From: Daniel B. <ba...@ke...> - 2013-02-27 19:10:15
|
Hello, I got a page to work with JSMol by loading all of the script files individually using the <script> tag. But when I only specify 'JSmol.min.js', it gives me a 'syntax error'. See: http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm Did anyone get the single-file 'min' javascript to work? If so, I'd like to see an example. Thanks. Daniel |
From: Michael E. <ev...@il...> - 2013-02-27 20:05:29
|
Dan, The version of JSmol I'm using is a bit dated, but see here: http://www.metallacycle.com/play/netmol/jmol/?use=html5 Cheers, Mike On Wednesday, February 27, 2013, Daniel Barich wrote: > Hello, > > I got a page to work with JSMol by loading all of the script files > individually using the <script> tag. But when I only specify > 'JSmol.min.js', it gives me a 'syntax error'. See: > > http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm > > Did anyone get the single-file 'min' javascript to work? If so, I'd like > to see an example. > > Thanks. > > Daniel > -- --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign |
From: Paul P. <pau...@ac...> - 2013-02-27 20:07:37
|
This link works for me (OsX10.6, Chrome) Le 27 févr. 2013 à 19:55, Daniel Barich a écrit : > Hello, > > I got a page to work with JSMol by loading all of the script files individually using the <script> tag. But when I only specify 'JSmol.min.js', it gives me a 'syntax error'. See: > > http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm > > Did anyone get the single-file 'min' javascript to work? If so, I'd like to see an example. > > Thanks. > > Daniel |
From: A. H. <ang...@ua...> - 2013-02-27 20:29:02
|
> http://biology.kenyon.edu/BMB/biomolecules_jsmol.htm Working for me , too (Firefox on WIn7) Clear your cache, maybe |
From: Daniel B. <ba...@ke...> - 2013-02-27 21:17:43
|
My page is still not working, and neither is this sample page on my jsmol installation: http://biology.kenyon.edu/BMB/jsmol/simple2.htm Does this link work for anyone else. The other examples work, but my page still doesn't work. The link again is: http://biology.kenyon.edu/BMB/jsmol/simple2.htm Daniel |
From: Michael E. <ev...@il...> - 2013-02-27 21:21:08
|
Works for me, big guy. The page loads using Java but the HTML5 Version link works fine for me. Cheers, Mike --- Michael Evans Department of Chemistry University of Illinois, Urbana-Champaign On Wed, Feb 27, 2013 at 3:16 PM, Daniel Barich <ba...@ke...> wrote: > My page is still not working, and neither is this sample page on my jsmol > installation: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Does this link work for anyone else. The other examples work, but my page > still doesn't work. The link again is: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Daniel > > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Robert H. <ha...@st...> - 2013-02-27 23:33:00
|
all good. HTML5 link on the page works as well. On Wed, Feb 27, 2013 at 3:16 PM, Daniel Barich <ba...@ke...> wrote: > My page is still not working, and neither is this sample page on my jsmol > installation: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Does this link work for anyone else. The other examples work, but my page > still doesn't work. The link again is: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Daniel > > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Otis R. <osr...@ch...> - 2013-02-27 22:03:08
|
Daniel, On your page, a Resolver load works after the initial page error. Your initial load is from PubChem, and that gives an error for this URL: http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d I'm not sure what's causing that cid # error. On my JSmol page, I go after Resolver and PubChem with my own server side scripts, but I tried the following from my page just to see what happens: load $tylenol load :tylenol The above does not use my server side scripts. The $ load (Resolver) works. The : load (PubChem) produces the same URL as your page. I'm not sure that I am offering a solution to your problem, but I found that working with my own server side scripts for remote loads made a lot of problems go away. Bob's scripts can, of course, be run from your server. On your original page, I was not seeing the syntax error that you mentioned - Safari (most recent) Mac Lion. Otis -- Otis Rothenberger ot...@ch... http://chemagic.com On Feb 27, 2013, at 4:16 PM, Daniel Barich wrote: > My page is still not working, and neither is this sample page on my jsmol installation: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Does this link work for anyone else. The other examples work, but my page still doesn't work. The link again is: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Daniel > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: A. H. <ang...@ua...> - 2013-02-27 23:08:11
|
> http://biology.kenyon.edu/BMB/jsmol/simple2.htm Yes! Same result as Mike: first it loads the Java applet, but the HTML5 links loads the JSmol version OK |
From: Robert H. <ha...@st...> - 2013-02-27 23:33:30
|
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d ah, I probably broke something. That number means "not a number" in Jmol. On Wed, Feb 27, 2013 at 3:55 PM, Otis Rothenberger <osr...@ch...>wrote: > Daniel, > > On your page, a Resolver load works after the initial page error. Your > initial load is from PubChem, and that gives an error for this URL: > > > http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d > > I'm not sure what's causing that cid # error. > > On my JSmol page, I go after Resolver and PubChem with my own server side > scripts, but I tried the following from my page just to see what happens: > > load $tylenol > load :tylenol > > The above does not use my server side scripts. The $ load (Resolver) > works. The : load (PubChem) produces the same URL as your page. > > I'm not sure that I am offering a solution to your problem, but I found > that working with my own server side scripts for remote loads made a lot of > problems go away. Bob's scripts can, of course, be run from your server. > > On your original page, I was not seeing the syntax error that you > mentioned - Safari (most recent) Mac Lion. > > Otis > > > -- > Otis Rothenberger > ot...@ch... > http://chemagic.com > > > > > On Feb 27, 2013, at 4:16 PM, Daniel Barich wrote: > > My page is still not working, and neither is this sample page on my jsmol > installation: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Does this link work for anyone else. The other examples work, but my page > still doesn't work. The link again is: > > http://biology.kenyon.edu/BMB/jsmol/simple2.htm > > Daniel > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > > http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2013-02-28 00:19:40
|
Yes, my bad. See http://chemapps.stolaf.edu/jmol/jsmol.zip Note that this round of JSmol improves isosurface creation speed by close to a factor of 2 -- half the time of previous versions. (Additional key optimization of Java code and the Java2Script library.) The minimized core file is also about 8% smaller than it was, as well. On Wed, Feb 27, 2013 at 5:32 PM, Robert Hanson <ha...@st...> wrote: > > http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d > > ah, I probably broke something. That number means "not a number" in Jmol. > > > On Wed, Feb 27, 2013 at 3:55 PM, Otis Rothenberger <osr...@ch...>wrote: > >> Daniel, >> >> On your page, a Resolver load works after the initial page error. Your >> initial load is from PubChem, and that gives an error for this URL: >> >> >> http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d >> >> I'm not sure what's causing that cid # error. >> >> On my JSmol page, I go after Resolver and PubChem with my own server side >> scripts, but I tried the following from my page just to see what happens: >> >> load $tylenol >> load :tylenol >> >> The above does not use my server side scripts. The $ load (Resolver) >> works. The : load (PubChem) produces the same URL as your page. >> >> I'm not sure that I am offering a solution to your problem, but I found >> that working with my own server side scripts for remote loads made a lot of >> problems go away. Bob's scripts can, of course, be run from your server. >> >> On your original page, I was not seeing the syntax error that you >> mentioned - Safari (most recent) Mac Lion. >> >> Otis >> >> >> -- >> Otis Rothenberger >> ot...@ch... >> http://chemagic.com >> >> >> >> >> On Feb 27, 2013, at 4:16 PM, Daniel Barich wrote: >> >> My page is still not working, and neither is this sample page on my jsmol >> installation: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Does this link work for anyone else. The other examples work, but my >> page still doesn't work. The link again is: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Daniel >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Daniel B. <ba...@ke...> - 2013-03-02 01:29:14
|
Thanks - my pages work great with the new JSmol version. Incidentally, I find that the following page, which has a large molecule view, runs much smoother in Chrome than Firefox: http://biology.kenyon.edu/BMB/jmodel/index.htm Do others experience the same? Daniel On Wed, Feb 27, 2013 at 6:32 PM, Robert Hanson <ha...@st...> wrote: > > http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d > > ah, I probably broke something. That number means "not a number" in Jmol. > > > On Wed, Feb 27, 2013 at 3:55 PM, Otis Rothenberger <osr...@ch...>wrote: > >> Daniel, >> >> On your page, a Resolver load works after the initial page error. Your >> initial load is from PubChem, and that gives an error for this URL: >> >> >> http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/-2147483648/SDF?record_type=3d >> >> I'm not sure what's causing that cid # error. >> >> On my JSmol page, I go after Resolver and PubChem with my own server side >> scripts, but I tried the following from my page just to see what happens: >> >> load $tylenol >> load :tylenol >> >> The above does not use my server side scripts. The $ load (Resolver) >> works. The : load (PubChem) produces the same URL as your page. >> >> I'm not sure that I am offering a solution to your problem, but I found >> that working with my own server side scripts for remote loads made a lot of >> problems go away. Bob's scripts can, of course, be run from your server. >> >> On your original page, I was not seeing the syntax error that you >> mentioned - Safari (most recent) Mac Lion. >> >> Otis >> >> >> -- >> Otis Rothenberger >> ot...@ch... >> http://chemagic.com >> >> >> >> >> On Feb 27, 2013, at 4:16 PM, Daniel Barich wrote: >> >> My page is still not working, and neither is this sample page on my jsmol >> installation: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Does this link work for anyone else. The other examples work, but my >> page still doesn't work. The link again is: >> >> http://biology.kenyon.edu/BMB/jsmol/simple2.htm >> >> Daniel >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Rolf H. <rh...@fl...> - 2013-03-05 12:51:51
|
On 02/28/2013 09:19 PM, Daniel Barich wrote: > Thanks - my pages work great with the new JSmol version. Incidentally, I > find that the following page, which has a large molecule view, runs much > smoother in Chrome than Firefox: > > http://biology.kenyon.edu/BMB/jmodel/index.htm > > Do others experience the same? > Daniel, your question got delayed somehow, so my answer comes a little late. It is the same on my system (OpenSuse 11.4, Firefox 16.0.2, Chromium 25.0). Generally I would not recommend setting 'spin' on by default with JSmol and protein structures in a large canvas because JSmol is about ten times slower than Jmol in most browsers in my experience. (At least it was several weeks ago.) With JSmol the speed is not only dependent from the CPU speed but also from the browser Javascript speed. Somewhat strange seems that spinning in Firefox is much slower (and stuttering) than free rotation with the mouse, which is quite fluent with your example protein containing only about 3500 atoms. Free rotation with the mouse is also even speedier in Chromium. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Robert H. <ha...@st...> - 2013-03-05 13:54:29
|
On Tue, Mar 5, 2013 at 6:26 AM, Rolf Huehne <rh...@fl...> wrote: > On 02/28/2013 09:19 PM, Daniel Barich wrote: > > Thanks - my pages work great with the new JSmol version. Incidentally, I > > find that the following page, which has a large molecule view, runs much > > smoother in Chrome than Firefox: > > > > http://biology.kenyon.edu/BMB/jmodel/index.htm > > > > Do others experience the same? > > > Daniel, your question got delayed somehow, so my answer comes a little > late. > > It is the same on my system (OpenSuse 11.4, Firefox 16.0.2, Chromium 25.0). > > Generally I would not recommend setting 'spin' on by default with JSmol > and protein structures in a large canvas because JSmol is about ten > times slower than Jmol in most browsers in my experience. (At least it > was several weeks ago.) With JSmol the speed is not only dependent from > the CPU speed but also from the browser Javascript speed. > > I agree completely about spin. That's one of the least worked-out aspects of JSmol. Small molecules -- no problem; large molecules, more of a problem. It would be good to check this out again. I've done some pretty significant optimizations recently. Surface creation, for example, is much much faster. (small protein solvent-accessible surface in 1.5 sec.) > Somewhat strange seems that spinning in Firefox is much slower (and > stuttering) than free rotation with the mouse, which is quite fluent > with your example protein containing only about 3500 atoms. Free > rotation with the mouse is also even speedier in Chromium. > > This something I can probably look at.. Since JavaScript does not have multiple threading, I've played some pretty fancy tricks to get spinning at all. Certainly room for optimization there, but it is a LOT of rendering. > Regards, > Rolf > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rh...@fl... > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph > Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |