Re: [Jmol-users] JSmol submenus not working in iOS
My observation (iPad) is that it opens but none of the links work and you close it by trying to drag it. > On Oct 20, 2016, at 10:39 AM, Otis Rothenberger <osrot...@icloud.com> wrote: > > Nick and Bob, > > I keep my eyes on iPad/Jmol performance pretty closely. I don’t think this > ever worked. You can’t even touch-close the console if you open it with the > console command. I just assumed this was an iPad thing. That’s why I include > my own text field for Jmol Script. > > JQuery does have mobile touch events, but I have not had time to play around > with them on iPad. I don’t even know if they work on iPad. I mention this > because touch and touch-hold are distinct events. Neither works with the Jmol > menu. > > Otis > > -- > Otis Rothenberger > o...@chemagic.org <mailto:o...@chemagic.org> > http://chemagic.org > >> On Oct 20, 2016, at 8:51 AM, Robert Hanson <hans...@stolaf.edu >> <mailto:hans...@stolaf.edu>> wrote: >> >> I tried Safari and Firefox on a desktop and found no problem. Is it the >> touch interface? >> >> On Thu, Oct 13, 2016 at 1:47 PM, Greeves, Nick <ngree...@liverpool.ac.uk >> <mailto:ngree...@liverpool.ac.uk>> wrote: >> I’ve tested an iPhone and an iPad running iOS 10. >> >> Load a page running JSmol, click on the logo, choose any of the items with a >> submenu e.g. Console or Surfaces, nothing happens for me. >> >> I’m pretty certain this used to work. Anyone else? >> Best regards >> Nick >> -- >> Nick Greevesvia OS X Mail >> Director of Teaching and Learning >> Department of Chemistry >> University of Liverpool >> Donnan and Robert Robinson Laboratories >> Crown Street, LIVERPOOL L69 7ZD U.K. >> Email address:ngree...@liverpool.ac.uk <mailto:ngree...@liverpool.ac.uk> >> WWW Pages:http://www.chemtube3d.com <http://www.chemtube3d.com/> >> Tel:+44 (0)151-794-3506 (3500 secretary) >> Dept Fax: +44 (0)151-794-3588 <tel:%2B44%20%280%29151-794-3588> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org <http://slashdot.org/>! >> http://sdm.link/slashdot <http://sdm.link/slashdot> >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> <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 <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 >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org <http://slashdot.org/>! >> http://sdm.link/slashdot___ >> <http://sdm.link/slashdot___> >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! > http://sdm.link/slashdot___ > 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Write 2 PDB models?
Bob: Don’t know if you picked up in the midst of the rapamycin discussion last week that there is an issue loading spartan files. In my observation, a *.spardir does not load local file but does using drag and drop. Trying to load as a local file give a “not atoms” error. That is on a mac, using the latest jsmol.htm and Spartan 14. Phil > On Jul 24, 2016, at 2:13 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > I found a solution. In the situation where there are models from multiple > files being saved, Jmol will give every atom a unique atom number. In this > way, the CONECT records at the end of the file will properly point to the > correct atoms. > > Jmol.___JmolVersion="14.6.1_2016.07.24" > > bug fix: write x.pdb for multimodel file does not work. > > Will release later today. > > Bob > > On Sun, Jul 24, 2016 at 12:59 PM, Angel Herráez <angel.herr...@uah.es > <mailto:angel.herr...@uah.es>> wrote: > Dear Bob, that makes sense. I did not realize. > Additional problem is that saved pdf file (with 1st model empty) cannot be > loaded back into Jmol, it hangs with the spinning cursor forever. > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev <http://sdm.link/zohodev2dev> > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <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 <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 > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
D yes not load anything for me?? > On Jul 19, 2016, at 3:03 PM, Angel Herráez <angel.herr...@uah.es> wrote: > > a little fun: browse rapamycin structures at PDB: > > http://biomodel.uah.es/JSmol/rapamycin.htm > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Yea. I had just found that. > On Jul 19, 2016, at 12:38 PM, Angel Herráez <angel.herr...@uah.es> wrote: > > Hi Phil > > Going to PubChem, Compound Summary for CID 5284616 > has a "download" menu that offers no 3D structure but says "Protein-bound > 3D structures" -- their format are not helpful, but you can search in PDB for > rapamycin and will find this ligand as RAP > > Hence, Jmol console > load ==RAP > and you have it! > > Of course, you can browse the different proteins to check the actual "real" > 3D structure they bind > > · > Dr. Angel Herráez > Biochemistry and Molecular Biology, > Dept. of Systems Biology, University of Alcalá > E-28871 Alcalá de Henares (Madrid), Spain > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
I have looked at it a little more. Turns out that the exported structures do load into JSmol (…. 06.30) with the odd exception of the .spardir. It will load by dropping it one the JSmol window, but will not with the load local file. For that I get a “no atoms found” error. That is true of the structure I was working with and with n-hexane. A file reading glitch in the load sequence? > On Jul 19, 2016, at 12:19 PM, Otis Rothenberger <osrot...@icloud.com> wrote: > > Phil, > > Resolver is string entry “smart,” so you can use load $IDENTIFIER from the > console or a script. You might need the InChI= in the IDENTIFIER string. When > I tried this, it was flat! > > While CORINA docs state that there is no atom limit, you have to get through > CORINA’s ensemble creation front door. I suspect, that this step is failing > with the return of the 2D. Recall that CORINA needs to break molecules into > known ensembles which are then reassembled as 3D. FYI, CORINA DOCS. > > I have no clue what’s going on in SPARTAN. > > Otis > > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > >> On Jul 19, 2016, at 11:49 AM, Philip Bays <pb...@saintmarys.edu> wrote: >> >> I was intrigued by the structure of the macrolide rapamycin after reading >> the article in C yesterday. So I went after the 3-D structure. >> >> I could not find it in any of the databases used by standard JSmol so I went >> off the Wikipedia and copied the smiles and inche strings. >> >> Using the console I was able to load from the smiles string, though the >> image was flat. Thinking Spartan would be faster at minimization, I >> exported from JSmol as a mol file which I loaded into Spartan and minimized. >> It was fast, but the result was ridiculous; a part of the molecule >> threaded through the macrocycle. >> >> I went back to JSmol and used the minimization function to begin a 3-D >> structure. I did not let it go to completion, but exported it as a mol file >> to load into Spartan. Spartan minimized it. I saved it as Spartan directory >> and as a mol file. For the mol file I was told that there were 8 >> unidentified atoms that were counted as dummy atoms. Neither would load >> into JSmol. It takes a while, but JSmol minimizes the structure to >> something reasonable. >> >> I then tried to load the inche string from the JSmol console using load >> inche “string”. Got a load error. What is the proper syntax for this and >> what is going on with Spartan?? >> >> >> Phil >> >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >> patterns at an interface-level. Reveals which users, apps, and protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Rapamycin
I was intrigued by the structure of the macrolide rapamycin after reading the article in C yesterday. So I went after the 3-D structure. I could not find it in any of the databases used by standard JSmol so I went off the Wikipedia and copied the smiles and inche strings. Using the console I was able to load from the smiles string, though the image was flat. Thinking Spartan would be faster at minimization, I exported from JSmol as a mol file which I loaded into Spartan and minimized. It was fast, but the result was ridiculous; a part of the molecule threaded through the macrocycle. I went back to JSmol and used the minimization function to begin a 3-D structure. I did not let it go to completion, but exported it as a mol file to load into Spartan. Spartan minimized it. I saved it as Spartan directory and as a mol file. For the mol file I was told that there were 8 unidentified atoms that were counted as dummy atoms. Neither would load into JSmol. It takes a while, but JSmol minimizes the structure to something reasonable. I then tried to load the inche string from the JSmol console using load inche “string”. Got a load error. What is the proper syntax for this and what is going on with Spartan?? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [n = {*}[0].molecule;show n] bug
rs@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> <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 <http://www.stolaf.edu/people/hansonr> >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Larson-Anderson Professor of Chemistry >>> St. Olaf College >>> Northfield, MN >>> http://www.stolaf.edu/people/hansonr <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 >>> >>> -- >>> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape >>> <http://sdm.link/attshape>___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> <https://lists.sourceforge.net/lists/listinfo/jmol-users> >> >> -- >> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape <http://sdm.link/attshape> >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> <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 <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 >> >> -- >> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape___ >> <http://sdm.link/attshape___> >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape___ > 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 -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] RCSB
In today’s version (…..6.28) the RCSB protein files in jsmol.htm do not load correctly. Yesterday’s version (….6.27) worked. Can anyone else confirm that? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol audio (applet and Application; Java and JavaScript)
Bob: You have a typo in your link. > On Jun 27, 2016, at 1:51 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > Isn't HTML5 is great?? > > Jmol.___JmolVersion="14.7.0_2016.06.27" > > new feature: load AUDIO audiofilename > -- Java and JavaScript applet can read WAV, MP3, and OGG files > -- application can read WAV files only > > See http://chemapp.stolaf.edu/jmol/zip/jmol-14.7.0_2016.06.27.zip > <http://chemapp.stolaf.edu/jmol/zip/jmol-14.7.0_2016.06.27.zip> > > (uploading now) > > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > -- > Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______ > 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 -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Seems to Be Broken 14.6.0_2016 05 24
Sorry. Intended for someone else.
> On Jun 23, 2016, at 10:14 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> ??
>
> On Wed, Jun 22, 2016 at 2:16 PM, Philip Bays <pb...@saintmarys.edu
> <mailto:pb...@saintmarys.edu>> wrote:
> Steve was actually looking at ones that were nominally mine. I know one was
> my laptop and another was the desktop. I think we had some mac laptops at
> one point that are gone. All of the ip’s he had for for Apple devices. We
> decided to cancel them all and see who complains:-)
>
>
>> On Jun 22, 2016, at 1:03 PM, Robert Hanson <hans...@stolaf.edu
>> <mailto:hans...@stolaf.edu>> wrote:
>>
>> Yes, that helps. Broken in 14.5.5. Fixed in next release. (tonight)
>>
>> On Fri, Jun 17, 2016 at 10:54 AM, Otis Rothenberger <osrot...@icloud.com
>> <mailto:osrot...@icloud.com>> wrote:
>> Bob,
>>
>> If it helps, 14.4.4_2016.03.25 is a few days after you fixed the click
>> invert and compare IS WORKING in this version.
>>
>> Otis
>> --
>> Otis Rothenberger
>> o...@chemagic.org <mailto:o...@chemagic.org>
>> http://chemagic.org <http://chemagic.org/>
>>
>> > On Jun 16, 2016, at 3:40 PM, Otis Rothenberger <osrot...@icloud.com
>> > <mailto:osrot...@icloud.com>> wrote:
>> >
>> > Bob,
>> >
>> > I think compare might be broken in 14.6.0_2016 05 24. The following script
>> > reports diastereomers when enantiomers are in the window:
>> >
>> > var i = {*}.atomno.max + 1;var t = {*}.atomno.min;select within(branch,
>> > {atomno=i}, {atomno=t});var x = compare({selected}, {not selected},
>> > "ISOMER");print x
>> >
>> > 05 17 on the test2.html page shows the same result.
>> >
>> > Perhaps it’s the selection method, but playing with coloring atoms to
>> > follow selections suggests that my selection is OK.
>> >
>> > Wild Guess: A while back the act of click inversion was broken, and you
>> > fixed it. Is it possible that the following line in SmilesMatcher.js was
>> > affected by the click inversion fix?
>> >
>> > check = (this.areEqual ("/invertstereo/" + smiles2, smiles1) > 0);
>> >
>> > Otis
>> >
>> > --
>> > Otis Rothenberger
>> > o...@chemagic.org <mailto:o...@chemagic.org>
>> > http://chemagic.org <http://chemagic.org/>
>> >
>>
>>
>> --
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning
>> reports. http://sdm.link/zohomanageengine <http://sdm.link/zohomanageengine>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> <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 <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
>>
>> ------
>> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape___
>> <http://sdm.link/attshape___>
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> <https://lists.sourceforge.net/lists/listinfo/jmol-users>
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre
Re: [Jmol-users] Compare Seems to Be Broken 14.6.0_2016 05 24
Steve was actually looking at ones that were nominally mine. I know one was my
laptop and another was the desktop. I think we had some mac laptops at one
point that are gone. All of the ip’s he had for for Apple devices. We
decided to cancel them all and see who complains:-)
> On Jun 22, 2016, at 1:03 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Yes, that helps. Broken in 14.5.5. Fixed in next release. (tonight)
>
> On Fri, Jun 17, 2016 at 10:54 AM, Otis Rothenberger <osrot...@icloud.com
> <mailto:osrot...@icloud.com>> wrote:
> Bob,
>
> If it helps, 14.4.4_2016.03.25 is a few days after you fixed the click invert
> and compare IS WORKING in this version.
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org <mailto:o...@chemagic.org>
> http://chemagic.org <http://chemagic.org/>
>
> > On Jun 16, 2016, at 3:40 PM, Otis Rothenberger <osrot...@icloud.com
> > <mailto:osrot...@icloud.com>> wrote:
> >
> > Bob,
> >
> > I think compare might be broken in 14.6.0_2016 05 24. The following script
> > reports diastereomers when enantiomers are in the window:
> >
> > var i = {*}.atomno.max + 1;var t = {*}.atomno.min;select within(branch,
> > {atomno=i}, {atomno=t});var x = compare({selected}, {not selected},
> > "ISOMER");print x
> >
> > 05 17 on the test2.html page shows the same result.
> >
> > Perhaps it’s the selection method, but playing with coloring atoms to
> > follow selections suggests that my selection is OK.
> >
> > Wild Guess: A while back the act of click inversion was broken, and you
> > fixed it. Is it possible that the following line in SmilesMatcher.js was
> > affected by the click inversion fix?
> >
> > check = (this.areEqual ("/invertstereo/" + smiles2, smiles1) > 0);
> >
> > Otis
> >
> > --
> > Otis Rothenberger
> > o...@chemagic.org <mailto:o...@chemagic.org>
> > http://chemagic.org <http://chemagic.org/>
> >
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
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> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
> <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 <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
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
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Re: [Jmol-users] JmolApplet.jar
Is it posible to do the following: Keep the java in the distribution Put all of the examples and scripts in separate directory. This would of course require changing the script to find the required files, but they would be available for playing with for development purposes (I find them very helpful!), but could be removed when transferring the relevant files to the server. Phil > On May 18, 2016, at 5:38 AM, Angel Herráez <angel.herr...@uah.es> wrote: > > I certainly would prefer to have Java available in the distribution. For > large > proteins and complexes there is still a significant difference in performance. > > Maybe the nonsigned variant can be dropped / separated into the other > download > > On the other hand, I would vote for not having the extra files in the > distribution like examples, scripts, copy of jQuery etc > Just leave what is needed for an operative JSmol, HTML5+Java > > > > > -- > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > ___ > 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 -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.4.4_2016.04.21
Not sure why you are pulling it but I do have some comments on mutf.htm. What is quaternion difference and what does it mean in the protein world? I find that auth generates the cartoon model and DSSP appears to do nothing. > On Apr 22, 2016, at 7:40 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > sorry, had to delete that build. > > -- > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ > 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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] window resizer test
I think the "load file" and "load url” button are reversed. The load url gives the file browsing option. > On Apr 20, 2016, at 3:02 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Oops. No, I just didn't realize I had clipped my local path. > > http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm > <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> > > One of the things I am trying here is switching to asynchronous transport for > binary files. This is supposed to be better for compatibility with Safari, > but I'm not sure that is the case. > > -- > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ > 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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] window resizer test
Bob: This works in Mac Safari for me. But if I copy your file to the most recently release, all it does is show the platform speed selections. The applet does not load nor any of the buttons. What am I missing? Phil > On Apr 20, 2016, at 3:02 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Oops. No, I just didn't realize I had clipped my local path. > > http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm > <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> > > One of the things I am trying here is switching to asynchronous transport for > binary files. This is supposed to be better for compatibility with Safari, > but I'm not sure that is the case. > > -- > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ > 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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and MMTF for testing
Is the mmtf file supposed top be a part of the release, or is it only on your
server? I do not find it in the jsmol directory.
> On Apr 20, 2016, at 2:07 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> and
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip
> <http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip>
>
> needs testing; highly experimental.
>
> Bob
>
>
> Jmol.___JmolVersion="14.5.4_2016.04.19"
>
> FEATURE NOTE: DSSP calculation at http://www.cmbi.ru.nl/dssp.html
> <http://www.cmbi.ru.nl/dssp.html> as changed
> from the original version, now emphasizing pi-helices (type
> "helix-5")
> insteda of alpha. The pi-helix set is determined first, then
> alpha helices
> (helix-4), then 3-10 helices (helix-3). I am not changing the
> order of
> determination in Jmol because I think this is a bug in that
> algorithm.
>
> new feature: preliminary MMTF reader
> -- MacroMolecular Transmission Format (MMTF, from RTSB)
> -- see https://github.com/rcsb/mmtf/blob/master/spec.md#overview
> <https://github.com/rcsb/mmtf/blob/master/spec.md#overview>
> -- binary format for file transfer and molecule construction
> -- uses MessagePack binary JSON format
> -- entirely experimental; not for general consumption
> -- biomolecule processing works
> -- DSSP secondary structure is read
> -- use LOAD =.mmtf for quick loading
>
> *
> * JmolData RCSB MMTF (macromolecular transmission format) file reader
> *
> * see https://github.com/rcsb/mmtf/blob/master/spec.md
> <https://github.com/rcsb/mmtf/blob/master/spec.md>
> *
> * /full/ specification as of 2016.4.18 is implemented,including:
> *
> * reading atoms, bonds, and DSSR secondary structure
> *
> * load =1f88.mmtf
> *
> *
> * reading space groups and unit cells, and using those as per other readers
> *
> * load =1crn.mmtf {1 1 1}
> *
> * reading bioassemblies (biomolecules) and applying those transformations
> *
> * load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P"
> *
> * reading biomolecules and lattices, and loading course-grained
> *
> * load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0;
> color property symop
> *
> *
>
> bug fix: certain viral capsid CIF files will fail to load due to this line:
> XAU '(X0)(1-10,21-25)' A,B,C
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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
>
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
--
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Re: [Jmol-users] Jmol and MMTF for testing
Otis:
What about NCI loads? I am getting no response. But it is not unique to this
version apparently.
> On Apr 20, 2016, at 9:27 AM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> I see the same behavior as Phil, but I see two other things in Safari,
> probably because I have developer tools turned on:
>
> 1) Load Pop-up
>
> JSmolCore.js: synchronous binary file transfer is requested but not available
>
> 2) JS Console
>
> XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S)
> requests made from the window context.
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org <mailto:o...@chemagic.org>
> http://chemagic.org
>
>> On Apr 20, 2016, at 9:01 AM, Philip Bays <pb...@saintmarys.edu
>> <mailto:pb...@saintmarys.edu>> wrote:
>>
>> Mac Safari does not like the mufti.htm file load from your site.
>> Unrecognized format for 1crn. Chrome and Firefox work fine.
>>
>>
>>> On Apr 20, 2016, at 2:07 AM, Robert Hanson <hans...@stolaf.edu
>>> <mailto:hans...@stolaf.edu>> wrote:
>>>
>>> see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm
>>> <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> and
>>> http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip
>>> <http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip>
>>>
>>> needs testing; highly experimental.
>>>
>>> Bob
>>>
>>>
>>> Jmol.___JmolVersion="14.5.4_2016.04.19"
>>>
>>> FEATURE NOTE: DSSP calculation at http://www.cmbi.ru.nl/dssp.html
>>> <http://www.cmbi.ru.nl/dssp.html> as changed
>>> from the original version, now emphasizing pi-helices (type
>>> "helix-5")
>>> insteda of alpha. The pi-helix set is determined first,
>>> then alpha helices
>>> (helix-4), then 3-10 helices (helix-3). I am not changing
>>> the order of
>>> determination in Jmol because I think this is a bug in that
>>> algorithm.
>>>
>>> new feature: preliminary MMTF reader
>>> -- MacroMolecular Transmission Format (MMTF, from RTSB)
>>> -- see https://github.com/rcsb/mmtf/blob/master/spec.md#overview
>>> <https://github.com/rcsb/mmtf/blob/master/spec.md#overview>
>>> -- binary format for file transfer and molecule construction
>>> -- uses MessagePack binary JSON format
>>> -- entirely experimental; not for general consumption
>>> -- biomolecule processing works
>>> -- DSSP secondary structure is read
>>> -- use LOAD =.mmtf for quick loading
>>>
>>> *
>>> * JmolData RCSB MMTF (macromolecular transmission format) file reader
>>> *
>>> * see https://github.com/rcsb/mmtf/blob/master/spec.md
>>> <https://github.com/rcsb/mmtf/blob/master/spec.md>
>>> *
>>> * /full/ specification as of 2016.4.18 is implemented,including:
>>> *
>>> * reading atoms, bonds, and DSSR secondary structure
>>> *
>>> * load =1f88.mmtf
>>> *
>>> *
>>> * reading space groups and unit cells, and using those as per other readers
>>> *
>>> * load =1crn.mmtf {1 1 1}
>>> *
>>> * reading bioassemblies (biomolecules) and applying those transformations
>>> *
>>> * load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P"
>>> *
>>> * reading biomolecules and lattices, and loading course-grained
>>> *
>>> * load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0;
>>> color property symop
>>> *
>>> *
>>>
>>> bug fix: certain viral capsid CIF files will fail to load due to this line:
>>> XAU '(X0)(1-10,21-25)' A,B,C
>>>
>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Department of Chemistry
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr <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
>>>
>>> --
>>> Find
Re: [Jmol-users] Jmol and MMTF for testing
Mac Safari does not like the mufti.htm file load from your site. Unrecognized
format for 1crn. Chrome and Firefox work fine.
> On Apr 20, 2016, at 2:07 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> and
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip
> <http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip>
>
> needs testing; highly experimental.
>
> Bob
>
>
> Jmol.___JmolVersion="14.5.4_2016.04.19"
>
> FEATURE NOTE: DSSP calculation at http://www.cmbi.ru.nl/dssp.html
> <http://www.cmbi.ru.nl/dssp.html> as changed
> from the original version, now emphasizing pi-helices (type
> "helix-5")
> insteda of alpha. The pi-helix set is determined first, then
> alpha helices
> (helix-4), then 3-10 helices (helix-3). I am not changing the
> order of
> determination in Jmol because I think this is a bug in that
> algorithm.
>
> new feature: preliminary MMTF reader
> -- MacroMolecular Transmission Format (MMTF, from RTSB)
> -- see https://github.com/rcsb/mmtf/blob/master/spec.md#overview
> <https://github.com/rcsb/mmtf/blob/master/spec.md#overview>
> -- binary format for file transfer and molecule construction
> -- uses MessagePack binary JSON format
> -- entirely experimental; not for general consumption
> -- biomolecule processing works
> -- DSSP secondary structure is read
> -- use LOAD =.mmtf for quick loading
>
> *
> * JmolData RCSB MMTF (macromolecular transmission format) file reader
> *
> * see https://github.com/rcsb/mmtf/blob/master/spec.md
> <https://github.com/rcsb/mmtf/blob/master/spec.md>
> *
> * /full/ specification as of 2016.4.18 is implemented,including:
> *
> * reading atoms, bonds, and DSSR secondary structure
> *
> * load =1f88.mmtf
> *
> *
> * reading space groups and unit cells, and using those as per other readers
> *
> * load =1crn.mmtf {1 1 1}
> *
> * reading bioassemblies (biomolecules) and applying those transformations
> *
> * load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P"
> *
> * reading biomolecules and lattices, and loading course-grained
> *
> * load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0;
> color property symop
> *
> *
>
> bug fix: certain viral capsid CIF files will fail to load due to this line:
> XAU '(X0)(1-10,21-25)' A,B,C
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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
>
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
> 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
--
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Re: [Jmol-users] RasMol terms
I will pass for the moment. I have solved my questions.
> On Apr 14, 2016, at 1:59 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote:
>
> On 04/14/2016 07:19 PM, Robert Hanson wrote:
>> Phil, you should check out DSSR. It is amazing! Sorry this is not
>> documented yet:
>>
>> new feature: select shortcuts for nucleic acid structures
>> -- for example: select junctions; select kissingloops
>> -- activated after load =/dssr or calculate structure dssr
>> -- includes:
>> "@bulges within(dssr,'bulges')",
>> "@coaxStacks within(dssr,'coaxStacks')",
>> "@hairpins within(dssr,'hairpins')",
>> "@hbonds within(dssr,'hbonds')",
>> "@helices within(dssr,'helices')",
>> "@iloops within(dssr,'iloops')",
>> "@isoCanonPairs within(dssr,'isoCanonPairs')",
>> "@junctions within(dssr,'junctions')",
>> "@kissingLoops within(dssr,'kissingLoops')",
>> "@multiplets within(dssr,'multiplets')",
>> "@nonStack within(dssr,'nonStack')",
>> "@nts within(dssr,'nts')",
>> "@naChains within(dssr,'naChains')",
>> "@pairs within(dssr,'pairs')",
>> "@ssSegments within(dssr,'ssSegments')",
>> "@stacks within(dssr,'stacks')",
>> "@stems within(dssr,'stems')",
>>
>>
>>
>> load =1d66/dssr
>> $ print _M.dssr.pairs.select("(nt*) where bp='C-G' or bp='G-C'")
>> |1|E|DG|38
>> |1|D|DC|1
>> |1|E|DG|37
>> |1|D|DC|2
>> ...
>> |1|D|DG|19
>>
>> $ x= _M.dssr.pairs.select("(nt*) where bp='C-G' or bp='G-C'")
>> $ select x
>>
>>
>> Works for RNA and DNA
>>
> I tried 'select within(dssr,"basePairs")' and 'select
> within(basepair,"GCAT")' for PDB entry '3cro' at
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (see examples below) and
> didn't get the expected results.
>
> In example 1 also about 300 protein atoms were selected, and in example
> 2 also about 900 protein atoms were selected.
>
> In example 3 two basepairs were not recognized, but at least no protein
> atoms were selected. Adding 'calculate structure dssr' didn't make a
> difference.
>
> - Example 1
> load =3cro
> calculate structure dssr
> cartoon only
> selectionhalos on
> select within(dssr,"basePairs")
>
> - Example 2
> load =3cro/dssr
> cartoon only
> selectionhalos on
> select within(dssr,"basePairs")
>
> - Example 3
> load =3cro
> cartoon only
> selectionhalos on
> select within(basepair,"GCAT")
>
>
> Regards,
> Rolf
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone: +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail: rolf.hue...@leibniz-fli.de
> Website: http://www.leibniz-fli.de
>
> Scientific Director: Prof. Dr. K. Lenhard Rudolph
>Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Burkhard Zinner
>
> VAT No: DE 153 925 464
> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
>
>
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
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Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
--
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[Jmol-users] RasMol terms
This is for the biomolecular people: How does one use the term “Selected”? Seems to me that it is redundant. In the Nucleic Acid area: How does one use CG and AT to select base pairing? Perhaps these are not implemented in Jmol? PS I am finding today’s version to work well for my purposes, which are limited. And HEM now works:-) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.4.4_2106.04.11
mz)"
> "xyzOriginal" : "-x,-y,-z,m"
> }
>
>In addition, all possible keys of this array may be used as well for
> outputType. These include:
>
>"axisVector", "cartesianTranslation", "centeringVector",
> "fractionalTranslation",
> "inversionCenter", "label", "matrix", "plane", "rotationAngle",
> "timeReversal", "unitTranslation", "xyz", and "xyzOriginal"
>
> Three of these that may be less than obvious are explained below:
>
> "centeringVector" For operations that are pure lattice translations,
> returns the vector
> for this centering in fractional coordinates.
>
> "timeReversal" This quantity is 0 for standard space groups.
> Magnetic space group
> operations also include the possibility of inversion
> of the spin
> along with any 3D symmetry operation. This inversion
> characteristic
> is referred to as "time reversal" and takes the value
> of 1 or -1.
>
> "unitTranslation" Symmetry operations involving two atoms may include
> an extra
> lattice translation if the two atoms are in different
> unit cells.
> This translation is above and beyond any fractional
> lattice centering
> that this operator incorporates for a face- or
> body-centered space group.
>
> new feature: show spacegroup/x
>
> -- selects lines from a space group report similar to the way show
> state/ works
> -- example:
>
> load =ams/quartz 1
> show spacegroup/Class
>
> new feature: show/draw symop @1 @2
> -- gives full list of matching symmetry operations
> -- example:
>
> $ load =magndata/1.23 {444 555 1} packed
> $ show symop @153 @299
>
> 1x+2,y,z2(mx,my,mz)translation: 2 0 -2
> 5-x,-y,-z(mx,my,mz)Ci: 0 0 0
> 11x+2,-y,-z(-mx,my,mz)2-fold screw axis|translation: 2 0
> 0|time-reversed
> 15-x,y,z2(-mx,my,mz)c-glide plane|translation: 0 0
> -2|time-reversed
>
> new feature: show/draw symop @1 @2 n
> -- shows or draws the nth symmetry operation relating atom 1 to atom 2
> -- example:
>
> $ load =magndata/1.23 {444 555 1} packed
> $ show symop @153 @299 3
>
> 11x+2,-y,-z(-mx,my,mz)2-fold screw axis|translation: 2 0
> 0|time-reversed
>
> new feature: print pointgroup("spacegroup", @1)
> -- analyzes the point group (crystal class) of a crystal.
> -- uses three irrational-coordinate points to generate all possible operators
> -- creates a map with keys (somewhat variable depending upon axes present):
>
> C2
> C3
> Ci
> Cs
> S6
> detail
> distanceTolerance
> linearTolerance
> nAtoms
> nC2
> nC3
> nCi
> nCn
> nCs
> nS6
> nSn
> nTotal
> name
> points
> principalAxis
>
> new feature: draw SPACEGROUP
> -- draws all operations in space group
>
> new feature: draw POINTGROUP SPACEGROUP
> -- draws crystal class symmetry operations for a space group
> -- uses point group style, with circular planes
>
> new feature: @1.find("crystalClass", pt)
> -- generates a list of points based on a model's crystal class (point group)
> -- uses @1 just to find the unit cell and space group
> -- optional pt is used as a generator (defaults to @1)
> -- example:
>load =ams/calcite 1
> x = @3.find("crystalClass")
>print pointgroup(x).name
>draw points @x
>polyhedra ID p {0 0 0} to @x
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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
>
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
> 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
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[Jmol-users] Symbols
Some days/weeks ago someone posted the symbols used for the various databases (i.e. $ for NCl) I cannot find that post which I know I saved:-( Can someone refresh it for me. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Protein Loading
You should not have looked at that page:-( It has not been updated in a long time and needs some work, but it also uses a much older version of jsmol — 12/14/13. It also works for me to drag and drop onto that. But simply replacing it with the new version throws a bunch of javascript errors on loading. Will look at what that is all about tomorrow— maybe. Phil > On Apr 1, 2016, at 6:31 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Drag-drop can't utilize jsmol.php, because it is not a "file" per se, just a > bunch of bytes. But try it in your installation at > http://sites.saintmarys.edu/~pbays/ <http://sites.saintmarys.edu/~pbays/> -- > worked for me there > > Bob > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ > 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Protein Loading
OK. It does not work with my implementation on any of the browsers on the mac, but it does with your jsmol.htm file. So it’s me:-( > On Apr 1, 2016, at 4:24 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > > > On Fri, Apr 1, 2016 at 2:52 PM, Philip Bays <pb...@saintmarys.edu > <mailto:pb...@saintmarys.edu>> wrote: > I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using > previous versions of jsmol.min, this file would load via drag-and-drop or > using the local-file load mechanism. In the latest version, jsmol version > (03.31) I get a "file not recognized" error. I can download the structure > directly from RCSB. > > with Firefox/Windows and Chrome/Windows I had no problem drag-dropping into > JSmol. > Is this perhaps browser/platform dependent? > > > > A definition question: In the various sample test files involving > macromolecules that I have looked at, Bob uses the terms “structure” and > “groups" as a color and display choices. I am not sure what I am looking at > in each case. I thought it might be 4° structure, but now I am not sure. > > > structure is type of secondary structure -- different types of helix, sheet, > etc. > > group is just 1->n within each chain. > > > Phil > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu <mailto:pb...@saintmarys.edu> > > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 > <http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140> > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ > 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Protein Loading
I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using previous versions of jsmol.min, this file would load via drag-and-drop or using the local-file load mechanism. In the latest version, jsmol version (03.31) I get a "file not recognized" error. I can download the structure directly from RCSB. A definition question: In the various sample test files involving macromolecules that I have looked at, Bob uses the terms “structure” and “groups" as a color and display choices. I am not sure what I am looking at in each case. I thought it might be 4° structure, but now I am not sure. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Ligands
Can JSmol pick out and display ligands in proteins? What is the script for that? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Open local files
Thanks. left out the “?":-( > On Mar 29, 2016, at 2:06 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > "Open Local File" is not a Jmol script command. Check > http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm > <http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm> to see how the "Load > File" link works. I believe it is just > > load ? > > > > On Tue, Mar 29, 2016 at 1:02 PM, Philip Bays <pb...@saintmarys.edu > <mailto:pb...@saintmarys.edu>> wrote: > I am putting together a page and want a link on it to open local files. I > know that you can do this through the JSmol frank menu, but I want the link > on the page. I have tried the following: > > console > > mailto:pb...@saintmarys.edu> > > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 > <http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140> > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ > 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Open local files
I am putting together a page and want a link on it to open local files. I know that you can do this through the JSmol frank menu, but I want the link on the page. I have tried the following: console http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.4.4_2016.03.21
And I am seeing on the campus website using the 0228 release. Possible that RCSB is down?? > On Mar 21, 2016, at 5:13 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > I am not seeing that. Others? > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___ > 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.4.4_2016.03.21
Bob:
I am seeing “unrecognized file format” errors in this release for both PubChem
and RCSB.
> On Mar 21, 2016, at 2:38 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> This update takes care of a few minor bugs and also introduces several
> powerful features in relation to polyhedra, unit cells, and SMILES.
>
> Jmol.___JmolVersion="14.4.4_2016.03.21"
> released
>
> new feature: moveto axis [a1-c4]
> -- extends moveto axis a|b|c to all for corners 1|2|3|4
> where 1 is upper left, 2 is upper right, 3 is lower right, and 4 is lower
> left
> -- for example, MOVETO AXIS a3
> -- defaults: a==a1, b==b1, c==c4
>
> new feature: axes OFFSET x.x
> -- applies offset of x.x in fractional coordinates in each axis direction
> -- AXES OFFSET -0.1 same as AXES CENTER {-0.1 -0.1 -0.1/1}
>
> new feature: expanded unitcell() function
> -- adds additional types: "A", "B", "C", "I", "F"
> -- default is the lattice type of the model's space group
> -- not just cubic; "BCC" is converted to "I"
> -- for example:
>
> load =ams/silicon 15 packed // Cmca
> draw id "uc" diameter 0.1 unitcell mesh nofill color black
> unitcell @{unitcell("primitive")}
> color unitcell red
> unitcell 0.1
> axes unitcell
> axes on
>
> new feature: expanded UNITCELL command to include PRIMITIVE option for any
> space group
>
> new feature: show smiles/NCI aka show smiles/CACTVS aka show
> smiles/canonical
>
> -- generates nonaromatic SMILES and sends that to NCI for canonicalization
>
> bug fix: SMILES matcher not allowing azulene to be aromatic
>
> bug fix: OpenSMILES matcher not allowing non-chemist Hueckel 4+2
> interpretation
>
> bug fix: SMILES generator not adding "-" for biphenyl Ar-Ar bond
>
> bug fix: set picking invertSTEREO does not work on open-ring systems
>
> bug fix: SMARTS [R] matching all atoms
>
> bug fix: dashed lines not visible in measurements, unit cells, and axes
>
> bug fix: axes 0.01 produces thick 20-pixel-wide lines
> -- solution was to drop that to 0.001 for this effect
>
> bug fix: Polyhedra with verticies that are also centers of polyhedra for
> atoms that were visible
> but are no longer visible do not update screen positions properly
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
> 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
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[Jmol-users] Malware
I struggled yesterday with a McAfee report of malware on my desktop Mac. The software does not provide a resizable window so I could not get the full path of the offending files. But it was identified as JS/Downloader……….. in a mail message. I finally got rid of it on the main machine and various backups. Is this a jmol file? Something that was attached to a jmol message? Anyone else seeing this? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] new InChI option
Some time ago I made a comment here about taxol. It was a molecule I went to when testing jsmol. It always loaded a nice 3D structure. Then, it changed to the 2D structure that now loads. > On Mar 8, 2016, at 9:29 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Whatever the problem is, it has to do with loading a trashy 2D structure > instead of a good 3D structure, apparently. > > I have placed a taxol structure in jsmol/data so you can see that it does > work: http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm > <http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm> > > I note that in creating this from the RCSB ligand TA1, I had to invent a new > way to write a MOL file: > > load ==TA1 > write MOL0 "taxol.mol" > > The new MOL0 format avoids use of the aromatic single and aromatic double > bond types 6 and 7. > (There is a bug in inchi.js that it cannot read these bond types.) > > > Bob > > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___ > 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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)
I confirm this behavior. You can go back and forth if they are loaded in tabs or different pages, but not via history. Same Safari version. In Firefox and Chrome, the applet reloads on return. > On Feb 11, 2016, at 1:41 PM, Jaime Prilusky <jaime.prilu...@weizmann.ac.il> > wrote: > > It seems that JSmol gets unloaded when a page gets out of focus, by flipping > between pages, on Safari Mac Version 9.0.3 (11601.4.4). > > 1. Open any page on Safari Mac (tested on Version 9.0.3) > > 2. Now open a page with JSMol on it, i.e. http://proteopedia.org/w/1dnn > > 3. Go to the previous page: History->Back or click on the ’Show the previous > page’ arrow > > 4. Go to the JSmol page: History->Forward or click on the ‘Show the next > page’ arrow > > JSmol is not longer reponsive. > > This doesn’t happen on Chrome or Firefox on Mac. Doesn’t happen either on > Safari when a page loose focus by opening another window on the same browser. > > Jaim > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 > ___ > 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 -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Taxol
Observation for both 12.23 and 01.01. When you load taxol from NCl it is not minimized; it is flat. It did not used to be that way. I suspect it is NCl since other molecules (cholesterol, tetracycline, etc.) are fine. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] test please
This link works in Safari, albeit slowly. That mat be because the console log is being displayed. Phil > On Dec 21, 2015, at 8:02 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > Brilliant, Paul! Very nice! > > I think I have http://chemapps.stolaf.edu/jmol/jsmol2/test2.htm > <http://chemapps.stolaf.edu/jmol/jsmol2/test2.htm> working now on Macs using > that -- please test -- I will get JSmol.min.js created and jsmol.htm there > working later tonight. > > Bob > > > -- > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] test please
Bob: Then link to your site does not work with Safari on the Mac, Works with Firefox and Chrome. When I launch the file test2.htm from the desktop, it again works in Firefox and Chrome but not Safari. In this case the list of files loading is visible and the crash comes at the following: TypeError: b.slice is not a function. (In 'b.slice(c, d)', 'b.slice' is undefined) Phil > On Dec 20, 2015, at 6:37 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > I have made some significant changes to the way JSmol handles arrays. This > needs wider testing -- Mac OS especially, JavaScript/HTML5 specifically. > > The full code is at: > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.0_2015.12.20.zip > <http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.0_2015.12.20.zip> > > > But you could also just test it at > > http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm > <http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm> > > if you want to. > > If something is wrong, it will be immediately obvious. Specific tests that > will be helpful are from the middle column and include anything that is > binary: the PyMOL session file, the water.xyz.gz, 1hxw.png, > square_planar.spartan, among others. > > Mostly what I did was to implement byte arrays (Int8Array in JavaScript) and > much faster array manipulation using .slice(). > > Maybe also making images. > > I think this may break Internet Explorer 9, but that might not be a big deal > -- there were just 300 visits out of 250,000 from that. But also Maybe Safari > 5.1 will break. again, only very few visits from that. Maybe time to move on. > > > Bob > > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > -- > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] test please
Addendum: I am running Safari 9.02. OS X 10.11.2 > On Dec 20, 2015, at 6:37 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > I have made some significant changes to the way JSmol handles arrays. This > needs wider testing -- Mac OS especially, JavaScript/HTML5 specifically. > > The full code is at: > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.0_2015.12.20.zip > <http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.0_2015.12.20.zip> > > > But you could also just test it at > > http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm > <http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm> > > if you want to. > > If something is wrong, it will be immediately obvious. Specific tests that > will be helpful are from the middle column and include anything that is > binary: the PyMOL session file, the water.xyz.gz, 1hxw.png, > square_planar.spartan, among others. > > Mostly what I did was to implement byte arrays (Int8Array in JavaScript) and > much faster array manipulation using .slice(). > > Maybe also making images. > > I think this may break Internet Explorer 9, but that might not be a big deal > -- there were just 300 visits out of 250,000 from that. But also Maybe Safari > 5.1 will break. again, only very few visits from that. Maybe time to move on. > > > Bob > > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > -- > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.4.1_2015.12.13 released - IMPORTANT
I concur with Otis, at least on my local server.
Phil
> On Dec 13, 2015, at 2:42 PM, Otis Rothenberger <osrot...@chemagic.com> wrote:
>
> Bob,
>
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm> on Chrome Mac (Latest
> versions OS and Chrome) works fine after cache clear.
>
> On my site, I swapped out JSmol.min.nojq.js and this also works fine after
> cache clear.
>
> “Fine” means a quick check. I’ll play around a bit to make sure.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com <mailto:o...@chemagic.com>
> http://chemagic.com
>
>> On Dec 13, 2015, at 1:56 PM, Robert Hanson <hans...@stolaf.edu
>> <mailto:hans...@stolaf.edu>> wrote:
>>
>> This new version is now available at SourceForge:
>>
>> Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB)
>> <https://sourceforge.net/projects/jmol/files/latest/download?source=files>
>>
>>
>> IMPORTANT: A very recent modification of Chrome makes Chrome unusable with
>> all previous versions of JSmol, at least until sometime in January. The
>> WebGL version of JSmol is not impacted.
>>
>> This appears to be the result of a well-meaning attempt by Chromium
>> developers to enhance smooth scrolling of pages by lowering the priority of
>> setTimeout calls. However, the unanticipated fallout of that change results
>> in extremely rough rotation of models. You can follow the issue here:
>> https://code.google.com/p/chromium/issues/detail?id=568725
>> <https://code.google.com/p/chromium/issues/detail?id=568725> Note that one
>> of the last comments on Dec. 11 indicates that there indicates this issue
>> will not be addressed until sometime in January.
>>
>> But there is a workaround. This release of Jmol 14.4.1 should correct that
>> problem and, at the same time, may improve performance with Microsoft Edge.
>>
>> I have put up two versions of JSmol that illustrate the problem and the fix:
>>
>> (original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>> <http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm>
>> (fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm
>> <http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm>
>>
>> Testing of that second site would be appreciated.
>>
>> The work-around is simple, and if you want, you can implement this yourself
>> on your site. Really (in terms of this bug) it is just a single coding
>> change in jsmol/js/JSmol.js, where one "setTimeout(f)" has been replaced
>> with "requestAnimationFrame(f)". Thus, if you prefer, you should be able to
>> just swap in a new JSmol.min.js or JSmol.min.nojq.js for the old one. I have
>> not tried this. Of course, if you do that, then the other bugs listed below
>> will still be there. If you want to try that, here is the link to that file
>> specifically:
>>
>> http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js
>> <http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js>
>>
>> Bob
>>
>> Jmol.___JmolVersion="14.4.1_2015.12.13"
>>
>> bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout
>> issues; uses requestAnimationFrame instead in JSmol.js
>> bug fix: zoomTo not setting time to 0 in the case of scriptWait
>> bug fix: set selectAllModels should restrict action of display/hide as well
>> bug fix: set selectAllModels not working appropriately
>> bug fix: set selectAllModels should not be saved in state
>> bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
>> select {visible}
>> bug fix: JmolData.jar -p flag does not work properly
>> bug fix: model 0 issued when more than one PDB file is open does not execute
>> model *
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Department of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr <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
>>
>> --
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> --
> ___
> 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
--
___
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Re: [Jmol-users] Jmol -- testing requested
Do these errors only show up on your web page, or do they show up using some of Bob’s sample pages? I have the newest on both a local server and on the campus server, but not integrated into my web pages yet. But I can access one of Bob's samples from that server to see what happens. I am running OS 10.10.5 and Safari 8.0.8. Phil On Aug 25, 2015, at 2:46 PM, Paul PILLOT paulpil...@gmail.com wrote: Thanks Otis, I am also running pages from my local web server (localhost). I haven’t spotted the setting you are referring to. I have made further tests with firefox 40 and Chrome 44. The three browsers give the same consistent error messages (that don’t prevent jsmol from working). Paul Le 25-08-2015 à 14:34, Otis Rothenberger osrot...@chemagic.com a écrit : Bob and Paul, I’m not seeing this (below) in MacOS X 10.10.4 (Yosemite) and Safari 8.0.7. I should mention that I’m running locally with internet connection - i.e. all my AJAX remote calls working. This means that I run Safari with “Disable Local File Restrictions” checked. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmol/jmse issue
I have played with this. At first I thought it had do with symmetry, but now I think it is the presence of an aromatic ring. For example, if you load toluene in the dismal applet, then rotate it to look down the methyl-ring bond, send it to jsme and then return it to jmol, it will rotate the structure (or re-download it) so that the ring is face-on. I do not see the issue in molecules without an aromatic ring, even substituted cyclohexane seem to retain the new orientation in jmol. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: jmol/jmse issue
PS: I can’t decide whether this is a bug or a feature. Begin forwarded message: From: Philip Bays pb...@saintmarys.edu Subject: jmol/jmse issue Date: August 19, 2015 at 11:06:29 AM EDT To: Jmol Jmol jmol-users@lists.sourceforge.net I have played with this. At first I thought it had do with symmetry, but now I think it is the presence of an aromatic ring. For example, if you load toluene in the dismal applet, then rotate it to look down the methyl-ring bond, send it to jsme and then return it to jmol, it will rotate the structure (or re-download it) so that the ring is face-on. I do not see the issue in molecules without an aromatic ring, even substituted cyclohexane seem to retain the new orientation in jmol. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] enlarging text in console and script editor windows
Is the new Font button missing in the console in ….07.29? On Jul 29, 2015, at 5:35 AM, Robert Hanson hans...@stolaf.edu wrote: A new [Font] button has been added to the console in Jmol 14.2 and 14.3; It allows five different font sizes, from tiny to extra large On Tue, Jul 28, 2015 at 6:54 PM, Angel Herráez angel.herr...@uah.es mailto:angel.herr...@uah.es wrote: Hi Margaret I think the answer is no. You may copy and paste code to/from a Notepad window -- that's what I often use to display text while projecting, it's easy to set the font size. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jsme jmol demo
Bob: Just for your information, while your new file solved problems for Safari, Chrome does not load any of the jsme demos locate in the jsmol directory. The first ( jsme.htm) results in a blank page and the other two which use both jsmol and jsme throw an error related to core/package for jsmol. Again, this is on a Mac running the latest iteration of OS X. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
That fixed it. Thanks. On Jun 19, 2015, at 6:43 PM, Robert Hanson hans...@stolaf.edu wrote: It was an error in JSmolJME.js that I have fixed. If you want to just download that, it goes in the jsmol/js directory. Find it at from http://chemapps.stolaf.edu/jmol/jsmol/js/JSmolJME.js http://chemapps.stolaf.edu/jmol/jsmol/js/JSmolJME.js On Fri, Jun 19, 2015 at 4:08 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: Bob, Angel, and Otis: Thanks for the suggestions. The width was not a problem for me. I had already gotten out of the box. However, I have discovered the issue.It manifests in all three of Bob’s samples for loading JSMe: jsme.htm, jsmetest.htm, and jsmetest2.htm. In each example, the applet loads correctly. All of the buttons along the top work as expected, except FG. None of the vertical buttons work as expected. In each case for these buttons (FG and vertical) the button has to be “touched” at the very bottom of the border to activate. Now all of this is in Safari on the Mac. Firefox works fine. However, Chrome on the two files that load both jsme and jsmol, the jmol applet fails to load, throwing javascript errors. I recognize that there are other ways to get the two applets on the same page, but something is problematic with these demos. I can, in fact, write code that loads just jsme, and the applet works as expected in Safari and Firefox. Still having some issues with Chrome (i.e. blank screen!). On Jun 18, 2015, at 7:58 PM, Robert Hanson hans...@stolaf.edu mailto:hans...@stolaf.edu wrote: I have increased the width of the JSME applet to be 350, even if I do like squares. :) Thanks, Angel. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users 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 mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
In the same folder as what? J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad On Jun 18, 2015, at 1:05 AM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, I'm at a loss other than saying that there is something inherent in Bob's JSmol/JSME page that is causing the problem. If you use jsmol/jsme/JSME.html in the same jsmol folder, then the problem goes away. Clicking anywhere in the FG icon drops the menu. Wild, I don’t have a clue, guess: Bob does redefine the JSME jsmeOnLoad function in his page. Peter’s page has a code comment that suggests that loading with this on load function is important with respect to proper applet element display. Maybe the new jsmeOnLoad function is causing the problem. Otis On Jun 17, 2015, at 11:03 PM, Philip Bays pb...@saintmarys.edu wrote: And that is specific to Safari. Works in Firefox. On the other hand, Chrome has issues throwing error messages. On Jun 17, 2015, at 9:31 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Bob is doing something on those pages that is way over my head! The hidden FG button actually throws a JS error when you expose it and click it. The way over my head part comes via: js/JSmolJME.js I can see that he’s integrating JSmol with JSME, but I get lost real fast if I try to get down to specifics in the .js file. As usual, Bob’s approach is elegant. It allows very simple communication between JSmol (multiple applets) and a single JSME applet with this code: Jmol.show2d(jmol, false) and Jmol.show2d(jmol, true) It may be that he is using 300X300 to hide the FG button because of something js/JSmolJME.js is doing that interferes with the button. I vaguely recall (years ago) some warnings from Bob about this implementation of Jmol with JME. The following JSME template would offer you an alternate approach: jsmol/jsme/JSME.html Alternatively, use http://chemagic.com/molecules/jsme.htm It’s stripped down to absolute bare bones. You have to write separate JavaScript to make JSmol and JSME talk to each other, but the JSME and JSmol functions are there to do that - Jmol functions that were not in place when Jmol first started using JME. Back then I was using a clumsy Jmol load-data approach. Jmol 2015 vs Jmol 2008: Thanks in large part to Bob, it’s come a long way. Otis On Jun 17, 2015, at 4:50 PM, Philip Bays pb...@saintmarys.edu wrote: OK. I have found the source of my issue, but not the solution yet. Please note the jsmoljsmetest2 file in the distribution. If you edit the file to expand the width to 400, you see the FG button. But if you try to use this applet, none of the vertical buttons work, nor does the FG. Since I was using that as my coding pattern, I reproduced the problem. Now to look at it in more detail tomorrow. On Jun 17, 2015, at 3:58 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Nah, Bob just likes squares! The JSME applet needs to be 400X300 to see all the buttons. The 300X300 applet just cuts off the buttons after cyclooctane. You could definitely teak the old JME FG button. Again this goes back to JME Java applet. In fact, it was not a button. It was a JavaScript drop down menu that could be modified by some type of cookie structure that remembered your drop entries. This is where I got the idea of using Local Storage to store JME structures. Users can store 50 JME structures in our application page that I linked to earlier. Otis On Jun 17, 2015, at 3:33 PM, Philip Bays pb...@saintmarys.edu wrote: If you look at some of Bob’s examples, you will find that they are biasing some of the buttons, including FG. I vaguely recall that there was a way to turn them on and off. On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com wrote: There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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 -- ___ Jmol-users mailing list Jmol
Re: [Jmol-users] JSME Qestion
Thanks
On Jun 18, 2015, at 11:59 AM, Angel Herráez angel.herr...@uah.es wrote:
It seems one of my former messages got lost.
Phil, this simplest code works fine:
!DOCTYPE HTML
html
head
script src=jsme/jsme.nocache.js type=text/javascript/script
script type=text/javascript
var JSMEditor;
function jsmeOnLoad() {
if ( document.getElementById('jsmeContainer') ) {
JSMEditor = new JSApplet.JSME(jsmeContainer, {
options : multipart,polarnitro,oldLook,atommovebutton,
});
JSMEditor.setMolecularAreaLineWidth(2);
}
}
/script
/head
body
div id=jsmeContainer style=width:400px; height:312px;/div
/body
/html
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Re: [Jmol-users] JSME Qestion
Otis: I am looking at the second link. The FG function works, even if I have not begun drawing. Mine does not. I will put together an separate test page and see if it does there. I note that you have the following options set: options : query,hydrogens,autoez,multipart,reaction,nocanonize”, However, no hydrogens appear when I draw a structure in your applet.What does that options thing do? (I know, that is a secondary question.) On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, I put JSME into an iFrame. Here is the main model application page: http://chemagic.com/molecules/mini.html http://chemagic.com/molecules/mini.html Here is the JSME page that is in the iFrame of the above page: http://chemagic.com/molecules/jsme.htm http://chemagic.com/molecules/jsme.htm There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Otis On Jun 17, 2015, at 2:08 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: I do not see where you set the options for jsme in your source. Do you have that in an ancillary file? On Jun 17, 2015, at 2:49 PM, Angel Herráez angel.herr...@uah.es mailto:angel.herr...@uah.es wrote: Hi Phil Not much documentation. I seem to remember that the display of buttons might depend on the size (width) of the JSME panel. See if my page gives you some insight: http://biomodel.uah.es/en/DIY/JSME/draw.en.htm http://biomodel.uah.es/en/DIY/JSME/draw.en.htm or http://bit.ly/DIYmol Yes, I do have the FG button there! -- ___ 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 mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
I have to go to a local ACS meeting in a while. I will get back to you in a day or so. At this point the file is not online yet. On Jun 17, 2015, at 2:33 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Can you point me to the page that is not working? Historical Note: In the history of JME/JSME, this menu went through some transitions. At one point, cookies were involved. That goes back to the Java applet, I think. This should just work out of the box, I think. Otis On Jun 17, 2015, at 2:22 PM, Philip Bays pb...@saintmarys.edu wrote: If you go to a jmol distribution to the following demo file (I am testing in the latest jmol release on 6/16): jmol0616/jsmol/jsme/JSME.html You will, see the FG button activated. When I try to do that on the gismo I have inserted on page, the button is present, but not active. That is, you do not get the menu of FG options. Perhaps that requires a file I do not have loaded on my site? I note that in the setup for jsme (which my spellchecker insists on replacing with gismo!) there is an “options” specifications. it is not clear to me that any of those are really sticking either. And I have seen pages using options that are not on the “list” from the official jsme site. On Jun 17, 2015, at 2:08 PM, Otis Rothenberger osrot...@chemagic.com wrote: Hi Phil, I use the version in Jmol, and FG works. Are you using it correctly? 1) Click FG to get drop menu. 2) Make a group selection . 3) The FG button stays gray, and your selection is now click atom active with the selection group item. Like other JME buttons FG is only active until you click another tool. Otis On Jun 17, 2015, at 1:16 PM, Philip Bays pb...@saintmarys.edu wrote: I am working with Jmol and Jsme. I cannot find some information about jsme and wonder if someone has a link. I see the files in the jmol distribution and have jsme running on several pages. However, in most of Bob’s examples he does not show the FG button. I want that and have it displayed. But I apparently do not have it set to be active. Is this specified in the options, and if so, how? Any help? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
If you look at some of Bob’s examples, you will find that they are biasing some of the buttons, including FG. I vaguely recall that there was a way to turn them on and off. On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com wrote: There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
I found the issue. Turns out all works well, except that you have to click the button at the very bottom, not in the center, That is true of the vertical elements as well as the FG button. Takes a steady hand. On Jun 17, 2015, at 9:31 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Bob is doing something on those pages that is way over my head! The hidden FG button actually throws a JS error when you expose it and click it. The way over my head part comes via: js/JSmolJME.js I can see that he’s integrating JSmol with JSME, but I get lost real fast if I try to get down to specifics in the .js file. As usual, Bob’s approach is elegant. It allows very simple communication between JSmol (multiple applets) and a single JSME applet with this code: Jmol.show2d(jmol, false) and Jmol.show2d(jmol, true) It may be that he is using 300X300 to hide the FG button because of something js/JSmolJME.js is doing that interferes with the button. I vaguely recall (years ago) some warnings from Bob about this implementation of Jmol with JME. The following JSME template would offer you an alternate approach: jsmol/jsme/JSME.html Alternatively, use http://chemagic.com/molecules/jsme.htm http://chemagic.com/molecules/jsme.htm It’s stripped down to absolute bare bones. You have to write separate JavaScript to make JSmol and JSME talk to each other, but the JSME and JSmol functions are there to do that - Jmol functions that were not in place when Jmol first started using JME. Back then I was using a clumsy Jmol load-data approach. Jmol 2015 vs Jmol 2008: Thanks in large part to Bob, it’s come a long way. Otis On Jun 17, 2015, at 4:50 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: OK. I have found the source of my issue, but not the solution yet. Please note the jsmoljsmetest2 file in the distribution. If you edit the file to expand the width to 400, you see the FG button. But if you try to use this applet, none of the vertical buttons work, nor does the FG. Since I was using that as my coding pattern, I reproduced the problem. Now to look at it in more detail tomorrow. On Jun 17, 2015, at 3:58 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Phil, Nah, Bob just likes squares! The JSME applet needs to be 400X300 to see all the buttons. The 300X300 applet just cuts off the buttons after cyclooctane. You could definitely teak the old JME FG button. Again this goes back to JME Java applet. In fact, it was not a button. It was a JavaScript drop down menu that could be modified by some type of cookie structure that remembered your drop entries. This is where I got the idea of using Local Storage to store JME structures. Users can store 50 JME structures in our application page that I linked to earlier. Otis On Jun 17, 2015, at 3:33 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: If you look at some of Bob’s examples, you will find that they are biasing some of the buttons, including FG. I vaguely recall that there was a way to turn them on and off. On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users 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 mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip
Re: [Jmol-users] JSME Qestion
And that is specific to Safari. Works in Firefox. On the other hand, Chrome has issues throwing error messages. On Jun 17, 2015, at 9:31 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Bob is doing something on those pages that is way over my head! The hidden FG button actually throws a JS error when you expose it and click it. The way over my head part comes via: js/JSmolJME.js I can see that he’s integrating JSmol with JSME, but I get lost real fast if I try to get down to specifics in the .js file. As usual, Bob’s approach is elegant. It allows very simple communication between JSmol (multiple applets) and a single JSME applet with this code: Jmol.show2d(jmol, false) and Jmol.show2d(jmol, true) It may be that he is using 300X300 to hide the FG button because of something js/JSmolJME.js is doing that interferes with the button. I vaguely recall (years ago) some warnings from Bob about this implementation of Jmol with JME. The following JSME template would offer you an alternate approach: jsmol/jsme/JSME.html Alternatively, use http://chemagic.com/molecules/jsme.htm http://chemagic.com/molecules/jsme.htm It’s stripped down to absolute bare bones. You have to write separate JavaScript to make JSmol and JSME talk to each other, but the JSME and JSmol functions are there to do that - Jmol functions that were not in place when Jmol first started using JME. Back then I was using a clumsy Jmol load-data approach. Jmol 2015 vs Jmol 2008: Thanks in large part to Bob, it’s come a long way. Otis On Jun 17, 2015, at 4:50 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: OK. I have found the source of my issue, but not the solution yet. Please note the jsmoljsmetest2 file in the distribution. If you edit the file to expand the width to 400, you see the FG button. But if you try to use this applet, none of the vertical buttons work, nor does the FG. Since I was using that as my coding pattern, I reproduced the problem. Now to look at it in more detail tomorrow. On Jun 17, 2015, at 3:58 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Phil, Nah, Bob just likes squares! The JSME applet needs to be 400X300 to see all the buttons. The 300X300 applet just cuts off the buttons after cyclooctane. You could definitely teak the old JME FG button. Again this goes back to JME Java applet. In fact, it was not a button. It was a JavaScript drop down menu that could be modified by some type of cookie structure that remembered your drop entries. This is where I got the idea of using Local Storage to store JME structures. Users can store 50 JME structures in our application page that I linked to earlier. Otis On Jun 17, 2015, at 3:33 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: If you look at some of Bob’s examples, you will find that they are biasing some of the buttons, including FG. I vaguely recall that there was a way to turn them on and off. On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users 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 mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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
[Jmol-users] JSME Qestion
I am working with Jmol and Jsme. I cannot find some information about jsme and wonder if someone has a link. I see the files in the jmol distribution and have jsme running on several pages. However, in most of Bob’s examples he does not show the FG button. I want that and have it displayed. But I apparently do not have it set to be active. Is this specified in the options, and if so, how? Any help? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSME Qestion
OK. I have found the source of my issue, but not the solution yet. Please note the jsmoljsmetest2 file in the distribution. If you edit the file to expand the width to 400, you see the FG button. But if you try to use this applet, none of the vertical buttons work, nor does the FG. Since I was using that as my coding pattern, I reproduced the problem. Now to look at it in more detail tomorrow. On Jun 17, 2015, at 3:58 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Nah, Bob just likes squares! The JSME applet needs to be 400X300 to see all the buttons. The 300X300 applet just cuts off the buttons after cyclooctane. You could definitely teak the old JME FG button. Again this goes back to JME Java applet. In fact, it was not a button. It was a JavaScript drop down menu that could be modified by some type of cookie structure that remembered your drop entries. This is where I got the idea of using Local Storage to store JME structures. Users can store 50 JME structures in our application page that I linked to earlier. Otis On Jun 17, 2015, at 3:33 PM, Philip Bays pb...@saintmarys.edu mailto:pb...@saintmarys.edu wrote: If you look at some of Bob’s examples, you will find that they are biasing some of the buttons, including FG. I vaguely recall that there was a way to turn them on and off. On Jun 17, 2015, at 2:21 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: There is no option setting for FG, it should just be there. At least I think that’s the case. You can check my options in the above JSME page. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu mailto:pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol use tops 5,000,000 page views per year
Bob: Your link does not work. File not found error. On Apr 6, 2015, at 8:15 AM, Robert Hanson hans...@stolaf.edu wrote: [reposting] FYI http://chemapps.stolaf.edu/jmol/img/JSmol-stats-2014-03-31_2015-04-01.png http://chemapps.stolaf.edu/jmol/img/JSmol-stats-2014-03-31_2015-04-01.png From April 1, 2014 to Mar 31, 2015, the Google Analytics tag in the JSmol distribution has recorded 5,666,193 page views and 2,291,928 sessions. There is close to a doubling of use since this time last year (87% increase in page views and 78% increase in session count comparing March of 2015 vs March of 2014), but some of that is probably attributable to a higher rate of conversion to JavaScript from Java last year than this year. I wish I had time to dig deeper into this, but for now that's all I have. Just thought this list might be interested. Feel free to post that image or use it in any way you wish. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] reset lighting
I note today that with the 12.09 release and 12.16 release, I am not getting
structures from NCI. I think the former worked earlier. Is this a Jmol or NCI
issue?
On Dec 16, 2014, at 9:55 PM, Robert Hanson hans...@stolaf.edu wrote:
See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2014.12.16.zip
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2014.12.16.zip
JmolVersion=14.3.11_2014.12.15
new feature: reset LIGHTING
public void resetLighting() {
vwr.setIntProperty(ambientPercent, 45);
vwr.setIntProperty(celShadingPower, 10);
vwr.setIntProperty(diffusePercent, 84);
vwr.setIntProperty(phongExponent, 64);
vwr.setIntProperty(specularExponent, 6); // log2 of phongExponent
vwr.setIntProperty(specularPercent, 22);
vwr.setIntProperty(specularPower, 40);
vwr.setIntProperty(zDepth, 0);
vwr.setIntProperty(zShadePower, 3);
vwr.setIntProperty(zSlab, 50);
vwr.setBooleanProperty(specular,true);
vwr.setBooleanProperty(celShading, false);
vwr.setBooleanProperty(zshade, false);
}
On Tue, Dec 9, 2014 at 8:33 PM, Eric Martz ema...@microbio.umass.edu
mailto:ema...@microbio.umass.edu wrote:
It seems to me that (low priority) a 'reset lighting' would be useful.
It would set all lighting parameters to their defaults.
Eric
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http://www.stolaf.edu/people/hansonr http://www.stolaf.edu/people/hansonr
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Re: [Jmol-users] Safari reloading JSmol over and over
. Certainly that must run far deeper than Jmol. Not much we can do about that. A bad week for Apple, perhaps. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users Eric Martz mailto:ema...@microbio.umass.edu September 29, 2014 at 6:20 PM With JSmol (either at Proteopedia JSmol 14.3.5_2014.08.09, or FirstGlance JSmol 14.3.7_2014.09.20), using Safari 7.1 in OS 10.9.5, fairly often the browser window suddenly goes blank white and a gray bar appears at the top saying A problem occurred with this webpage so it was reloaded A small window appears with OK to send a report to Apple. The page is reloaded and appears fine until the next problem a few minutes later. I have seen this dozens of times in recent weeks with FirstGlance and once now with Proteopedia. I don't think I saw it with the previous version of Safari, 7.0. I have not seen this (yet?) in Firefox or Chrome. Is anyone else seeing this? -Eric -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com mailto:o...@chemagic.com http://chemagic.com http://chemagic.com/ -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Local File Access
On Sep 4, 2014, at 6:47 AM, Robert Hanson hans...@stolaf.edu wrote: What was the final word on the 6/28 8/25 issue? The situation for me is this. I am using OSX 10.9.4 with the latest versions of Safari (7.0.6) and Chrome. As we have seen elsewhere, Chrome will not launch test2 from the desktop in either edition of jmolJS. I have not tried Otis’ workaround. Safari (and related browsers) is a different issue. test2.htm will launch fine locally in the 6/28 version, but will not in any subsequent version, including 8/25. Disabling local file restrictions in the developer menu allows it to run. I have copied the alert I get when it fails and will send it to you off-line as an attachment. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Running JSmol Locally on Mac Chrome
Angel and Otis: I would only comment that you need not go to the preferences in Safari as per Otis’ instructions. Once you have the browser open, simply go to the Develop menu and set turn the local file restrictions off. The launch you html file. Phil On Sep 4, 2014, at 2:47 PM, Angel Herráez angel.herr...@uah.es wrote: Otis, I've added your info in http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Chrome.2FMac Please check if it's ok Thanks -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Local File Access
Thanks. That solves the issue for Safari and newer jmol versions. However, I
still do not understand the problem in this sense: the release of 6/28 works
fine without having to make the file restrictions change, but the 8/25 version
does not. Same version of OS and Safari. Has something changed in jmol in the
intervening time that causes that, or is it something else?
In addition, I have moved copies of booth versions to my website. In this
case, accessing from home,6/28/test2 works, but I get a permissions error for
8/25. Still working to see what is different.
The links I am trying to access via the web are:
www.saintmarys.edu/~pbays/jmol0628/jsmol/test2.htm
www.saintmarys.edu/~pbays/jmol0825/jsmol/test2.htm
Phil
On Sep 3, 2014, at 9:07 AM, Otis Rothenberger osrot...@chemagic.com wrote:
Hi Phil,
In Safari Preferences, go to Advanced and check Show Develop menu in menu
bar.
In the resulting Develop toolbar drop-down, there is a Disable Local File
Restrictions check toggle item. Select this if it is not checked.
On the Chrome (37.0.2062.94 on Mavericks) issue that I wrote about yesterday,
there are two ways to avoid the terminal directly if you have some
familiarity with the Apple Automator.
Open Automator. Choose Application. Select Utilities. Drag Run AppleScript to
the Automator window. Copy/paste one of the following scripts into the
resulting text window. Save the app to desktop. Double click OR Drag/Drop htm
file depending on approach you selected.
FOR DOUBLE CLICKABLE AUTOMATOR APP
on run {input, parameters}
do shell script open -a /Applications/Google\\ Chrome.app --args
--allow-file-access-from-files
end run
FOR DRAG/DROP AUTOMATOR APP
on run {input, parameters}
tell application Finder
set filename to input as text
set filepath to POSIX path of filename
end tell
do shell script open /Applications/Google\\ Chrome.app --args
--allow-file-access-from-files file:/// filepath
end run
Again, it is most important that Chrome is closed when you do this. If Chrome
is open, neither script will work properly. Late night last night. What a
weird scripting language! I have not dealt with AppleScript since my first
Macintosh LONG ago.
Otis
On Mon, Sep 1, 2014 at 10:07 AM, Philip Bays pb...@saintmarys.edu wrote:
I think I was the one who raised this issue (#3). Perhaps I was not clear,
or perhaps I am dense.
I am not talking about the Java applet. I am trying to launch test2 in
Safari with JSmol by double clicking it. The applet tries to load but then
fails. I see the opportunity in Safari...Preferences…Security to white list
various plug-ins: things like Flash, Adobe, Quicktime, etc. I believe this
is where Java also appears if it is on the system. But I see no preference
for JSmol except to “enable javascript”.
What am I missing?
Phil
On Wed, Aug 20, 2014 at 1:25 PM, Robert Hanson hans...@stolaf.edu wrote:
Issue #3 JSmol/Java applet will not run in Safari for local pages
(Mavericks OS 10.9.4)
Solution: Open a local page accessing the JSmol/Java and then using
Safari...Preferences...Security, enable local file reading
See http://sourceforge.net/p/jmol/mailman/message/31570102/
Outcome: Reloading the page, you should get the standard alerts about running
Java applets, then the Jmol applet will start.
Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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Re: [Jmol-users] Local File Access
Yes. I got the permission issue resolved.
J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN
Sent from my iPad
On Sep 3, 2014, at 11:55 AM, Otis Rothenberger osrot...@chemagic.com
wrote:
Phil,
I don't know about the local issue, but both URL's open for me in Chrome and
Safari (Version 7.0.6 (9537.78.2)) on Mavericks: OS X 10.9.4 (13E28)
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University Normal, IL 61790-4160
http://chemagic.org
From: Philip Bays pb...@saintmarys.edu
Sent: Wednesday, September 03, 2014 10:17 AM
To: Jmol Jmol jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Local File Access
Thanks. That solves the issue for Safari and newer jmol versions. However,
I still do not understand the problem in this sense: the release of 6/28
works fine without having to make the file restrictions change, but the 8/25
version does not. Same version of OS and Safari. Has something changed in
jmol in the intervening time that causes that, or is it something else?
In addition, I have moved copies of booth versions to my website. In this
case, accessing from home,6/28/test2 works, but I get a permissions error for
8/25. Still working to see what is different.
The links I am trying to access via the web are:
www.saintmarys.edu/~pbays/jmol0628/jsmol/test2.htm
www.saintmarys.edu/~pbays/jmol0825/jsmol/test2.htm
Phil
On Sep 3, 2014, at 9:07 AM, Otis Rothenberger osrot...@chemagic.com wrote:
?Hi Phil,
?In Safari Preferences, go to Advanced and check Show Develop menu in menu
bar.
In the resulting Develop toolbar drop-down, there is a Disable Local File
Restrictions check toggle item. Select this if it is not checked.
On the Chrome (37.0.2062.94 on Mavericks) issue that I wrote about
yesterday, there are two ways to avoid the terminal directly if you have
some familiarity with the Apple Automator.
Open Automator. Choose Application. Select Utilities. Drag Run AppleScript
to the Automator window. Copy/paste one of the following scripts into the
resulting text window. Save the app to desktop. Double click OR Drag/Drop
htm file depending on approach you selected.
FOR DOUBLE CLICKABLE AUTOMATOR APP
on run {input, parameters}
do shell script open -a /Applications/Google\\ Chrome.app --args
--allow-file-access-from-files
end run
FOR DRAG/DROP AUTOMATOR APP
on run {input, parameters}
tell application Finder
set filename to input as text
set filepath to POSIX path of filename
end tell
do shell script open /Applications/Google\\ Chrome.app --args
--allow-file-access-from-files file:/// filepath
end run
Again, it is most important that Chrome is closed when you do this. If
Chrome is open, neither script will work properly. Late night last night.
What a weird scripting language! I have not dealt with AppleScript since my
first Macintosh LONG ago.
Otis
On Mon, Sep 1, 2014 at 10:07 AM, Philip Bays pb...@saintmarys.edu wrote:
I think I was the one who raised this issue (#3). Perhaps I was not clear,
or perhaps I am dense.
I am not talking about the Java applet. I am trying to launch test2 in
Safari with JSmol by double clicking it. The applet tries to load but then
fails. I see the opportunity in Safari...Preferences…Security to white
list various plug-ins: things like Flash, Adobe, Quicktime, etc. I
believe this is where Java also appears if it is on the system. But I see
no preference for JSmol except to “enable javascript”.
What am I missing?
Phil
On Wed, Aug 20, 2014 at 1:25 PM, Robert Hanson hans...@stolaf.edu wrote:
Issue #3 JSmol/Java applet will not run in Safari for local pages
(Mavericks OS 10.9.4)
Solution: Open a local page accessing the JSmol/Java and then using
Safari...Preferences...Security, enable local file reading
See http://sourceforge.net/p/jmol/mailman/message/31570102/
Outcome: Reloading the page, you should get the standard alerts about
running Java applets, then the Jmol applet will start.
Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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Philip Bays
Emeritus
[Jmol-users] Local File Access
I think I was the one who raised this issue (#3). Perhaps I was not clear, or perhaps I am dense. I am not talking about the Java applet. I am trying to launch test2 in Safari with JSmol by double clicking it. The applet tries to load but then fails. I see the opportunity in Safari...Preferences…Security to white list various plug-ins: things like Flash, Adobe, Quicktime, etc. I believe this is where Java also appears if it is on the system. But I see no preference for JSmol except to “enable javascript”. What am I missing? Phil On Wed, Aug 20, 2014 at 1:25 PM, Robert Hanson hans...@stolaf.edu wrote: Issue #3 JSmol/Java applet will not run in Safari for local pages (Mavericks OS 10.9.4) Solution: Open a local page accessing the JSmol/Java and then using Safari...Preferences...Security, enable local file reading See http://sourceforge.net/p/jmol/mailman/message/31570102/ Outcome: Reloading the page, you should get the standard alerts about running Java applets, then the Jmol applet will start. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Test2
I am using the latest version of Safari (7.0.6). Test2 runs locally using Firefox and SeaMonkey, but fails with Chrome, Chromium, Opera, and Safari. I have removed Java from my machine, so I cannot test with Jmol.jar. I will play a little more to see if it works via web access, though someone else may be able to answer that faster than I. Otis?. Phil On Aug 19, 2014, at 8:57 AM, Robert Hanson hans...@stolaf.edu wrote: Have you recently updated MacOS? It could be that Macs are now blocking local file access by AJAX . What browser are you using? a) try another browser b) note that this is only a local-file problem c) look for a way to enable local file access in your browser, for example, on Windows: see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Current_limitations_of_JSmol Q: Can you double-click on the Jmol.jar application and see it run? Or do you get a security error there as well? Bob On Mon, Aug 18, 2014 at 9:25 PM, Philip Bays pb...@saintmarys.edu wrote: When I try to launch locally by double clicking test2, I get the following error in the applet load process. Error: NETWORK_ERR: XMLHttpRequest Exception 101 Mac OS 10.9.4, jmol release …8.17b Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ 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, Department 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 -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Test2
I get the same error on the ….8.03 release. So perhaps something happened between 6.29 and 8.03. I have been in and out of town so have not been testing each release. Phil On Aug 19, 2014, at 10:43 AM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, I get this error message with Chrome. Safari Loads test2 OK, BUT I'm using Jmol 14.2.2_2014_06.29. Updating Jmol on one of my servers has become a very slow process, so I have to admit that I'm not keeping up on some of the latest versions. I'll check the latest version, but I thought the 14.2.2_2014_06.29 double click information might be useful. OSX 10.9.4 and Safari 7.0.6 (9537.78.2). More thoughts on running locally in a subsequent post... Otis Philip Bays August 19, 2014 at 10:11 AM I am using the latest version of Safari (7.0.6). Test2 runs locally using Firefox and SeaMonkey, but fails with Chrome, Chromium, Opera, and Safari. I have removed Java from my machine, so I cannot test with Jmol.jar. I will play a little more to see if it works via web access, though someone else may be able to answer that faster than I. Otis?. Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Robert Hanson August 19, 2014 at 8:57 AM Have you recently updated MacOS? It could be that Macs are now blocking local file access by AJAX . What browser are you using? a) try another browser b) note that this is only a local-file problem c) look for a way to enable local file access in your browser, for example, on Windows: see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Current_limitations_of_JSmol Q: Can you double-click on the Jmol.jar application and see it run? Or do you get a security error there as well? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays August 18, 2014 at 10:25 PM When I try to launch locally by double clicking test2, I get the following error in the applet load process. Error: NETWORK_ERR: XMLHttpRequest Exception 101 Mac OS 10.9.4, jmol release …8.17b Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Test2
When I try to launch locally by double clicking test2, I get the following error in the applet load process. Error: NETWORK_ERR: XMLHttpRequest Exception 101 Mac OS 10.9.4, jmol release …8.17b Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Survey Question re Run Jmol Locally
On Jul 28, 2014, at 10:55 AM, Otis Rothenberger osrot...@chemagic.com wrote: I'm putting together a presentation, and I have a question about an issue the comes up from time to time on this list. Specifically, there are questions related to running Jmol locally. Since my main interest is small molecules, I have moved totally to JSmol, but I'm interested in general answers to this multiple choice question: Why do you want to run Jmol locally? A) I have local data files that I need to load, BUT I have nothing against requiring user Internet connectivity. Primarily when I am writing code. It is easier to launch them locally than to move them to the campus server for testing. B) I have local data files that I need to load, AND I want to free my user from Internet connectivity. No. C) I want my Jmol pages to act like double clickable applications that do not require a server, BUT I have nothing against requiring user Internet connectivity. This is much like A — testing purposes only. D) I want my Jmol pages to act like double clickable applications that do not require a server, AND I want the Internet totally out of the picture. No E) Other Thanks in advance for any replies... Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071iu=/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 -- Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.1.15 released
Bob: it appears to me that the PubChem links are broken in test2 in today’s
new version.
On May 7, 2014, at 3:05 AM, Robert Hanson hans...@stolaf.edu wrote:
___JmolVersion=14.1.15
JmolVersion=14.1.15_2014.05.06
bug fix: CIF reader not filtering atoms by element
bug fix: structure command may not properly remove residues from structures
(F. Reichsman)
bug fix: FRAME n setting frame to n - 1. (F. Reichsman)
bug fix: unitcell {0 0 0}; in state leaves unit cell on
bug fix: modulation of anisotropic parameters broken
bug fix: Jana2006 reader does not accept filter MODAVE
bug fix: msCIF with filter MODAXES=X broken
JmolVersion=14.1.15_2014.05.04
new feature: reset PRINT
-- clears the output buffer (scriptWait, scriptEcho, evaluateVar
bug fix: color property x does not pass script check, so not allowed in web
command box
bug fix: echo @{xxx} may fail
but fix: print @b fails for referred variable an array
bug fix: xxx.format(%8.-3p) does not work
bug fix: [array].format(%8.3p) does not work
bug fix: PDB Reader skips first ANISOU record
bug fix: SFTP not supported
bug fix: fix for measurements not updating with modulation x.x
new feature: replace()
-- no arguments means clean whitespace to single space and trim
new feature: replace(x, y, TRUE)
-- all occurrences of characters of x will be replaced with y.
new feature: mCIF reader
-- Bilbao Crystallographic Server format
-- magnetic extension to CIF reader
new feature: set vectorsCentered
-- centers vibration vector on atom
-- vector is never animated
-- useful for magnetic/spin properties
new feature: select xyz 1.0
-- xyz, fxyz, fuxyz, uxyz, vxyz
-- uses length
--
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
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Saint Mary's College
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pb...@saintmarys.edu
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Re: [Jmol-users] Jmol 14.1.14 released
But should it ultimately load the structure? It does not. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad On Apr 30, 2014, at 6:30 PM, Robert Hanson hans...@stolaf.edu wrote: On Tue, Apr 29, 2014 at 4:01 PM, Philip Bays pb...@saintmarys.edu wrote: I am now testing from my local network server and still get the errors for the asynchronous file transfer and subsequent unknown file type error in Safari. I have captured an error alert and can send it to you separately if you wish. But it will be delayed through the list. That´s not an error, that´s a feature. It is correct to do that with Safari. You are tapping into the St. Olaf page, and you need to know that. Phil On Apr 29, 2014, at 10:58 AM, Robert Hanson hans...@stolaf.edu wrote: You should always see the alert in Safari, I think, if you are loading those files from a LOCAL installation of JSmol. Or do you see that as well at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm ? On Tue, Apr 29, 2014 at 9:54 AM, Robert Hanson hans...@stolaf.edu wrote: Yes - thanks - just noticed that myself and have removed that release (again!). Shoot! I accidentally deleted the url address for NCI in the list of known databases. I might be able to still get this done today; probably tomorrow. On Tue, Apr 29, 2014 at 8:53 AM, Philip Bays pb...@saintmarys.edu wrote: Observations on this release: Mac OSX 10.9.2, Safari 7.0.3, Firefox 28.0 (Have not looked at 29.0 released this morning.) Safari: NCI links give file format error Both cyclohexane animations, mo homo SQUARED, load data/1hxw.png (image), load data/square_planar.spartan , and load data/water.xyz.gz These are preceded by the asynchronous file alert. Firefox: NCI links do not work here either All others seem to work well On Apr 28, 2014, at 11:56 PM, Robert Hanson hans...@stolaf.edu wrote: OK, this is re-released. Please test. I would like to release it as 14.0.14 soon. I did not check the Safari synchronous file transfer business. http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled
Re: [Jmol-users] Jmol 14.1.14 released
Observations on this release: Mac OSX 10.9.2, Safari 7.0.3, Firefox 28.0 (Have not looked at 29.0 released this morning.) Safari: NCI links give file format error Both cyclohexane animations, mo homo SQUARED, load data/1hxw.png (image), load data/square_planar.spartan , and load data/water.xyz.gz These are preceded by the asynchronous file alert. Firefox: NCI links do not work here either All others seem to work well On Apr 28, 2014, at 11:56 PM, Robert Hanson hans...@stolaf.edu wrote: OK, this is re-released. Please test. I would like to release it as 14.0.14 soon. I did not check the Safari synchronous file transfer business. http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.1.14 released
Bob: I do not see those issues on the link you provided, but I note that is using an earlier version of JSmol. This morning I was doing a local launch of test2. I downloaded the fix (from the airport) and that works fine for Firefox (now 29.0) and the NCI links now work in both Safari and Firefox. I am now testing from my local network server and still get the errors for the asynchronous file transfer and subsequent unknown file type error in Safari. I have captured an error alert and can send it to you separately if you wish. But it will be delayed through the list. Phil On Apr 29, 2014, at 10:58 AM, Robert Hanson hans...@stolaf.edu wrote: You should always see the alert in Safari, I think, if you are loading those files from a LOCAL installation of JSmol. Or do you see that as well at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm ? On Tue, Apr 29, 2014 at 9:54 AM, Robert Hanson hans...@stolaf.edu wrote: Yes - thanks - just noticed that myself and have removed that release (again!). Shoot! I accidentally deleted the url address for NCI in the list of known databases. I might be able to still get this done today; probably tomorrow. On Tue, Apr 29, 2014 at 8:53 AM, Philip Bays pb...@saintmarys.edu wrote: Observations on this release: Mac OSX 10.9.2, Safari 7.0.3, Firefox 28.0 (Have not looked at 29.0 released this morning.) Safari: NCI links give file format error Both cyclohexane animations, mo homo SQUARED, load data/1hxw.png (image), load data/square_planar.spartan , and load data/water.xyz.gz These are preceded by the asynchronous file alert. Firefox: NCI links do not work here either All others seem to work well On Apr 28, 2014, at 11:56 PM, Robert Hanson hans...@stolaf.edu wrote: OK, this is re-released. Please test. I would like to release it as 14.0.14 soon. I did not check the Safari synchronous file transfer business. http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu
Re: [Jmol-users] Jmol 14.1.14 released
isosurface range broken (Lucy Cusinato) bug fix: script compiler error: x.x*x.x requiring space: x.x * x.x (Alexander Rose) bug fix: lost H atoms of PDB-designated water bug fix: mouse rotation can cause loss of model bug fix: Jana2006 reader not reading groups correctly (still work TODO) bug fix: functions called in script defined by script called by this script must be lower case. bug fix: clickable atoms may not be considered visible for hover bug fix: select color=red should be color=red to allow for variable after color= code: upgrade of Apache Commons CLI (Command Line Interface) to 1.2 from 1.0 code: T4 generalized as extending T3, allowing 4D mesh reading. code: implementation of Andrew Hanson's 3D Ball Roll mouse algorithm -- no significant practical improvement, but nicer mathematics -- a bit more involved, but this is once per mouse move. Doesn't matter. -- 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 -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ 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 -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Test2.htm CONFIRMATION
I see the same issue on my iMac running 10.9.2, Safari 7.0.3 or Firefox 27.0.1 and JSmol ….4.10 running locally or over the network.Have not tried other browsers. It’s as if something is going on in the background. For me the manipulation of the structure is quite jerky, freezes, then is jerky, and finally disappears. I am having a different issue with Safari as well. I run a local network at home. All browsers work fine using [network name].local/~[account name]/ except for Safari. I get a “cannot connect to server error”. I am required to use the ip address approach as the URL. This arose with OSX 9.2. All other browsers are fine using the local network name, and I can access it with a PC or my iPad using the network name. On Apr 13, 2014, at 9:56 PM, Otis Rothenberger osrot...@chemagic.com wrote: I'm running 14.1.12_2014.3.21 and it's OK Mac Safari, Chrome, and Firefox. This is OS 10.9.2 Mavericks. I've been keeping a close eye on iPad, and this version of JSmol runs really well on iPad Air and iPad 2. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 13, 2014, at 8:05 PM, Eric Martz ema...@microbio.umass.edu wrote: From the online URL http://chemapps.stolaf.edu/jmol/jsmol/test2.htm In addition to Firefox, I also see the disappearance with slight rotation in Safari and Chrome (again, on Mac OS 10.9.1 Mavericks). Those browsers will not run test2.htm from local files (network error is reported), so I can only test them from the server. Eric -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Local
Bob: Not sure what you are asking. Do you want to set up a local server on the back that is accessed from that mac or anyone on the local network? Phil On Feb 17, 2014, at 5:22 PM, Robert Hanson hans...@stolaf.edu wrote: Can some one summarize for me what the instructions are for getting Safari or Firefox on a Mac reading local files? http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Browser_considerations_for_local_file_access_.28JSmol.29 needs completion. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/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 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Local
Try this: https://discussions.apple.com/docs/DOC-3083 On Feb 17, 2014, at 5:22 PM, Robert Hanson hans...@stolaf.edu wrote: Can some one summarize for me what the instructions are for getting Safari or Firefox on a Mac reading local files? http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Browser_considerations_for_local_file_access_.28JSmol.29 needs completion. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/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 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol broken on Mac Safari back button
Two comments: I see the difference that you do except that the applet works fine in Safari when I come back to the page. That is, I do not see a broken applet, it is just not refreshed. (Mac OS 10.9.1) I thought that the Safari behavior was the normal for the back button. I hate it when I am reading and article, click a link to another page, and then when I come back to the original, the page reloads and I have to search for where I was. On Jan 30, 2014, at 3:32 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Is there a way to force loading JSmol when loading/rendering a page? JQuery should be able to do this. This is why we might need to start with a fresh loaded JSmol: When clicking a ‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders non-operational. On Firefox 26.0, same Mac, it works Ok. To test (better than the previous explanation): 1. go to http://proteopedia.org/w/3rec 2. verify if JSmol is working, ie mouse rotates model, zooms, etc. 3. go to another page by clicking a link, like ‘About Proteopedia’ in the bottom mid section 4. click on the browser’s ‘back to previous page’ button to display again the page 3rec 5. verify if JSmol is working, ie mouse rotates model, zooms, etc. The main difference is that Firefox actually reloads JSmol on page back. Safari simply tries to work with what’s available, rendering a broken applet. Jaim -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/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 -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question: How is Info intended to be used?
Did I send you the article about the moss in Northern Canada?
On Jan 28, 2014, at 12:54 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Chuck and Angle,
I think I'm in basic agreement with Angle. I look at this as a scratch pad
per the following JS function:
function scratchPad(header, content) {
header = (!header) ? : header;
content = (!content) ? : content;
if (header == content == ) { Jmol.setInfo(jmolApplet0,
content, false); return null; }
jmolApplet0._infoHeader = header;
Jmol.setInfo(jmolApplet0, content, true);
return null;
}
I write to it as needed using the above - e.g. display pdb header or pdb
content. Storage of a given content/header pair would have to be in some type
of global variable. Long term storage would have to be server side, although
for small bits of information I've used cookies.
Only because I found out the hard way, 10 cholesterol molfile cookies will
break the cookie jar. I did not realize what a pain a broken cookie jar could
be for the user!
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 28, 2014, at 12:16 PM, Angel Herráez angel.herr...@uah.es wrote:
Hi, Chuck
this is how I see it (but I may not be right)
There is not your variable and Jmol's variable. The single Info
variable belongs to the Jmol Object once you invoke getApplet.
What you do is initialize some values/parameters that are part of the
Info variable (which is more properly a Javascript object with many
name/value pairs). Jmol has defaults for all of them and will change
just the ones you state.
So I am not suprised at all that Jmol writes in the Info variable.
In summary
1. a single Info variable
2. has defaults for all its properties or parts or parameters
3. the defaults are overwritten by your data
4. Jmol will be using all the time the single Info variable
Ah, of course if you have two Jmols they may use separate Infos,
that's why you need to assign Info in the Jmol.getApplet() call.
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Notre Dame, IN 46556
pb...@saintmarys.edu
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Re: [Jmol-users] Jmol 14.0.6 released
Bob: As I recall, several years ago you wrote the java applet to compare -smiles strings. The issue for me before that came along was that drawing a structure in JME could result in more than one “correct” smiles string, depending on how it was drawn, particularly in regards to stereochemistry. (Sorry for that sentence!!) I do not know if that is still an issue or not, but would like to know. On Jan 21, 2014, at 3:06 PM, Robert Hanson hans...@stolaf.edu wrote: Why not just use Jmol's SMILES and SMARTS matching? Certainly there is no need to go get an InChIkey for that, right? Just match the JME or Jmol structure with a representative SMILES string or with each other's SMILES string. Why the interest in InChI or InChIKey? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Will unsigned applet be blocked soon?
Henry: I am using the same OS but downloaded last evening’s release of jmol (14.0.3). I test using my sites local network server on an iMac, which should behave like an outside server. My test was to access test2.htm in the jsmol directory. It runs fine with HTML5 and the signed applet. But does not do so when simply launched as a file. I did have to change permissions on the jmol directory. In my java console (security tabmanage certificates, I see the Integrated Graphics certificate as trusted (That has been true since originally specified several iterations of jmol ago. However, when I try your link, I get the same results as you do. On Dec 30, 2013, at 8:25 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: On 29 Dec 2013, at 20:00, Robert Hanson hans...@stolaf.edu wrote: I'm guessing it will be January 14: https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias http://www.oracle.com/technetwork/topics/security/alerts-086861.html As I understand it, all applets must be updated. signed or not -- all must be signed, and local file reading now requires the JNLP files as well in the directory of the JAR files. (Note that these JNLP files allow the applet to be started outside a browser as well.) Using Jmol 14.0.2 (14th December) uploaded to a server, I can indeed no longer get the applet to load (OS X Mavericks/Safari or Firefox). Application blocked by security settings”. It also (falsely) tells me that the Java security settings have prevented this application from running. You may change this behaviour in the Java control panel”. Well, I could not. This did not happen with eg 13.3.9. There are four JNLP files in this build of Jmol in the Java directory (including eg JmolApplet.jnlp and JmolAppletSigned.jnlp), but their presence has not prevented the above message. Am struggling slightly. Could it be that our Apache server has no MIMEtype defined for JNLP? Or that OS X Mavericks Java is broken in this regard? Or that some other configuration which I have omitted is needed? The relevant page is http://www.ch.ic.ac.uk/rzepa/WEO/ja061400a/?JAVA (which is an ancient page from ~2007 which I thought I might try to rescue). -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] another Mac surprise
I would think that they both rely on the java console. I wonder what is going on with that? On Mon, Dec 30, 2013 at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote: It appears that Safari has a very strange feature -- at least on my machine, everything works fine using http, but with file://, if I download Jmol, open the zip file, extract the jsmol directory, and start simple2.htm, and immediately clicking on the Signed link to get the signed version, the applet fails to load. However, if I first open the applet in Firefox, then Safari will open it. If Safari has opened the file, and I change the directory name, then the next time I try this, Safari will not start the applet. However, if I then open that local page in Firefox and then try again in Safari, all is good. What could possibly be going on? I don't know. But the fact that this is a new problem suggested to me that it's something recent. I remembered that recently I changed Safari settings to using the applet tag instead of object. Well, guess what? When I switch back to using the object tag, everything works normally. No directory problems; no load issues. Go figure. For whatever reason, it looks like we cannot use the applet tag in Safari. I'm sure I had a reason for switching to that, but I can't remember that. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/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 Saint Mary's College Notre Dame, IN 46556 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] another Mac surprise
I was having a problem this afternoon with some debugging. I typically disable cache in the developer menu, and use private browsing. nevertheless, I would make a change in my code and the change was not reflected in the browser reload. In fact, I had a line that called on a nonexistent function. I deleted the line, but it kept appearing in the error messages. Somehow, Safari was caching when it was not supposed to be. I did not have time to explore it further, but will tomorrow and see if I can reproduce it. I did not try loading with Firefox and then again with Safari. On Dec 30, 2013, at 7:48 PM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, Exactly. That's what I'm thinking. Safari won't cache it, but it will pull it from cache. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Dec 30, 2013, at 7:28 PM, J. Philip Bays pb...@saintmarys.edu wrote: I would think that they both rely on the java console. I wonder what is going on with that? On Mon, Dec 30, 2013 at 4:27 PM, Robert Hanson hans...@stolaf.edu wrote: It appears that Safari has a very strange feature -- at least on my machine, everything works fine using http, but with file://, if I download Jmol, open the zip file, extract the jsmol directory, and start simple2.htm, and immediately clicking on the Signed link to get the signed version, the applet fails to load. However, if I first open the applet in Firefox, then Safari will open it. If Safari has opened the file, and I change the directory name, then the next time I try this, Safari will not start the applet. However, if I then open that local page in Firefox and then try again in Safari, all is good. What could possibly be going on? I don't know. But the fact that this is a new problem suggested to me that it's something recent. I remembered that recently I changed Safari settings to using the applet tag instead of object. Well, guess what? When I switch back to using the object tag, everything works normally. No directory problems; no load issues. Go figure. For whatever reason, it looks like we cannot use the applet tag in Safari. I'm sure I had a reason for switching to that, but I can't remember that. Bob -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] iPad reserved term
One of my tutorials which does not involve jmol and has run for many years on all sorts of computerist and OS's, fails to run correctly on the iPad. I have tested it one early and late models and versions of iOS. I was looking at the code this week to try to figure out why and narrowed the issue down to a declared global array which was not being read. My son and I then tried to figure out why — clearly read on anything but an iPad on which it returns “undefined. On a whim he changed the name of the array and all dependencies; things worked. The array was originally named: orientation[ ]. It appears that the term “orientation” is reserved by iOS for a 90° rotation of the device. Insert an alert using orientation into your javascript and see what happens. Since we are concerned about molecular orientations, this is a warning to not use that term as a variable name in javascript, unless you mean it:-) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol popup menu on an iPad
Bob: That works but the positioning is sometimes barely visible and the menu links do not work at all on an iPad. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad On Dec 27, 2013, at 1:15 PM, Bob Hanson hans...@stolaf.edu wrote: Doesn't clicking on the logo work? Sent from my stupid iPhone On Dec 25, 2013, at 12:31 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: Whilst the JSmol menu on a “normal” computer pops up nicely, there is no “right click” on a tablet. Is it possible to invoke (set up?) in some other way. Please excuse if its a FAQ. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Mavericks Local Server
This is primarily addressed to newer jmol Mac users. For a long time Apple provided a web Sharing option in the Sharing control panel. That disappeared a couple of OSX iterations ago. This allowed you to use the Sites directory in your home account as a local network server. This is handy since it allows you to drag and drop your web pages into the Sites directory during development and serve them from there. If your public server is like ours, uploads can take a long time; this is instantaneous Furthermore, you can test your site with a variety of devices you may have on your local network: my wife’s Windows machine, my iMac (on which the server is located) and MacBook Pro, and my iOS devices, for example. It also by-passes the problem of trying to launch the Java applets from your desktop. That is, it works just like your external public server. It also provides a way to serve your site locally when giving a talk. Most of you longtime Mac users already know all this. But, after having done it a number of years ago when Apple told you how to do it, I went through the process of setting it up under Mavericks where the web serving option is no longer presented. The following document is the best I found for a step-by-step how to: https://discussions.apple.com/docs/DOC-3083 I would add only a couple additional points. If, when you get it all set up, you have permissions errors trying to access the site, check the permissions settings on your home directory and the Sites directory. Everyone must have read access for this to work. The local host name of your new website is: YourMachineName.local. (I have a very complex machine name which is a pain to type in every time I want to access the site.) In the sharing panel, you can change that in the edit option without changing your machine name. a.local works just fine. If you do not want to go to Terminal to turn off and on the apache server, the following link gives you a preference pane for doing so. http://clickontyler.com/web-sharing/ Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final(?) testing: jmol-13.3.9_2013.12.03b
On Dec 4, 2013, at 12:50 AM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.03b.zip -- local installations Get file format errors loading structures from NCI http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- general HTML5 operation Get file format errors loading structures from NCI http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm --- file loading Get file format errors loading structures from NCIe --- image creation This loads the various images of cyclohexane --- command-line entry with immediate script checking feedback and up-down arrow key history navigation I am not a “scripter yet:-( See what you can find! Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/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 -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] progress ... ?
Unfortunately, neither work with Safari. jsmol loads the applet only if the error console is open. Without that, a null pointer is reported. I can send you the message, but I think we have see it before. I can’t get simple2 to do anything. Test2 loads the HTML applet, but now the java applets seem to load, but not display a structure. If it is any consolation, everything works fine with Safari on my new iPad — iOS7. Like Otis, I went to the Apple site. I can find no listing for downloading Safari 7. Perhaps we ought to bail on it for the moment to see what they are doing in Cupertino. I may drop by the Apple store today and ask some questions. Phil On Dec 3, 2013, at 7:10 AM, Robert Hanson hans...@stolaf.edu wrote: Mac testers: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm would be good for this test. Do check out the new command input box in simple2.htm. It's responsive to each character typed and should have a history buffer accessible with the up- and down-arrow keys. Bob On Tue, Dec 3, 2013 at 6:07 AM, Robert Hanson hans...@stolaf.edu wrote: OK, if Safari testers could try that again, I would appreciate it. The error reports will now mean something, as JSmol.min.js and j2s/core/core.z.js are no longer compressed. On Tue, Dec 3, 2013 at 3:35 AM, Greeves, Nick ngree...@liverpool.ac.uk wrote: Bob et al, Using http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and Mac OS. Firefox is fine, Chrome is fine, Safari 7.0 fails to load the applet. But as has been noted elsewhere http://chemapps.stolaf.edu/jmol/jsmol/test2.htm loads slowly but does work and uses the 2nd Dec version of JSmol. I’m not clear what the difference between jsmol.htm and test2.htm is. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.02b.zip http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr Having failed to load http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm in Safari I displayed the Safari error console and this is the result [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 391) (anonymous function) (core.z.js, line 2200) (anonymous function) (core.z.js, line 2193) (anonymous function) (core.z.js, line 2169) instantialize (JSmol.min.js, line 347) (anonymous function) (core.z.js, line 2168) (anonymous function) (core.z.js, line 2218) (anonymous function) (core.z.js, line 902) (anonymous function) (core.z.js, line 891) (anonymous function) (core.z.js, line 882) instantialize (JSmol.min.js, line 347) (anonymous function) (core.z.js, line 878) $fz (GenericApplet.js, line 52) (anonymous function) (GenericApplet.js, line 46) (anonymous function) (core.z.js, line 495) instantialize (JSmol.min.js, line 347) (anonymous function) (core.z.js, line 494) __startAppletJS (JSmol.min.js, line 260) __nextExecution (JSmol.min.js, line 257) I then reloaded the page with the console active and the page loads fine! Philip has noted similar behaviour, I think. Best regards Nick -- Nick Greevesvia OS X Mail Director of Teaching and Learning Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories Crown Street, LIVERPOOL L69 7ZD U.K. Email address:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame
Re: [Jmol-users] progress ... ?
Here it is. [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (favicon.ico, line 0) [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 10826) (anonymous function) (core.z.js, line 46479) (anonymous function) (core.z.js, line 46391) (anonymous function) (core.z.js, line 46117) instantialize (JSmol.min.js, line 15481) (anonymous function) (core.z.js, line 46099) (anonymous function) (core.z.js, line 46786) (anonymous function) (core.z.js, line 20424) (anonymous function) (core.z.js, line 20264) (anonymous function) (core.z.js, line 20143) instantialize (JSmol.min.js, line 15491) (anonymous function) (core.z.js, line 20079) $fz (GenericApplet.js, line 52) (anonymous function) (GenericApplet.js, line 46) (anonymous function) (core.z.js, line 13308) instantialize (JSmol.min.js, line 15491) (anonymous function) (core.z.js, line 13293) __startAppletJS (JSmol.min.js, line 11982) __nextExecution (JSmol.min.js, line 11911) On Dec 3, 2013, at 8:39 AM, Robert Hanson hans...@stolaf.edu wrote: Do clear your cache and try again on the site -- I would very much like to see the error report. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] progress ... ?
Boolean
function () {
Clazz_instantialize (this, arguments);
}
Boolean.FALSE
Object
valueOf: function () {return b;}
__proto__: Object
Boolean.TRUE
Object
valueOf: function () {return b;}
__proto__: Object
On Dec 3, 2013, at 10:00 AM, Robert Hanson hans...@stolaf.edu wrote:
Now we are getting somewhere!
In the developer console, enter
Boolean
and then
Boolean.TRUE
and then
Boolean.FALSE
and tell me what you see.
--
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
--
Rapidly troubleshoot problems before they affect your business. Most IT
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Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Re: [Jmol-users] Safari test -- fixes Boolean issue?
Bob: You had a mighty profitable 1.5 hours between 11:30 and 1:00 today to have accomplished the “unsolvable”!! Looks really good — both hosted and local. The community owes you a huge round of thanks — though I know there are always bugs to fix. Phil On Dec 3, 2013, at 1:11 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.03a.zip -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol for testing....
Bob: I privately sent you some error messages earlier this morning. Did you get the email? I have a Safari 7.0 update As I reported in that prior message, jsmol.htm does not load the applet from your site. I have put a copy of the jsmol directory on my campus server. The applet in jsmol.htm does not load from there either. HOWEVER, test2.htm works from both your and my servers, in all three modes — HTML5, Signed, and unsigned — and that is without the error console. The HTML5 version stalls a little on loading at the Elements.js point, particularly the first time, but goes ahead and loads. I have not fully tested the other links. However, both Firefox and Chrome will not load the surface for the caffeine MMFF link though they do load the initial structure. Safari not only will not load the surface, but then freezes the page altogether. Hope this helps. Phil On Dec 1, 2013, at 9:42 PM, Robert Hanson hans...@stolaf.edu wrote: Thanks, Phil. I left /jsmol out of a bunch of those links; the download link is right. (Isn't it nice to have trusted-signed applets? Perhaps we will soon forget the days of all those warning messages.) By the way, at least for me, Chrome and MSIE are working for non-binary file formats on local drives with file:// protocol. http access tests : http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA loading caffeine loading 1hxw loading Pymol session loading =blu saving PNG image -- http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm?_USE=SIGNED searching for a compound name, CAS number, SMILES, InChI, etc. going back and forth 2D/3D -- http://chemapps.stolaf.edu/jmol/jsmol/jsv.htm spectrum loads http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm molecule interactive with spectra. -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Local testing
Following are the results of launching pages locally: Safari jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet loads, but neither java applet loads. giving the following error alert java.lang.reflect.InvocationTargetException Firefox jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet loads rapidly; I sometimes get an alert that jquery is busy, but the continue button continues the load Signed applet loads fine Unsigned applet throws AccessControl Exception Chrome jsmol.htm — HTML5 applet does not load test2.htm — HTML5 applet does not load; stalls at: loading... j2s/J/awtjs2d/Platform.js I note that for server loading of the WebGL version, Safari seems to require that you turn WebGL on in the developer menu. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Local testing
I agree. On Dec 2, 2013, at 4:17 PM, Miller, Benjamin mill...@janelia.hhmi.org wrote: For safari (jsmol.htm), can you check the browser console for error? I was seeing a null pointer exception. Once the console ws open, doing a refresh allowed jsmol to load. On 12/2/13, 4:10 PM, Philip Bays pb...@saintmarys.edu wrote: Following are the results of launching pages locally: Safari jsmol.htm ‹ HTML5 applet does not load test2.htm ‹ HTML5 applet loads, but neither java applet loads. giving the following error alert java.lang.reflect.InvocationTargetException Firefox jsmol.htm ‹ HTML5 applet does not load test2.htm ‹ HTML5 applet loads rapidly; I sometimes get an alert that jquery is busy, but the continue button continues the load Signed applet loads fine Unsigned applet throws AccessControl Exception Chrome jsmol.htm ‹ HTML5 applet does not load test2.htm ‹ HTML5 applet does not load; stalls at: loading... j2s/J/awtjs2d/Platform.js I note that for server loading of the WebGL version, Safari seems to require that you turn WebGL on in the developer menu. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktr k ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol for testing....
Bob: I think that your links here are not correct. And is the download link right?? Sent from my iPad On Dec 1, 2013, at 9:05 PM, Robert Hanson hans...@stolaf.edu wrote: again! http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.01.zip http access tests : http://chemapps.stolaf.edu/jmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol.htm?_USE=SIGNED http://chemapps.stolaf.edu/jmol/jsmol.htm?_USE=JAVA loading caffeine loading 1hxw loading Pymol session loading =blu saving PNG image -- http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm?_USE=SIGNED searching for a compound name, CAS number, SMILES, InChI, etc. going back and forth 2D/3D -- http://chemapps.stolaf.edu/jmol/jsv.htm spectrum loads http://chemapps.stolaf.edu/jmol/testjsv_mol.htm molecule interactive with spectra. -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Happy Thanksgiving!! Mac OSX 9 (Mavericks), Safari 7.0 Firefox works both locally and from Bob’s site using the three links below. The only issue is that test2 running locally gives an access control exception with the unsigned applet. Safari 7.0 is the issue with the HTML5 code. The hosted the applet will not load unless the error console is on. I posted the error thrown last night. Locally, test.htm and test2.htm load fine. jsmol.htm will not load hosted without the error console This morning I have looked at three files: simplej.htm, simpleOpt.htm, and supersimple.htm. All three purport to do the same thing. I have not looked at the code to see what is different. simplej.htm is fine both locally and hosted without the error console, albeit slowly. The other two, both locally and hosted, require the error console to be open to load the applet. If the console is closed, the code thrown is the same as I posted last evening. As I indicated last evening On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Firefox/Mac loads Signed local Jmol but not Unsigned
Addendum: The local test was run using the new version posted last night. I have found that locally 25c seems to behave best and that seems to be what is also on Bob’s site. On Nov 27, 2013, at 1:05 AM, Robert Hanson hans...@stolaf.edu wrote: OK. Tomorrow is Mac-testing day for me. Tell me your woes Please do try the latest, at http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.26b.zip and http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=HTML5 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED By the way, those _USE attributes are standard now for any JSmol page. Also: _JAR=http://. (some other java location) _J2S=http://. (some other j2s location) These should really help with remote debugging of different sites. If you haven't tried http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm http://chemapps.stolaf.edu/jmol/jsmol/jsv.htm http://chemapps.stolaf.edu/jmol/jsmol/jsv.htm?USE=SIGNED http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm?_USE=SIGNED be sure to try those. The last four demonstrate Robert Lancashire's and my work this past couple of months getting JSpecView up and running in JavaScript and in association with Jmol. -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Firefox/Mac loads Signed local Jmol but not Unsigned
Final note on the jsme and jsv links: Safari JME test neither applet loads JME Test2 JME loads, jmol does not JSV Spectrum loads, jmol does not JSV signed jmol does not load jv_mol nothing loads jv_mol signed works Firefox jsmetestworks jsmetest2 works jsv spectrum loads, jmol does not jsv signed spectrum loads, jmol does not testjsv_mol works testjsv_mol signed works On Nov 27, 2013, at 1:05 AM, Robert Hanson hans...@stolaf.edu wrote: OK. Tomorrow is Mac-testing day for me. Tell me your woes Please do try the latest, at http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.26b.zip and http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=HTML5 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED By the way, those _USE attributes are standard now for any JSmol page. Also: _JAR=http://. (some other java location) _J2S=http://. (some other j2s location) These should really help with remote debugging of different sites. If you haven't tried http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm http://chemapps.stolaf.edu/jmol/jsmol/jsv.h`tm http://chemapps.stolaf.edu/jmol/jsmol/jsv.htm?USE=SIGNED http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm http://chemapps.stolaf.edu/jmol/jsmol/testjsv_mol.htm?_USE=SIGNED be sure to try those. The last four demonstrate Robert Lancashire's and my work this past couple of months getting JSpecView up and running in JavaScript and in association with Jmol. -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Problems
Bob: The bondset issue is still there when running locally from the ….27 directory. On Nov 27, 2013, at 4:44 PM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip fixes the bondset problem. How do I get to your site to test this? On Wed, Nov 27, 2013 at 2:16 PM, Otis Rothenberger osrot...@chemagic.com wrote: I apologize in advance for starting a new thread here, but I'm getting really confused on issues. My focus here is this note from Bob this morning. From Bob... OK. Tomorrow is Mac-testing day for me. Tell me your woes Please do try the latest, at http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.26b.zip End from Bob With Mac Chrome, our model kit loads, but there is considerable whining during the load about waiting for the ISU server. Once loaded, most script links seem dead. I cannot even bring up the console or check the Jmol right-click menu. With Safari, the model does not load. I get the same error that Phil is getting about a missing BondSet.js file Otis -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
I have just had time to see if the applets load from your site. Java and signed load fine. HTML5 only loads if the error console is open. Error comments are as follows: [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2236) (anonymous function) (core.z.js, line 2228) (anonymous function) (core.z.js, line 2205) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 2204) (anonymous function) (core.z.js, line 2253) (anonymous function) (core.z.js, line 937) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 505) (anonymous function) (core.z.js, line 503) instantialize (JSmol.min.js, line 344) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 258) __nextExecution (JSmol.min.js, line 263) On Nov 27, 2013, at 7:53 PM, Robert Hanson hans...@stolaf.edu wrote: OK --- that's ready. tests: for local downloading: http://chemapps.stolaf.edu/jmol/jsmol/jmol-13.3.9_2013.11.27d.zip for hosted site checking: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED I await your word Bob Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Safari errors
I am looking at your web site the test2. Works fine in firefox. In safari both jsmol and jmol initially load fine. However, with the jsmol, after clicking number of links in the database column, the browser hangs and the page has to be reloaded. In addition, I get the following error alert popping up with a protein structure: Javascript JmolCore.js synchronus binary file transfer is requested but not available. Clicking OK on this alert allows that structure and a few others to load, but then it again freezes. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Addendum
I do not have the aforementioned issue running from my desktop using ….25c. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Firefox/Mac loads Signed local Jmol but not Unsigned
I agree with Nick on this for the most part. However, for me Firefox hangs after several loads from the database column; the culprit seems to be caffeine with MMFF force field. On Nov 26, 2013, at 5:48 PM, Greeves, Nick ngree...@liverpool.ac.uk wrote: With this version and test2.htm Firefox loads the signed Jmol just fine but Unsigned gives an AccessControlException error. Is this expected? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
