Re: [Jmol-users] old Jmol, new JSmol

Bob Many thanks for this. IE9 now works perfectly from files on my laptop, but not via the www from my server (still perfect with FF, Chrome, Safari). Actually your demo file shows the same symptoms: no blue outline seen, title tab still shows original wording not ‘jmolApplet0 is ready’. File

Re: [Jmol-users] old Jmol, new JSmol

you haven't updated js/JSmolCore.js On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane wrote: > Bob > > Many thanks for this. IE9 now works perfectly from files on my laptop, but > not via the www from my server (still perfect with FF, Chrome, Safari). > > Actually your demo file shows the sam

Re: [Jmol-users] old Jmol, new JSmol

(and other files in that directory) On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote: > you haven't updated js/JSmolCore.js > > > > > On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane < > richard.ste...@ntlworld.com> wrote: > >> Bob >> >> Many thanks for this. IE9 now works perfectly from f

Re: [Jmol-users] old Jmol, new JSmol

More problems than that -- turns out MSIE 10 has the same problem (at least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip Also includes optimization of molecular orbital calculations, and a cool link called "make a nanotube" On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote

Re: [Jmol-users] old Jmol, new JSmol

Bob I’m fairly sure all the files in the js directory are up to date. Richard From: Robert Hanson Sent: Friday, March 15, 2013 3:19 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] old Jmol, new JSmol More problems than that -- turns out MSIE 10 has the same problem (at least

[Jmol-users] phosphate of phosphorylated amino acids defined as mainchain

Hi, It looks like P and O bound to P in phosphorylated amino acids are incorrectly included in the predefined mainchain atom set, perhaps a knock-on from the correct assignment of such atoms to the mainchain of nucleic acids? For example chain A, residue 638 of 3iw4: select 638a # 11 atoms selec

Re: [Jmol-users] old Jmol, new JSmol

Get the latest file; I changed a few aspects so that MSIE of any version will not do this. On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane < richard.ste...@ntlworld.com> wrote: > Bob > > I’m fairly sure all the files in the js directory are up to date. > > Richard > > *From:* Robert Hanson

Re: [Jmol-users] old Jmol, new JSmol

Which file/folder? From: Robert Hanson Sent: Friday, March 15, 2013 4:52 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] old Jmol, new JSmol Get the latest file; I changed a few aspects so that MSIE of any version will not do this. On Fri, Mar 15, 2013 at 10:36 AM, Richar

Re: [Jmol-users] Jmol | lcaocartoon

On 3/11/2013 2:18 PM, Robert Hanson wrote: Since when are they sp2 ? ;) Since freshman chemistry covered hybridization? I am guessing that there is no simple fix... PM On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak > wrote: On 3/11/2013 12:58 PM, Robert

Re: [Jmol-users] Jmol | lcaocartoon

I think the point here is that CO2 has simple sp hybridization, not sp2... 2013/3/15 Pshemak Maslak > On 3/11/2013 2:18 PM, Robert Hanson wrote: > > Since when are they sp2 ? ;) > > Since freshman chemistry covered hybridization? > > I am guessing that there is no simple fix... > > PM > > > >

Re: [Jmol-users] Jmol | lcaocartoon

On 3/15/2013 1:42 PM, Simone Sturniolo wrote: I think the point here is that CO2 has simple sp hybridization, not sp2... We are talking about lone pairs on oxygens (not about carbon hybridization). PM 2013/3/15 Pshemak Maslak mailto:p...@chem.psu.edu>> On 3/11/2013 2:18 PM, Robert Hans

Re: [Jmol-users] Jmol | lcaocartoon

There seems to be a philosophical and technological debate brewing here. Rigorously, the lone pairs of CO2 are not sp2-hybridized; a canonical calculation of the MOs reveals that. But on another note, how would Jmol even know where to put the sp2 hybridized lone pairs? The two ends of CO2 would ha

Re: [Jmol-users] phosphate of phosphorylated amino acids defined as mainchain

Ah, thank you for spotting that. See http://chemapps.stolaf.edu/jmol/Jmol-13.zip http://chemapps.stolaf.edu/jmol/jsmol.zip On Fri, Mar 15, 2013 at 11:42 AM, Matthew Betts < matthew.be...@bioquant.uni-heidelberg.de> wrote: > Hi, > > It looks like P and O bound to P in phosphorylated amino aci

Re: [Jmol-users] Jmol | lcaocartoon

But I would argue that CO2 is sp hybridized, and the six left-over p orbitals form two orthogonal three-orbital pi sets. Isn't that necessary from symmetry considerations? Bob On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak wrote: > On 3/11/2013 2:18 PM, Robert Hanson wrote: > > Since when

Re: [Jmol-users] old Jmol, new JSmol

sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane < richard.ste...@ntlworld.com> wrote: > Which file/folder? > > *From:* Robert Hanson > *Sent:* Friday, March 15, 2013 4:52 PM > *To:* jmol-users@lists.sourceforge.net > *Subject:* Re: [Jmol-u

Re: [Jmol-users] Jmol | lcaocartoon

On 3/15/2013 2:11 PM, Michael Evans wrote: There seems to be a philosophical and technological debate brewing here. Rigorously, the lone pairs of CO2 are not sp2-hybridized; a canonical calculation of the MOs reveals that. I do not think that CARTOON orbitals inspire a philosophical debate; :-)

Re: [Jmol-users] Jmol | lcaocartoon

On 3/15/2013 2:21 PM, Robert Hanson wrote: But I would argue that CO2 is sp hybridized, and the six left-over p orbitals form two orthogonal three-orbital pi sets. Isn't that necessary from symmetry considerations? Bob In the MO-sense, yes, but I am thinking about simple (freshman-level) h

[Jmol-users] second request - Please unsubsribe

Mogus D Mochena Professor of Physics Florida A & M University Tallahassee, Florida 32307 Tel: 850-412-5740 Fax: 850-599-3577 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download

Re: [Jmol-users] Jmol | lcaocartoon

OK, I suggest we leave the philosophy out of it -- sorry I brought it up! Yes, you can put lobes anywhere and any direction you want. The MOLECULAR keyword indicates that you want to indicate directions based on xyz axes and not use the hybridization algorithm. Just make sure your model lines up o

Re: [Jmol-users] Jmol | lcaocartoon

lcaocartoon ID "lp1" center {_O}[1] lobe {0 -0.866 -0.5 0.7} looks to me to be a decent sp2 orbital for which the associated p orbital is along x. The first three numbers are the axis direction; the last one is the ratio of width to length. Will that do, Pshemak? Bob On Fri, Mar 15, 201

Re: [Jmol-users] Jmol | lcaocartoon

On 3/15/2013 4:38 PM, Robert Hanson wrote: > lcaocartoon ID "lp1" center {_O}[1] lobe {0 -0.866 -0.5 0.7} > > looks to me to be a decent sp2 orbital for which the associated p > orbital is along x. > > The first three numbers are the axis direction; the last one is the > ratio of width to lengt

Re: [Jmol-users] Jmol | lcaocartoon

just switch LONEPAIR for LOBE. On Fri, Mar 15, 2013 at 4:09 PM, Pshemak Maslak wrote: > On 3/15/2013 4:38 PM, Robert Hanson wrote: > > lcaocartoon ID "lp1" center {_O}[1] lobe {0 -0.866 -0.5 0.7} > > > > looks to me to be a decent sp2 orbital for which the associated p > > orbital is along x.

Re: [Jmol-users] old Jmol, new JSmol

I updated to the latest version of jmol. The molecule was working fine before, but now it works in Chrome but not in Firefox. Any idea why? http://biology.kenyon.edu/BMB/biomolecules.htm Thanks. Daniel On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson wrote: > sorry -- http://chemapps.stolaf.

Re: [Jmol-users] old Jmol, new JSmol

Hello Daniel I am seeing your problem (same as mine) with IE9, but Firefox and Chrome display that page correctly . IE9 is still not quite working at my end, despite complete new upload. Could it be anything to do with synchronous cross-domain file transfer? Is anyone seeing a molecule at: htt

Re: [Jmol-users] old Jmol, new JSmol

That page is working correctly for me in Firefox, MSIE 9, MSIE 10, Chrome, and Opera on Windows 8. The Opera implementation has clunky rotation. I really think this is just a caching problem for you. It's harder than you think to clear the caches in MSIE. If http://chemapps.stolaf.edu/jmol/jsmol/

[Jmol-users] one last upload for the week

http://chemapps.stolaf.edu/jmol/jsmol.zip -- improved performance for script variable math, isosurface, MO, and pmesh creation, rendering, crystallographic symmetry, more -- final optimizations of several Java classes, including Arrays, Hashtable, and ArrayList using the latest Java2Script compil

Re: [Jmol-users] old Jmol, new JSmol

Here's the error I get with my page at http://biology.kenyon.edu/BMB/biomolecules.htm: getValue MINIMIZATIONCallback = null getValue PICKCallback = null getValue RESIZECallback = null getValue SCRIPTCallback = null getValue SYNCCallback = null language=en_US getValue script = null Jmol applet myJm