[Jmol-users] R: Firefox 17

2012-11-21 Thread pino.stricc...@libero.it
I have the same answer from firefox on mac. Pino Messaggio originale Da: pb...@saintmarys.edu Data: 20/11/2012 21.00 A: Jmol Jmoljmol-users@lists.sourceforge.net Ogg: [Jmol-users] Firefox 17 Forefox 17 was released today. I downloaded to see if it will now run JSMol. It will not.

[Jmol-users] Application oddities - V13.1.9_dev

2012-11-21 Thread Rolf Huehne
Hi all, while working with the Jmol application (13.1.9_dev) I noticed some odd behaviour: 1) The set selectionHalos on setting is not stable. It is switched off for example after clicking any of the toolbar icons in the third or fourth group. 2) Entering the mouse selection mode by

[Jmol-users] JSmol - three months in

2012-11-21 Thread Robert Hanson
Well, it's been a busy three months! Hard to believe that I started this Aug 26, and we basically now have a fully functional Jmol applet without Java. I have updated http://chemapps.stolaf.edu/jmol/jsmol.zip http://chemapps.stolaf.edu/jmol/jsmol/test2.htm demonstrates reading binary Spartan

Re: [Jmol-users] Application oddities - V13.1.9_dev

2012-11-21 Thread Robert Hanson
On Wed, Nov 21, 2012 at 10:52 AM, Rolf Huehne rhue...@fli-leibniz.dewrote: Hi all, while working with the Jmol application (13.1.9_dev) I noticed some odd behaviour: 1) The set selectionHalos on setting is not stable. It is switched off for example after clicking any of the toolbar

Re: [Jmol-users] Application oddities - V13.1.9_dev

2012-11-21 Thread Angel Herráez
2) Entering the mouse selection mode by using the toolbar icon deselects all atoms. This doesn't happen if the popup menu is used instead I see this logical. If I go into mouse selection I am not expecting to work against an already selected full set. So the previous select none

Re: [Jmol-users] Application oddities - V13.1.9_dev

2012-11-21 Thread Rolf Huehne
On 11/21/2012 06:12 PM, Robert Hanson wrote: On Wed, Nov 21, 2012 at 10:52 AM, Rolf Huehne rhue...@fli-leibniz.dewrote: Hi all, while working with the Jmol application (13.1.9_dev) I noticed some odd behaviour: 1) The set selectionHalos on setting is not stable. It is switched off

Re: [Jmol-users] Application oddities - V13.1.9_dev

2012-11-21 Thread Rolf Huehne
On 11/21/2012 06:33 PM, Angel Herráez wrote: 2) Entering the mouse selection mode by using the toolbar icon deselects all atoms. This doesn't happen if the popup menu is used instead I see this logical. If I go into mouse selection I am not expecting to work against an already

Re: [Jmol-users] JSmol - three months in

2012-11-21 Thread Rolf Huehne
On 11/21/2012 06:02 PM, Robert Hanson wrote: Well, it's been a busy three months! Hard to believe that I started this Aug 26, and we basically now have a fully functional Jmol applet without Java. I have updated http://chemapps.stolaf.edu/jmol/jsmol.zip I tried the new version but Firefox

Re: [Jmol-users] JSmol - three months in

2012-11-21 Thread Robert Hanson
thanks. This is a step I forget because it doesn't affect my browser. Those are byte-order marks I don't know how to prevent but I know how to remove. Please try that again at http://chemapps.stolaf.edu/jmol/jsmol/test2.htm or http://chemapps.stolaf.edu/jmol/jsmol.zip On Wed, Nov 21, 2012 at

[Jmol-users] JSmol - three months in

2012-11-21 Thread Greeves, Nick
Bob et al, I am pleased to report that loading of Spartan files e.g.molecule.spardir works beautifully. It just keeps getting more like Jmol. Thanks Bob! All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) On 21 Nov

Re: [Jmol-users] JSmol - three months in

2012-11-21 Thread Otis Rothenberger
This now works on Mac Firefox 17.0 - very fast load even after cache is cleared. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 21, 2012, at 2:52 PM, Robert Hanson wrote: thanks. This is a step I forget because it doesn't affect my browser. Those are byte-order

Re: [Jmol-users] JSmol - three months in

2012-11-21 Thread Angel Herráez
Yeah, I was just checking that. I downloaded JSmol.zip this morning and I am getting error in loading core.z.js After checking the js console errors, I located many lines that have a strange invisible character at the beginning of line. I could select one (together with the next few letters)

Re: [Jmol-users] two JSmols in the page

2012-11-21 Thread Angel Herráez
Ok, after sorting out my problems with the JSmol file set, I can now --again-- assert that where one JSmol works, two don't. This is my test code: var myJmol1,myJmol2; var myInfo = { height: '50%', width: '100%', jarFile: JmolApplet.jar, jarPath: '..',

[Jmol-users] JSmol - three months in... and compression

2012-11-21 Thread Paul Pillot
I've tried minifying JSmol (yes, again), with the new version. After gziping by the server, the results are : - 720kB with WebGL - 666kB without WebGL (including 4kB just for the HTML page) (I don't have the extra download of 40+ files, as I had previously so the minifying process works as

[Jmol-users] Molecular Orbitals squaring

2012-11-21 Thread Leonardo Matheus Marion Jorge
Dear Jmol users, Can you please help me? I need to plot the weighted sum of the squares of Molecular Orbitals from a Molden output file. The first problem I had is that the code I used didn't add a space between the (Atoms) and (Angs) keywords, and Jmol was expecting that space (Molden gave

Re: [Jmol-users] two JSmols in the page

2012-11-21 Thread Robert Hanson
OK, Angel, That's a good test. A few problems there. (1) a bug in the Java2Script library was causing the location of j2sjmol.lib to be miscalculated -- fixed (see http://chemapps.stolaf.edu/jmol/jsmol/j2s/j2sjmol.js, line 3791, Renjian) (2) incomplete Info object -- You need an explicit

Re: [Jmol-users] Molecular Orbitals squaring

2012-11-21 Thread Robert Hanson
Q: What is the physical significance of sum of squares of orbitals? Electron density would be the square of the sum, not the sum of the squares. Right? Bob On Wed, Nov 21, 2012 at 9:22 PM, Leonardo Matheus Marion Jorge leo...@usp.br wrote: Dear Jmol users, Can you please help me? I need to

[Jmol-users] JSmol limitations

2012-11-21 Thread Robert Hanson
OK. Found one. Minimization is not feasible. Just way too slow. -- 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

Re: [Jmol-users] Molecular Orbitals squaring

2012-11-21 Thread Leonardo Matheus Marion Jorge
A: I want to examine the excitons, using the approach of http://pubs.acs.org/doi/abs/10.1021/jz200472a to look at the spatial distribution of electron and hole. Thanks, Leonardo Jorge PhD Student, USP - Brazil Nanomol group http://nanomol.if.usp.br Date: Wed, 21 Nov 2012 21:38:56 -0600