> work.
>>
>>
>> On Fri, Jun 14, 2013 at 3:02 PM, Otis Rothenberger > > wrote:
>>
>>> Hi Angel and Daniel,
>>>
>>> I can't see any JavaScript errors either, but as I play with it in my
>>> error/code console, I see myJmol as being undefined. Something's messing up
>>> myJmol as a global window property even though the applet is loading.
>>>
>>> I do not see an initial html tag. JavaScript global variables are really
>>> window properties. Is it possible that myJmol is being lost as a global
>>> JavaScript property of the window because of this apparent omission?
>>>
>>> By way of example:
>>>
>>> Jmol.script(myJmol,"select all;color red")
>>>
>>> does not work at all.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Jun 14, 2013, at 1:31 PM, Angel Herráez wrote:
>>>
>>> > Hi Daniel
>>> >
>>> > I am not seeing javascript errors. The buttons d not work, but their
>>> > syntax is wrong. You have
>>> >
>>> > Jmol.jmolButton("select all; wireframe on; etc
>>> > and you need
>>> >
>>> > Jmol.jmolButton(myJmol, "select all; wireframe on; etc
>>> >
>>> >
>>> >
>>> >
>>> >
>>> --
>>> > This SF.net email is sponsored by Windows:
>>> >
>>> > Build for Windows Store.
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>>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>>
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>>>
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>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>> --
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
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>>
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>>
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>>
>
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Re: [Jmol-users] Jsmol page buttons not working
On Fri, Jun 14, 2013 at 3:33 PM, Otis Rothenberger wrote:
> Daniel,
>
> Try a global declaration of myJmol - i.e.
>
> var myJmol;
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Jun 14, 2013, at 3:24 PM, Daniel Barich wrote:
>
> I added a DOCTYPE and an html tag at the top, but the buttons still don't
> work.
>
>
> On Fri, Jun 14, 2013 at 3:02 PM, Otis Rothenberger
> wrote:
>
>> Hi Angel and Daniel,
>>
>> I can't see any JavaScript errors either, but as I play with it in my
>> error/code console, I see myJmol as being undefined. Something's messing up
>> myJmol as a global window property even though the applet is loading.
>>
>> I do not see an initial html tag. JavaScript global variables are really
>> window properties. Is it possible that myJmol is being lost as a global
>> JavaScript property of the window because of this apparent omission?
>>
>> By way of example:
>>
>> Jmol.script(myJmol,"select all;color red")
>>
>> does not work at all.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Jun 14, 2013, at 1:31 PM, Angel Herráez wrote:
>>
>> > Hi Daniel
>> >
>> > I am not seeing javascript errors. The buttons d not work, but their
>> > syntax is wrong. You have
>> >
>> > Jmol.jmolButton("select all; wireframe on; etc
>> > and you need
>> >
>> > Jmol.jmolButton(myJmol, "select all; wireframe on; etc
>> >
>> >
>> >
>> >
>> >
>> --
>> > This SF.net email is sponsored by Windows:
>> >
>> > Build for Windows Store.
>> >
>> > http://p.sf.net/sfu/windows-dev2dev
>> > ___
>> > Jmol-users mailing list
>> > Jmol-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
>
> http://p.sf.net/sfu/windows-dev2dev___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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Re: [Jmol-users] Jsmol page buttons not working
I added a DOCTYPE and an html tag at the top, but the buttons still don't
work.
On Fri, Jun 14, 2013 at 3:02 PM, Otis Rothenberger wrote:
> Hi Angel and Daniel,
>
> I can't see any JavaScript errors either, but as I play with it in my
> error/code console, I see myJmol as being undefined. Something's messing up
> myJmol as a global window property even though the applet is loading.
>
> I do not see an initial html tag. JavaScript global variables are really
> window properties. Is it possible that myJmol is being lost as a global
> JavaScript property of the window because of this apparent omission?
>
> By way of example:
>
> Jmol.script(myJmol,"select all;color red")
>
> does not work at all.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Jun 14, 2013, at 1:31 PM, Angel Herráez wrote:
>
> > Hi Daniel
> >
> > I am not seeing javascript errors. The buttons d not work, but their
> > syntax is wrong. You have
> >
> > Jmol.jmolButton("select all; wireframe on; etc
> > and you need
> >
> > Jmol.jmolButton(myJmol, "select all; wireframe on; etc
> >
> >
> >
> >
> >
> --
> > This SF.net email is sponsored by Windows:
> >
> > Build for Windows Store.
> >
> > http://p.sf.net/sfu/windows-dev2dev
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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Re: [Jmol-users] Jsmol page buttons not working
Oops, I had converted the page from jmol and forgot the correct syntax for
jsmol. I fixed the syntax, but the buttons still don't work. I cleared
the cache, but it still doesn't work:
http://biology.kenyon.edu/BMB/Chime2/2002/T4injector/FRAMES/start.htm
Daniel
On Fri, Jun 14, 2013 at 1:31 PM, Angel Herráez wrote:
> Hi Daniel
>
> I am not seeing javascript errors. The buttons d not work, but their
> syntax is wrong. You have
>
> Jmol.jmolButton("select all; wireframe on; etc
> and you need
>
> Jmol.jmolButton(myJmol, "select all; wireframe on; etc
>
>
>
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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[Jmol-users] Jsmol page buttons not working
Hi everybody, Could somebody look at this page for me? The molecule loads, but none of the buttons work. The JavaScript console shows an undefined method in jsmol.min.js even though I set up the latest download from SourceForge. http://biology.kenyon.edu/BMB/Chime2/2002/T4injector/FRAMES/start.htm My other pages are working fine. Thanks. Daniel -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol upload
I still can't open this link in Windows Explorer either. It says the file is invalid. On Thu, Mar 28, 2013 at 2:59 PM, Oliver Stueker < revilo2...@users.sourceforge.net> wrote: > Hi, > > The jsmol.zip that I have just downloaded seems to be broken: > > $ unzip jsmol.zip > Archive: jsmol.zip > End-of-central-directory signature not found. Either this file is not > a zipfile, or it constitutes one disk of a multi-part archive. In the > latter case the central directory and zipfile comment will be found on > the last disk(s) of this archive. > unzip: cannot find zipfile directory in one of jsmol.zip or > jsmol.zip.zip, and cannot find jsmol.zip.ZIP, period. > > > > The file's timestamp on the webserver is evening of Mar 25th ( ~6:30 pm > Central time if I converted the timezone correctly). > > Oliver > > > On Mon, Mar 25, 2013 at 3:00 PM, Robert Hanson wrote: > >> If you are doing anything with JSmol, I suggest uploading >> http://chemapps.stolaf.edu/jmol/jsmol.zip once more. It's got some >> changes in the way the .js files are organized and fixes some problems I >> introduced yesterday. >> >> Most importantly, if you are not loading binary files (PNGJ, ZIP, GZ, >> Spartan, for instance), and you use jQuery already on your page, this >> allows you to bypass JSmoljQuery.js and use what you are using already. >> That file is JSmol.min.nojq.js, and it is only 130K in size. >> >> This build also includes JSmol.lite.js (no jQuery) and JSmol.lite.jq.js >> (with jQuery) that are used in >> http://chemapps.stolaf.edu/jmol/jsmol/liteNCI.htm >> >> and it adds the jquery subdirectory, which includes the latest jQuery 1.9 >> library, which JSmol seems to be compatible with (but still needs the >> extensions we add for binary file transfer, MSIE cross-domain AJAX, and >> mouse binding). >> >> Bob >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Chemistry Department >> 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 >> >> >> >> -- >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] IE9 not working with my page
Bob, I replaced the file with the one you sent me, but it still doesn't work in IE9. http://biology.kenyon.edu/BMB/biomolecules.htm Daniel On Mon, Mar 25, 2013 at 3:50 PM, Robert Hanson wrote: > It's a test I inadvertently left in for checking performance. Replace your > JSmol.min.js with this: http://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js > and you should be good to go -- or at least further. Interesting that that > error is not showing up with "IE9" mode in IE10. But I see why: apparently > MSIE9 doesn't include the JSON class of functions. > > Bob > > > > > > On Mon, Mar 25, 2013 at 2:29 PM, Daniel Barich wrote: > >> I can't get IE9 to run JSmol on my page. Any idea why? >> >> http://biology.kenyon.edu/BMB/biomolecules.htm >> >> Thanks. >> >> Daniel >> >> >> -- >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> ___ >> 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 > Chair, Chemistry Department > 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 > > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] IE9 not working with my page
I can't get IE9 to run JSmol on my page. Any idea why? http://biology.kenyon.edu/BMB/biomolecules.htm Thanks. Daniel -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] old Jmol, new JSmol
Bob, I tried it again today, and the page now works fine in Firefox and even in IE. Thank you for all your hard work! Daniel On Sat, Mar 16, 2013 at 4:05 PM, Robert Hanson wrote: > That page looks great to me. Nice model! > > There is no longer any reference to "J.util.Point4f" in the libraries, so > this has to be due to the use of old files. So I'm guessing it's a caching > problem. I'm sorry about that -- it's always a problem when files are > changing as we go. I know I'm updating these pages rapidly, and it results > in issues like this. > > Bob > > > On Fri, Mar 15, 2013 at 7:30 PM, Daniel Barich wrote: > >> Here's the error I get with my page at >> http://biology.kenyon.edu/BMB/biomolecules.htm: >> >> getValue MINIMIZATIONCallback = null >> getValue PICKCallback = null >> getValue RESIZECallback = null >> getValue SCRIPTCallback = null >> getValue SYNCCallback = null >> language=en_US >> getValue script = null >> Jmol applet myJmol_object__269579045037469__ ready >> call loadScript jsmol\core\corescript.z.js >> call loadScript jsmol\J\util\Point4f.js >> Jmol._readyCallback failed java.lang.IndexOutOfBoundsException >> >> >> On Fri, Mar 15, 2013 at 6:02 PM, Daniel Barich wrote: >> >>> I updated to the latest version of jmol. The molecule was working fine >>> before, but now it works in Chrome but not in Firefox. Any idea why? >>> >>> http://biology.kenyon.edu/BMB/biomolecules.htm >>> >>> Thanks. >>> >>> Daniel >>> >>> >>> On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson wrote: >>> >>>> sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip >>>> >>>> >>>> >>>> On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane < >>>> richard.ste...@ntlworld.com> wrote: >>>> >>>>> Which file/folder? >>>>> >>>>> *From:* Robert Hanson >>>>> *Sent:* Friday, March 15, 2013 4:52 PM >>>>> *To:* jmol-users@lists.sourceforge.net >>>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>>>> >>>>> Get the latest file; I changed a few aspects so that MSIE of any >>>>> version will not do this. >>>>> >>>>> >>>>> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane < >>>>> richard.ste...@ntlworld.com> wrote: >>>>> >>>>>> Bob >>>>>> >>>>>> I’m fairly sure all the files in the js directory are up to date. >>>>>> >>>>>> Richard >>>>>> >>>>>> *From:* Robert Hanson >>>>>> *Sent:* Friday, March 15, 2013 3:19 PM >>>>>> *To:* jmol-users@lists.sourceforge.net >>>>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>>>>> >>>>>> More problems than that -- turns out MSIE 10 has the same problem >>>>>> (at least it does today!) see >>>>>> http://chemapps.stolaf.edu/jmol/jsmol.zip >>>>>> >>>>>> Also includes optimization of molecular orbital calculations, and a >>>>>> cool link called "make a nanotube" >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: >>>>>> >>>>>>> (and other files in that directory) >>>>>>> >>>>>>> >>>>>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson >>>>>>> wrote: >>>>>>> >>>>>>>> you haven't updated js/JSmolCore.js >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane < >>>>>>>> richard.ste...@ntlworld.com> wrote: >>>>>>>> >>>>>>>>>Bob >>>>>>>>> >>>>>>>>> Many thanks for this. IE9 now works perfectly from files on my >>>>>>>>> laptop, but not via the www from my server (still perfect with FF, >>>>>>>>> Chrome, >>>>>>>>> Safari). >>>>>>>>> >>>>>>>>> Actually your demo file shows the same s
Re: [Jmol-users] old Jmol, new JSmol
Here's the error I get with my page at http://biology.kenyon.edu/BMB/biomolecules.htm: getValue MINIMIZATIONCallback = null getValue PICKCallback = null getValue RESIZECallback = null getValue SCRIPTCallback = null getValue SYNCCallback = null language=en_US getValue script = null Jmol applet myJmol_object__269579045037469__ ready call loadScript jsmol\core\corescript.z.js call loadScript jsmol\J\util\Point4f.js Jmol._readyCallback failed java.lang.IndexOutOfBoundsException On Fri, Mar 15, 2013 at 6:02 PM, Daniel Barich wrote: > I updated to the latest version of jmol. The molecule was working fine > before, but now it works in Chrome but not in Firefox. Any idea why? > > http://biology.kenyon.edu/BMB/biomolecules.htm > > Thanks. > > Daniel > > > On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson wrote: > >> sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip >> >> >> >> On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane < >> richard.ste...@ntlworld.com> wrote: >> >>> Which file/folder? >>> >>> *From:* Robert Hanson >>> *Sent:* Friday, March 15, 2013 4:52 PM >>> *To:* jmol-users@lists.sourceforge.net >>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>> >>> Get the latest file; I changed a few aspects so that MSIE of any >>> version will not do this. >>> >>> >>> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane < >>> richard.ste...@ntlworld.com> wrote: >>> >>>> Bob >>>> >>>> I’m fairly sure all the files in the js directory are up to date. >>>> >>>> Richard >>>> >>>> *From:* Robert Hanson >>>> *Sent:* Friday, March 15, 2013 3:19 PM >>>> *To:* jmol-users@lists.sourceforge.net >>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>>> >>>> More problems than that -- turns out MSIE 10 has the same problem >>>> (at least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip >>>> >>>> Also includes optimization of molecular orbital calculations, and a >>>> cool link called "make a nanotube" >>>> >>>> >>>> >>>> >>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: >>>> >>>>> (and other files in that directory) >>>>> >>>>> >>>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: >>>>> >>>>>> you haven't updated js/JSmolCore.js >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane < >>>>>> richard.ste...@ntlworld.com> wrote: >>>>>> >>>>>>>Bob >>>>>>> >>>>>>> Many thanks for this. IE9 now works perfectly from files on my >>>>>>> laptop, but not via the www from my server (still perfect with FF, >>>>>>> Chrome, >>>>>>> Safari). >>>>>>> >>>>>>> Actually your demo file shows the same symptoms: no blue outline >>>>>>> seen, title tab still shows original wording not ‘jmolApplet0 is ready’. >>>>>>> >>>>>>> File URLs: >>>>>>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html >>>>>>> http://www.biotopics.co.uk/jsmol/jsmol.htm >>>>>>> >>>>>>> I hope it’s just something simple! >>>>>>> >>>>>>> Thanks for any help. >>>>>>> >>>>>>> Richard Steane >>>>>>> *From:* Robert Hanson >>>>>>> *Sent:* Friday, March 15, 2013 3:20 AM >>>>>>> *To:* jmol-users@lists.sourceforge.net ; Zhou >>>>>>> Renjian >>>>>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>>>>>> >>>>>>> The problem with MSIE 9 is fixed. A newly optimized version of >>>>>>> JSmol is in http://chemapps.stolaf.edu/jmol/jsmol.zip >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Everyone hates slow websites. So do we. >>>>>>> Make your web apps faster with AppDynamics >>>>>>> Download AppDynamics Lite for free today: >>>>>&
Re: [Jmol-users] old Jmol, new JSmol
I updated to the latest version of jmol. The molecule was working fine before, but now it works in Chrome but not in Firefox. Any idea why? http://biology.kenyon.edu/BMB/biomolecules.htm Thanks. Daniel On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson wrote: > sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip > > > > On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane < > richard.ste...@ntlworld.com> wrote: > >> Which file/folder? >> >> *From:* Robert Hanson >> *Sent:* Friday, March 15, 2013 4:52 PM >> *To:* jmol-users@lists.sourceforge.net >> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >> >> Get the latest file; I changed a few aspects so that MSIE of any >> version will not do this. >> >> >> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane < >> richard.ste...@ntlworld.com> wrote: >> >>> Bob >>> >>> I’m fairly sure all the files in the js directory are up to date. >>> >>> Richard >>> >>> *From:* Robert Hanson >>> *Sent:* Friday, March 15, 2013 3:19 PM >>> *To:* jmol-users@lists.sourceforge.net >>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >>> >>> More problems than that -- turns out MSIE 10 has the same problem (at >>> least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip >>> >>> Also includes optimization of molecular orbital calculations, and a cool >>> link called "make a nanotube" >>> >>> >>> >>> >>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: >>> (and other files in that directory) On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: > you haven't updated js/JSmolCore.js > > > > > On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane < > richard.ste...@ntlworld.com> wrote: > >>Bob >> >> Many thanks for this. IE9 now works perfectly from files on my >> laptop, but not via the www from my server (still perfect with FF, >> Chrome, >> Safari). >> >> Actually your demo file shows the same symptoms: no blue outline >> seen, title tab still shows original wording not ‘jmolApplet0 is ready’. >> >> File URLs: >> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html >> http://www.biotopics.co.uk/jsmol/jsmol.htm >> >> I hope it’s just something simple! >> >> Thanks for any help. >> >> Richard Steane >> *From:* Robert Hanson >> *Sent:* Friday, March 15, 2013 3:20 AM >> *To:* jmol-users@lists.sourceforge.net ; Zhou >> Renjian >> *Subject:* Re: [Jmol-users] old Jmol, new JSmol >> >> The problem with MSIE 9 is fixed. A newly optimized version of >> JSmol is in http://chemapps.stolaf.edu/jmol/jsmol.zip >> >> >> -- >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> ___ >> 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 > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> -- >>> Robert M. Hanson >>> Larson-Anderson Professor of Chemistry >>> Chair, Chemistry Department >>> 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 >>> >>> -- >>> >>> -- >>> Everyone hates slow websites. So do we. >>> Make your web apps faster with AppDynamics >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_mar >>> -- >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> -- >>> Everyone hates slow websites. So do we. >>> Make your web apps faster wit
Re: [Jmol-users] JSMol not working with JSmol.min.js
Thanks - my pages work great with the new JSmol version. Incidentally, I find that the following page, which has a large molecule view, runs much smoother in Chrome than Firefox: http://biology.kenyon.edu/BMB/jmodel/index.htm Do others experience the same? Daniel On Wed, Feb 27, 2013 at 6:32 PM, Robert Hanson wrote: > > http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d > > ah, I probably broke something. That number means "not a number" in Jmol. > > > On Wed, Feb 27, 2013 at 3:55 PM, Otis Rothenberger > wrote: > >> Daniel, >> >> On your page, a Resolver load works after the initial page error. Your >> initial load is from PubChem, and that gives an error for this URL: >> >> >> http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d >> >> I'm not sure what's causing that cid # error. >> >> On my JSmol page, I go after Resolver and PubChem with my own server side >> scripts, but I tried the following from my page just to see what happens: >> >> load $tylenol >> load :tylenol >> >> The above does not use my server side scripts. The $ load (Resolver) >> works. The : load (PubChem) produces the same URL as your page. >> >> I'm not sure that I am offering a solution to your problem, but I found >> that working with my own server side scripts for remote loads made a lot of >> problems go away. Bob's scripts can, of course, be run from your server. >> >> On your original page, I was not seeing the syntax error that you >> mentioned - Safari (most recent) Mac Lion. >> >> Otis >> >> >> -- >> Otis Rothenberger >> o...@chemagic.com >> http://chemagic.com >> >> >> >> >> On Feb 27, 2013, at 4:16 PM, Daniel Barich wrote: >> >> My page is still not working, and neither is this sample page on my jsmol >> installation: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Does this link work for anyone else. The other examples work, but my >> page still doesn't work. The link again is: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Daniel >> >> >> >> -- >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_feb___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> -- >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> ___ >> 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 > Chair, Chemistry Department > 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 > > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSMol not working with JSmol.min.js
My page is still not working, and neither is this sample page on my jsmol installation: http://biology.kenyon.edu/BMB/jsmol/simple2.htm Does this link work for anyone else. The other examples work, but my page still doesn't work. The link again is: http://biology.kenyon.edu/BMB/jsmol/simple2.htm Daniel -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
