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

[Daniel Barich]

Here's the error I get with my page at
http://biology.kenyon.edu/BMB/biomolecules.htm:

getValue MINIMIZATIONCallback = null
getValue PICKCallback = null
getValue RESIZECallback = null
getValue SCRIPTCallback = null
getValue SYNCCallback = null
language=en_US
getValue script = null
Jmol applet myJmol_object__269579045037469__ ready
call loadScript jsmol\core\corescript.z.js
call loadScript jsmol\J\util\Point4f.js
Jmol._readyCallback failed java.lang.IndexOutOfBoundsException


On Fri, Mar 15, 2013 at 6:02 PM, Daniel Barich  wrote:

> I updated to the latest version of jmol.  The molecule was working fine
> before, but now it works in Chrome but not in Firefox.  Any idea why?
>
> http://biology.kenyon.edu/BMB/biomolecules.htm
>
> Thanks.
>
> Daniel
>
>
> On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson  wrote:
>
>> sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>>
>> On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>   Which file/folder?
>>>
>>>  *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 4:52 PM
>>> *To:* jmol-users@lists.sourceforge.net
>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>  Get the latest file; I changed a few aspects so that MSIE of any
>>> version will not do this.
>>>
>>>
>>> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane <
>>> richard.ste...@ntlworld.com> wrote:
>>>
   Bob

 I’m fairly sure all the files in the js directory are up to date.

 Richard

  *From:* Robert Hanson 
 *Sent:* Friday, March 15, 2013 3:19 PM
 *To:* jmol-users@lists.sourceforge.net
  *Subject:* Re: [Jmol-users] old Jmol, new JSmol

   More problems than that -- turns out MSIE 10 has the same problem
 (at least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip

 Also includes optimization of molecular orbital calculations, and a
 cool link called "make a nanotube"




 On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:

> (and other files in that directory)
>
>
> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>
>> you haven't updated js/JSmolCore.js
>>
>>
>>
>>
>>  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>Bob
>>>
>>> Many thanks for this. IE9 now works perfectly from files on my
>>> laptop, but not via the www from my server (still perfect with FF, 
>>> Chrome,
>>> Safari).
>>>
>>> Actually your demo file shows the same symptoms: no blue outline
>>> seen, title tab still shows original wording not ‘jmolApplet0 is ready’.
>>>
>>> File URLs:
>>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>>> http://www.biotopics.co.uk/jsmol/jsmol.htm
>>>
>>> I hope it’s just something simple!
>>>
>>> Thanks for any help.
>>>
>>> Richard Steane
>>>   *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 3:20 AM
>>> *To:* jmol-users@lists.sourceforge.net ; Zhou 
>>> Renjian
>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>  The problem with MSIE 9 is fixed. A newly optimized version of
>>> JSmol is in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday

[Jmol-users] one last upload for the week

[Robert Hanson]

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 compiler (thank you,
Zhou Renjian!)




-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

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

[Robert Hanson]

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/jsmol.htm  works, then your page
should as well.

Bob



On Fri, Mar 15, 2013 at 6:34 PM, Richard Steane  wrote:

>   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:
> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>
> (Thanks Bob for your past and future efforts!)
>
> Richard Steane
>
>
>
>
>  *From:* Daniel Barich 
> *Sent:* Friday, March 15, 2013 10:02 PM
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>
>   I updated to the latest version of jmol.  The molecule was working fine
> before, but now it works in Chrome but not in Firefox.  Any idea why?
> http://biology.kenyon.edu/BMB/biomolecules.htm
>
> Thanks.
>
> Daniel
>
>
> On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson  wrote:
>
>> sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>>
>> On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>   Which file/folder?
>>>
>>>  *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 4:52 PM
>>>  *To:* jmol-users@lists.sourceforge.net
>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>   Get the latest file; I changed a few aspects so that MSIE of any
>>> version will not do this.
>>>
>>>
>>> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane <
>>> richard.ste...@ntlworld.com> wrote:
>>>
   Bob

 I’m fairly sure all the files in the js directory are up to date.

 Richard

  *From:* Robert Hanson 
 *Sent:* Friday, March 15, 2013 3:19 PM
 *To:* jmol-users@lists.sourceforge.net
  *Subject:* Re: [Jmol-users] old Jmol, new JSmol

   More problems than that -- turns out MSIE 10 has the same problem
 (at least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip

 Also includes optimization of molecular orbital calculations, and a
 cool link called "make a nanotube"




 On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:

> (and other files in that directory)
>
>
> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>
>> you haven't updated js/JSmolCore.js
>>
>>
>>
>>
>>  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>Bob
>>>
>>> Many thanks for this. IE9 now works perfectly from files on my
>>> laptop, but not via the www from my server (still perfect with FF, 
>>> Chrome,
>>> Safari).
>>>
>>> Actually your demo file shows the same symptoms: no blue outline
>>> seen, title tab still shows original wording not ‘jmolApplet0 is ready’.
>>>
>>> File URLs:
>>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>>> http://www.biotopics.co.uk/jsmol/jsmol.htm
>>>
>>> I hope it’s just something simple!
>>>
>>> Thanks for any help.
>>>
>>> Richard Steane
>>>   *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 3:20 AM
>>> *To:* jmol-users@lists.sourceforge.net ; Zhou 
>>> Renjian
>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>  The problem with MSIE 9 is fixed. A newly optimized version of
>>> JSmol is in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it i

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

[Richard Steane]

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:
http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html

(Thanks Bob for your past and future efforts!)

Richard Steane




From: Daniel Barich 
Sent: Friday, March 15, 2013 10:02 PM
To: jmol-users@lists.sourceforge.net 
Subject: Re: [Jmol-users] old Jmol, new JSmol

I updated to the latest version of jmol.  The molecule was working fine before, 
but now it works in Chrome but not in Firefox.  Any idea why?
http://biology.kenyon.edu/BMB/biomolecules.htm


Thanks.

Daniel




On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson  wrote:

  sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip





  On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane 
 wrote:

Which file/folder?

From: Robert Hanson 
Sent: Friday, March 15, 2013 4:52 PM
To: jmol-users@lists.sourceforge.net 
Subject: Re: [Jmol-users] old Jmol, new JSmol

Get the latest file; I changed a few aspects so that MSIE of any version 
will not do this.




On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane 
 wrote:

  Bob

  I’m fairly sure all the files in the js directory are up to date.

  Richard

  From: Robert Hanson 
  Sent: Friday, March 15, 2013 3:19 PM
  To: jmol-users@lists.sourceforge.net 
  Subject: Re: [Jmol-users] old Jmol, new JSmol

  More problems than that -- turns out MSIE 10 has the same problem (at 
least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip


  Also includes optimization of molecular orbital calculations, and a cool 
link called "make a nanotube"






  On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

(and other files in that directory)




On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  
wrote:

  you haven't updated js/JSmolCore.js






  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane 
 wrote:

Bob

Many thanks for this. IE9 now works perfectly from files on my 
laptop, but not via the www from my server (still perfect with FF, Chrome, 
Safari).

Actually your demo file shows the same symptoms: no blue outline 
seen, title tab still shows original wording not ‘jmolApplet0 is ready’.

File URLs:
http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
http://www.biotopics.co.uk/jsmol/jsmol.htm

I hope it’s just something simple!

Thanks for any help.

Richard Steane
From: Robert Hanson 
Sent: Friday, March 15, 2013 3:20 AM
To: jmol-users@lists.sourceforge.net ; Zhou Renjian 
Subject: Re: [Jmol-users] old Jmol, new JSmol

The problem with MSIE 9 is fixed. A newly optimized version of 
JSmol is in  http://chemapps.stolaf.edu/jmol/jsmol.zip 



--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users





  -- 
  Robert M. Hanson
  Larson-Anderson Professor of Chemistry
  Chair, Chemistry Department
  St. Olaf College
  Northfield, MN
  http://www.stolaf.edu/people/hansonr


  If nature does not answer first what we want,
  it is better to take what answer we get. 

  -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





  -- 
  Robert M. Hanson
  Larson-Anderson Professor of Chemistry
  Chair, Chemistry Department
  St. Olaf College
  Northfield, MN
  http://www.stolaf.edu/people/hansonr


  If nature does not answer first what we want,
  it is better to take what answer we get. 

  -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



--

  
--
  Everyone hates slow websites. So do we.
  Make your web apps faster with AppD

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

[Daniel Barich]

I updated to the latest version of jmol.  The molecule was working fine
before, but now it works in Chrome but not in Firefox.  Any idea why?

http://biology.kenyon.edu/BMB/biomolecules.htm

Thanks.

Daniel


On Fri, Mar 15, 2013 at 2:22 PM, Robert Hanson  wrote:

> sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip
>
>
>
> On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane <
> richard.ste...@ntlworld.com> wrote:
>
>>   Which file/folder?
>>
>>  *From:* Robert Hanson 
>> *Sent:* Friday, March 15, 2013 4:52 PM
>> *To:* jmol-users@lists.sourceforge.net
>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>
>>  Get the latest file; I changed a few aspects so that MSIE of any
>> version will not do this.
>>
>>
>> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>   Bob
>>>
>>> I’m fairly sure all the files in the js directory are up to date.
>>>
>>> Richard
>>>
>>>  *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 3:19 PM
>>> *To:* jmol-users@lists.sourceforge.net
>>>  *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>   More problems than that -- turns out MSIE 10 has the same problem (at
>>> least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>> Also includes optimization of molecular orbital calculations, and a cool
>>> link called "make a nanotube"
>>>
>>>
>>>
>>>
>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>>>
 (and other files in that directory)


 On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:

> you haven't updated js/JSmolCore.js
>
>
>
>
>  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
> richard.ste...@ntlworld.com> wrote:
>
>>Bob
>>
>> Many thanks for this. IE9 now works perfectly from files on my
>> laptop, but not via the www from my server (still perfect with FF, 
>> Chrome,
>> Safari).
>>
>> Actually your demo file shows the same symptoms: no blue outline
>> seen, title tab still shows original wording not ‘jmolApplet0 is ready’.
>>
>> File URLs:
>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>> http://www.biotopics.co.uk/jsmol/jsmol.htm
>>
>> I hope it’s just something simple!
>>
>> Thanks for any help.
>>
>> Richard Steane
>>   *From:* Robert Hanson 
>> *Sent:* Friday, March 15, 2013 3:20 AM
>> *To:* jmol-users@lists.sourceforge.net ; Zhou 
>> Renjian
>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>
>>  The problem with MSIE 9 is fixed. A newly optimized version of
>> JSmol is in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_mar
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>> --
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar
>>> --
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster wit

Re: [Jmol-users] Jmol | lcaocartoon

[Robert Hanson]

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.
> >
> > The first three numbers are the axis direction; the last one is the
> > ratio of width to length.
> >
> > Will that do, Pshemak?
> >
> > Bob
> >
>
> Thanks Bob!  It works great.
>
> I did essentially the same with the isosurface (lobe) command.
>
> Can this be extended to "LONEPAIR" to get two electron dots that do not
> eclipse each other in some positions upon model rotations (i.e.
> reproduce the dots from lcaoCartoon LONEPAIR)?
>
> PM
>
> [...]
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

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 length.
>
> Will that do, Pshemak?
>
> Bob
>

Thanks Bob!  It works great.

I did essentially the same with the isosurface (lobe) command.

Can this be extended to "LONEPAIR" to get two electron dots that do not 
eclipse each other in some positions upon model rotations (i.e. 
reproduce the dots from lcaoCartoon LONEPAIR)?

PM

[...]


--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol | lcaocartoon

[Robert Hanson]

 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, 2013 at 3:31 PM, Robert Hanson  wrote:

> 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
> on an axis, and then create the orbitals. Probably simple sp2 ideas will
> work for one. We could consider adding something like sp2ya sp2yb sp2yc
> sp2xa sp2xb sp2xc, meaning: "Given the y (or x) axis as the p-orbital,
> depict the specified sp2 lobe.
>
> But first see if you can do it just with what we have now.
>
> Bob
>
>
> On Fri, Mar 15, 2013 at 2:42 PM, Pshemak Maslak  wrote:
>
>>  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)
>> hybridization scheme.
>>
>>
>> PM
>>
>>
>>
>>
>>
>>
>> On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak  wrote:
>>
>>>  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 Hanson wrote:

 Good catch, Michael. Yes, it's specifically a problem with "-sp3d" --
 easily fixed.

 See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
 http://chemapps.stolaf.edu/jmol/jsmol.zip


 Bob


 I have lcaocartoon-related questions. For CO2 (for example) the sp2
 lone pair lobes are shown as the sp lobes instead.  Similar outcome is
 observed for other linear molecules. Is that a general limitation?

 I know that the cartoons lobes can be drawn and oriented  (per demand)
 using "isosurface" command, but the lonepair dots are much harder if one
 wants them to keep up with molecular rotations and not eclipse each other
 at some orientations.

 Is there a simple way to deal with these issues?

 Thanks,

 PM







 On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote:

>  Jmol'ers,
> I am having trouble using lcaocartoon in a very specific case. If you
> look on this page, the antibonding orbitals render fine:
>
>  http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html
>
>  However, on this updated version of the same page using either JSmol
> or Jmol 13.0.12, the last antibonding orbitals (C3-H6 and C2-H8) fail to
> render properly.
>
>
> http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java
>
>  Those last antibonding orbitals use the "-sp3d" lobe, which appears
> not to render properly no matter what I try. I even tried back here with 
> no
> success:
>
>  http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
>
>  An sp3d lobe renders fine, but nothing happens when I try
> lcaocartoon create "-sp3d". Am I missing something?
>
>  Cheers, Mike
>
>  ---
> Michael Evans
> Department of Chemistry
> University of Illinois, Urbana-Champaign
>
>
> --
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
> http://p.sf.net/sfu/symantec-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



 --
 Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
 Wave(TM): Endpoint Security, Q1 2013 and

Re: [Jmol-users] Jmol | lcaocartoon

[Robert Hanson]

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
on an axis, and then create the orbitals. Probably simple sp2 ideas will
work for one. We could consider adding something like sp2ya sp2yb sp2yc
sp2xa sp2xb sp2xc, meaning: "Given the y (or x) axis as the p-orbital,
depict the specified sp2 lobe.

But first see if you can do it just with what we have now.

Bob


On Fri, Mar 15, 2013 at 2:42 PM, Pshemak Maslak  wrote:

>  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)
> hybridization scheme.
>
>
> PM
>
>
>
>
>
>
> On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak  wrote:
>
>>  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 Hanson wrote:
>>>
>>> Good catch, Michael. Yes, it's specifically a problem with "-sp3d" --
>>> easily fixed.
>>>
>>> See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
>>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>>
>>> Bob
>>>
>>>
>>> I have lcaocartoon-related questions. For CO2 (for example) the sp2 lone
>>> pair lobes are shown as the sp lobes instead.  Similar outcome is observed
>>> for other linear molecules. Is that a general limitation?
>>>
>>> I know that the cartoons lobes can be drawn and oriented  (per demand)
>>> using "isosurface" command, but the lonepair dots are much harder if one
>>> wants them to keep up with molecular rotations and not eclipse each other
>>> at some orientations.
>>>
>>> Is there a simple way to deal with these issues?
>>>
>>> Thanks,
>>>
>>> PM
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote:
>>>
  Jmol'ers,
 I am having trouble using lcaocartoon in a very specific case. If you
 look on this page, the antibonding orbitals render fine:

  http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

  However, on this updated version of the same page using either JSmol
 or Jmol 13.0.12, the last antibonding orbitals (C3-H6 and C2-H8) fail to
 render properly.


 http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

  Those last antibonding orbitals use the "-sp3d" lobe, which appears
 not to render properly no matter what I try. I even tried back here with no
 success:

  http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

  An sp3d lobe renders fine, but nothing happens when I try lcaocartoon
 create "-sp3d". Am I missing something?

  Cheers, Mike

  ---
 Michael Evans
 Department of Chemistry
 University of Illinois, Urbana-Champaign


 --
 Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
 Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
 endpoint security space. For insight on selecting the right partner to
 tackle endpoint security challenges, access the full report.
 http://p.sf.net/sfu/symantec-dev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users


>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>>
>>>
>>> --
>>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>>> endpoint security space. For insight on selecting the right partner to
>>> tackle endpoint security challenges, access the full report. 
>>> http://p.sf.net/sfu/symantec-dev2dev
>>>
>>>
>>>
>>> ___
>>> Jmol-users mailing 
>>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>> --
>>> Symant

[Jmol-users] second request - Please unsubsribe

[Mochena, Mogus D.]

Mogus D Mochena
Professor of Physics
Florida A & M University
Tallahassee, Florida 32307
Tel: 850-412-5740
Fax: 850-599-3577

--
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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

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) 
hybridization scheme.



PM






On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak > wrote:


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 mailto:p...@chem.psu.edu>> wrote:

On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
"-sp3d" -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example)
the sp2 lone pair lobes are shown as the sp lobes instead. 
Similar outcome is observed for other linear molecules. Is

that a general limitation?

I know that the cartoons lobes can be drawn and oriented 
(per demand) using "isosurface" command, but the lonepair

dots are much harder if one wants them to keep up with
molecular rotations and not eclipse each other at some
orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
mailto:evan...@illinois.edu>> wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding
orbitals (C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the "-sp3d" lobe,
which appears not to render properly no matter what I
try. I even tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I
try lcaocartoon create "-sp3d". Am I missing something?

Cheers, Mike

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign


--
Symantec Endpoint Protection 12 positioned as A LEADER
in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good
choice" in the
endpoint security space. For insight on selecting the
right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/jmol-users




-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev


___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net  

https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Symantec Endpoint Protection 12 positioned as A LEADER in The
Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good
choice" in the
endpoint security space. For insight on selecting the right
partner to
 

Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

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; :-)
I am strictly after the technical aspects.



But on another note, how would Jmol even know where to put the sp2 
hybridized lone pairs? The two ends of CO2 would have to know 
something about each other, since the lone pairs ought to be at right 
angles (I hope we can agree on that...). It seems a technological 
impossibility to lay down sp2 or even px and py lobes on the oxygens.
That is part of my question: is there a simple way (within lcaoCartoon) 
to draw sp2 lobes on oxygens and to do it in the correct relative 
orientation. As is, Jmol draws  sp lobes on oxygens. (There is a similar 
limitation for other linear molecules and other hybridization types).


p orbitals can be draw correctly by "manually" selecting their 
orientation  (px, py, or pz). Would it be possible to similarly define 
planes for lone pair lobes?


PM




Sounds like independent isosurfaces are the way to go.

On Friday, March 15, 2013, Pshemak Maslak wrote:

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 

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 Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem
with "-sp3d" -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for
example) the sp2 lone pair lobes are shown as the sp
lobes instead.  Similar outcome is observed for other
linear molecules. Is that a general limitation?

I know that the cartoons lobes can be drawn and
oriented  (per demand) using "isosurface" command, but
the lonepair dots are much harder if one wants them to
keep up with molecular rotations and not eclipse each
other at some orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
 wrote:

Jmol'ers,




--

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign



--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Make your web apps faster with AppDynamics
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Re: [Jmol-users] old Jmol, new JSmol

[Robert Hanson]

sorry -- http://chemapps.stolaf.edu/jmol/jsmol.zip



On Fri, Mar 15, 2013 at 12:07 PM, Richard Steane <
richard.ste...@ntlworld.com> wrote:

>   Which file/folder?
>
>  *From:* Robert Hanson 
> *Sent:* Friday, March 15, 2013 4:52 PM
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>
>  Get the latest file; I changed a few aspects so that MSIE of any version
> will not do this.
>
>
> On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane <
> richard.ste...@ntlworld.com> wrote:
>
>>   Bob
>>
>> I’m fairly sure all the files in the js directory are up to date.
>>
>> Richard
>>
>>  *From:* Robert Hanson 
>> *Sent:* Friday, March 15, 2013 3:19 PM
>> *To:* jmol-users@lists.sourceforge.net
>>  *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>
>>   More problems than that -- turns out MSIE 10 has the same problem (at
>> least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>> Also includes optimization of molecular orbital calculations, and a cool
>> link called "make a nanotube"
>>
>>
>>
>>
>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>>
>>> (and other files in that directory)
>>>
>>>
>>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>>>
 you haven't updated js/JSmolCore.js




  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
 richard.ste...@ntlworld.com> wrote:

>Bob
>
> Many thanks for this. IE9 now works perfectly from files on my laptop,
> but not via the www from my server (still perfect with FF, Chrome, 
> Safari).
>
> Actually your demo file shows the same symptoms: no blue outline seen,
> title tab still shows original wording not ‘jmolApplet0 is ready’.
>
> File URLs:
> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
> http://www.biotopics.co.uk/jsmol/jsmol.htm
>
> I hope it’s just something simple!
>
> Thanks for any help.
>
> Richard Steane
>   *From:* Robert Hanson 
> *Sent:* Friday, March 15, 2013 3:20 AM
> *To:* jmol-users@lists.sourceforge.net ; Zhou 
> Renjian
> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>
>  The problem with MSIE 9 is fixed. A newly optimized version of JSmol
> is in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Chemistry Department
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we want,
 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>> --
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_mar
>> --
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_mar
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/pe

Re: [Jmol-users] Jmol | lcaocartoon

[Robert Hanson]

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 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 Hanson wrote:
>>
>> Good catch, Michael. Yes, it's specifically a problem with "-sp3d" --
>> easily fixed.
>>
>> See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>> Bob
>>
>>
>> I have lcaocartoon-related questions. For CO2 (for example) the sp2 lone
>> pair lobes are shown as the sp lobes instead.  Similar outcome is observed
>> for other linear molecules. Is that a general limitation?
>>
>> I know that the cartoons lobes can be drawn and oriented  (per demand)
>> using "isosurface" command, but the lonepair dots are much harder if one
>> wants them to keep up with molecular rotations and not eclipse each other
>> at some orientations.
>>
>> Is there a simple way to deal with these issues?
>>
>> Thanks,
>>
>> PM
>>
>>
>>
>>
>>
>>
>>
>> On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote:
>>
>>>  Jmol'ers,
>>> I am having trouble using lcaocartoon in a very specific case. If you
>>> look on this page, the antibonding orbitals render fine:
>>>
>>>  http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html
>>>
>>>  However, on this updated version of the same page using either JSmol
>>> or Jmol 13.0.12, the last antibonding orbitals (C3-H6 and C2-H8) fail to
>>> render properly.
>>>
>>>
>>> http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java
>>>
>>>  Those last antibonding orbitals use the "-sp3d" lobe, which appears
>>> not to render properly no matter what I try. I even tried back here with no
>>> success:
>>>
>>>  http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
>>>
>>>  An sp3d lobe renders fine, but nothing happens when I try lcaocartoon
>>> create "-sp3d". Am I missing something?
>>>
>>>  Cheers, Mike
>>>
>>>  ---
>>> Michael Evans
>>> Department of Chemistry
>>> University of Illinois, Urbana-Champaign
>>>
>>>
>>> --
>>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>>> endpoint security space. For insight on selecting the right partner to
>>> tackle endpoint security challenges, access the full report.
>>> http://p.sf.net/sfu/symantec-dev2dev
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> --
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report. 
>> http://p.sf.net/sfu/symantec-dev2dev
>>
>>
>>
>> ___
>> Jmol-users mailing 
>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> --
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report.
>> http://p.sf.net/sfu/symantec-dev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> --
> Symantec Endpoint Protection 12 positioned as A LEADER 

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

[Robert Hanson]

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 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 selected
> select 638a and sidechain
> # 3 atoms selected
>
> Can you suggest a work around for this please? I'm trying to select the
> sidechains of all amino acids, modified or not.
>
> Thanks,
>
> Matthew
>
>
> --
> Matthew Betts PhD
> Russell Lab, CellNetworks Excellenz Cluster, University of Heidelberg
> BioQuant room 563, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
> http://www.russelllab.org/people/matthew/
> matthew.be...@bioquant.uni-heidelberg.de, +49 (0)6221 54 513 61
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Re: [Jmol-users] Jmol | lcaocartoon

[Michael Evans]

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 have to know something
about each other, since the lone pairs ought to be at right angles (I hope
we can agree on that...). It seems a technological impossibility to lay
down sp2 or even px and py lobes on the oxygens.

Sounds like independent isosurfaces are the way to go.

On Friday, March 15, 2013, Pshemak Maslak wrote:

>  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 
>
>  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 Hanson wrote:
>
> Good catch, Michael. Yes, it's specifically a problem with "-sp3d" --
> easily fixed.
>
> See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
> http://chemapps.stolaf.edu/jmol/jsmol.zip
>
>
> Bob
>
>
> I have lcaocartoon-related questions. For CO2 (for example) the sp2 lone
> pair lobes are shown as the sp lobes instead.  Similar outcome is observed
> for other linear molecules. Is that a general limitation?
>
> I know that the cartoons lobes can be drawn and oriented  (per demand)
> using "isosurface" command, but the lonepair dots are much harder if one
> wants them to keep up with molecular rotations and not eclipse each other
> at some orientations.
>
> Is there a simple way to deal with these issues?
>
> Thanks,
>
> PM
>
>
>
>
>
>
>
> On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote:
>
>  Jmol'ers,
>
>

-- 

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign
--
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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

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 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 mailto:p...@chem.psu.edu>> wrote:

On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
"-sp3d" -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example)
the sp2 lone pair lobes are shown as the sp lobes instead. 
Similar outcome is observed for other linear molecules. Is

that a general limitation?

I know that the cartoons lobes can be drawn and oriented 
(per demand) using "isosurface" command, but the lonepair

dots are much harder if one wants them to keep up with
molecular rotations and not eclipse each other at some
orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
mailto:evan...@illinois.edu>> wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding
orbitals (C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the "-sp3d" lobe,
which appears not to render properly no matter what I
try. I even tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I
try lcaocartoon create "-sp3d". Am I missing something?

Cheers, Mike

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign


--
Symantec Endpoint Protection 12 positioned as A LEADER
in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good
choice" in the
endpoint security space. For insight on selecting the
right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
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-- 
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




--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev


___
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--
Symantec Endpoint Protection 12 positioned as A LEADER in The
Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good
choice" in the
endpoint security space. For insight on selecting the right
partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
___

Re: [Jmol-users] Jmol | lcaocartoon

[Simone Sturniolo]

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
>
>
>
>
>
>
> On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak  wrote:
>
>>  On 3/11/2013 12:58 PM, Robert Hanson wrote:
>>
>> Good catch, Michael. Yes, it's specifically a problem with "-sp3d" --
>> easily fixed.
>>
>> See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>> Bob
>>
>>
>> I have lcaocartoon-related questions. For CO2 (for example) the sp2 lone
>> pair lobes are shown as the sp lobes instead.  Similar outcome is observed
>> for other linear molecules. Is that a general limitation?
>>
>> I know that the cartoons lobes can be drawn and oriented  (per demand)
>> using "isosurface" command, but the lonepair dots are much harder if one
>> wants them to keep up with molecular rotations and not eclipse each other
>> at some orientations.
>>
>> Is there a simple way to deal with these issues?
>>
>> Thanks,
>>
>> PM
>>
>>
>>
>>
>>
>>
>>
>> On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans wrote:
>>
>>>  Jmol'ers,
>>> I am having trouble using lcaocartoon in a very specific case. If you
>>> look on this page, the antibonding orbitals render fine:
>>>
>>>  http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html
>>>
>>>  However, on this updated version of the same page using either JSmol
>>> or Jmol 13.0.12, the last antibonding orbitals (C3-H6 and C2-H8) fail to
>>> render properly.
>>>
>>>
>>> http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java
>>>
>>>  Those last antibonding orbitals use the "-sp3d" lobe, which appears
>>> not to render properly no matter what I try. I even tried back here with no
>>> success:
>>>
>>>  http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
>>>
>>>  An sp3d lobe renders fine, but nothing happens when I try lcaocartoon
>>> create "-sp3d". Am I missing something?
>>>
>>>  Cheers, Mike
>>>
>>>  ---
>>> Michael Evans
>>> Department of Chemistry
>>> University of Illinois, Urbana-Champaign
>>>
>>>
>>> --
>>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>>> endpoint security space. For insight on selecting the right partner to
>>> tackle endpoint security challenges, access the full report.
>>> http://p.sf.net/sfu/symantec-dev2dev
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> --
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report. 
>> http://p.sf.net/sfu/symantec-dev2dev
>>
>>
>>
>> ___
>> Jmol-users mailing 
>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> --
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report.
>> http://p.sf.net/sfu/symantec-dev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> --
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on s

Re: [Jmol-users] Jmol | lcaocartoon

[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






On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak > wrote:


On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
"-sp3d" -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example) the
sp2 lone pair lobes are shown as the sp lobes instead.  Similar
outcome is observed for other linear molecules. Is that a general
limitation?

I know that the cartoons lobes can be drawn and oriented (per
demand) using "isosurface" command, but the lonepair dots are much
harder if one wants them to keep up with molecular rotations and
not eclipse each other at some orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
mailto:evan...@illinois.edu>> wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding orbitals
(C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the "-sp3d" lobe, which
appears not to render properly no matter what I try. I even
tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I try
lcaocartoon create "-sp3d". Am I missing something?

Cheers, Mike

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign


--
Symantec Endpoint Protection 12 positioned as A LEADER in The
Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good
choice" in the
endpoint security space. For insight on selecting the right
partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/jmol-users




-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev


___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net  
https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Symantec Endpoint Protection 12 positioned as A LEADER in The
Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice"
in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/jmol-users




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



--
Symantec Endpoint Protection 12 positioned as A LEADE

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

[Richard Steane]

Which file/folder?

From: Robert Hanson 
Sent: Friday, March 15, 2013 4:52 PM
To: jmol-users@lists.sourceforge.net 
Subject: Re: [Jmol-users] old Jmol, new JSmol

Get the latest file; I changed a few aspects so that MSIE of any version will 
not do this.




On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane  
wrote:

  Bob

  I’m fairly sure all the files in the js directory are up to date.

  Richard

  From: Robert Hanson 
  Sent: Friday, March 15, 2013 3:19 PM
  To: jmol-users@lists.sourceforge.net 
  Subject: Re: [Jmol-users] old Jmol, new JSmol

  More problems than that -- turns out MSIE 10 has the same problem (at least 
it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip


  Also includes optimization of molecular orbital calculations, and a cool link 
called "make a nanotube"






  On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

(and other files in that directory)




On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

  you haven't updated js/JSmolCore.js






  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane 
 wrote:

Bob

Many thanks for this. IE9 now works perfectly from files on my laptop, 
but not via the www from my server (still perfect with FF, Chrome, Safari).

Actually your demo file shows the same symptoms: no blue outline seen, 
title tab still shows original wording not ‘jmolApplet0 is ready’.

File URLs:
http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
http://www.biotopics.co.uk/jsmol/jsmol.htm

I hope it’s just something simple!

Thanks for any help.

Richard Steane
From: Robert Hanson 
Sent: Friday, March 15, 2013 3:20 AM
To: jmol-users@lists.sourceforge.net ; Zhou Renjian 
Subject: Re: [Jmol-users] old Jmol, new JSmol

The problem with MSIE 9 is fixed. A newly optimized version of JSmol is 
in  http://chemapps.stolaf.edu/jmol/jsmol.zip 



--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
___
Jmol-users mailing list
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  -- 
  Robert M. Hanson
  Larson-Anderson Professor of Chemistry
  Chair, Chemistry Department
  St. Olaf College
  Northfield, MN
  http://www.stolaf.edu/people/hansonr


  If nature does not answer first what we want,
  it is better to take what answer we get. 

  -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





  -- 
  Robert M. Hanson
  Larson-Anderson Professor of Chemistry
  Chair, Chemistry Department
  St. Olaf College
  Northfield, MN
  http://www.stolaf.edu/people/hansonr


  If nature does not answer first what we want,
  it is better to take what answer we get. 

  -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900



--

  --
  Everyone hates slow websites. So do we.
  Make your web apps faster with AppDynamics
  Download AppDynamics Lite for free today:
  http://p.sf.net/sfu/appdyn_d2d_mar 
--
  ___
  Jmol-users mailing list
  Jmol-users@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/jmol-users


  --
  Everyone hates slow websites. So do we.
  Make your web apps faster with AppDynamics
  Download AppDynamics Lite for free today:
  http://p.sf.net/sfu/appdyn_d2d_mar
  ___
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  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 w

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

[Robert Hanson]

Get the latest file; I changed a few aspects so that MSIE of any version
will not do this.


On Fri, Mar 15, 2013 at 10:36 AM, Richard Steane <
richard.ste...@ntlworld.com> wrote:

>   Bob
>
> I’m fairly sure all the files in the js directory are up to date.
>
> Richard
>
>  *From:* Robert Hanson 
> *Sent:* Friday, March 15, 2013 3:19 PM
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>
>  More problems than that -- turns out MSIE 10 has the same problem (at
> least it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip
>
> Also includes optimization of molecular orbital calculations, and a cool
> link called "make a nanotube"
>
>
>
>
> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:
>
>> (and other files in that directory)
>>
>>
>> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson wrote:
>>
>>> you haven't updated js/JSmolCore.js
>>>
>>>
>>>
>>>
>>>  On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
>>> richard.ste...@ntlworld.com> wrote:
>>>
Bob

 Many thanks for this. IE9 now works perfectly from files on my laptop,
 but not via the www from my server (still perfect with FF, Chrome, Safari).

 Actually your demo file shows the same symptoms: no blue outline seen,
 title tab still shows original wording not ‘jmolApplet0 is ready’.

 File URLs:
 http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
 http://www.biotopics.co.uk/jsmol/jsmol.htm

 I hope it’s just something simple!

 Thanks for any help.

 Richard Steane
   *From:* Robert Hanson 
 *Sent:* Friday, March 15, 2013 3:20 AM
 *To:* jmol-users@lists.sourceforge.net ; Zhou 
 Renjian
 *Subject:* Re: [Jmol-users] old Jmol, new JSmol

  The problem with MSIE 9 is fixed. A newly optimized version of JSmol
 is in  http://chemapps.stolaf.edu/jmol/jsmol.zip


 --
 Everyone hates slow websites. So do we.
 Make your web apps faster with AppDynamics
 Download AppDynamics Lite for free today:
 http://p.sf.net/sfu/appdyn_d2d_mar
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users


>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> Chair, Chemistry Department
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>  --
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
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[Jmol-users] phosphate of phosphorylated amino acids defined as mainchain

[Matthew Betts]

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 selected
select 638a and sidechain
# 3 atoms selected

Can you suggest a work around for this please? I'm trying to select the
sidechains of all amino acids, modified or not.

Thanks,

Matthew


-- 
Matthew Betts PhD
Russell Lab, CellNetworks Excellenz Cluster, University of Heidelberg
BioQuant room 563, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
http://www.russelllab.org/people/matthew/
matthew.be...@bioquant.uni-heidelberg.de, +49 (0)6221 54 513 61
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Re: [Jmol-users] old Jmol, new JSmol

[Richard Steane]

Bob

I’m fairly sure all the files in the js directory are up to date.

Richard

From: Robert Hanson 
Sent: Friday, March 15, 2013 3:19 PM
To: jmol-users@lists.sourceforge.net 
Subject: Re: [Jmol-users] old Jmol, new JSmol

More problems than that -- turns out MSIE 10 has the same problem (at least it 
does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip


Also includes optimization of molecular orbital calculations, and a cool link 
called "make a nanotube"






On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

  (and other files in that directory)




  On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

you haven't updated js/JSmolCore.js






On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane 
 wrote:

  Bob

  Many thanks for this. IE9 now works perfectly from files on my laptop, 
but not via the www from my server (still perfect with FF, Chrome, Safari).

  Actually your demo file shows the same symptoms: no blue outline seen, 
title tab still shows original wording not ‘jmolApplet0 is ready’.

  File URLs:
  http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
  http://www.biotopics.co.uk/jsmol/jsmol.htm

  I hope it’s just something simple!

  Thanks for any help.

  Richard Steane
  From: Robert Hanson 
  Sent: Friday, March 15, 2013 3:20 AM
  To: jmol-users@lists.sourceforge.net ; Zhou Renjian 
  Subject: Re: [Jmol-users] old Jmol, new JSmol

  The problem with MSIE 9 is fixed. A newly optimized version of JSmol is 
in  http://chemapps.stolaf.edu/jmol/jsmol.zip 


  
--
  Everyone hates slow websites. So do we.
  Make your web apps faster with AppDynamics
  Download AppDynamics Lite for free today:
  http://p.sf.net/sfu/appdyn_d2d_mar
  ___
  Jmol-users mailing list
  Jmol-users@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/jmol-users





-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





  -- 
  Robert M. Hanson
  Larson-Anderson Professor of Chemistry
  Chair, Chemistry Department
  St. Olaf College
  Northfield, MN
  http://www.stolaf.edu/people/hansonr


  If nature does not answer first what we want,
  it is better to take what answer we get. 

  -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900





--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar 



___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
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Re: [Jmol-users] old Jmol, new JSmol

[Robert Hanson]

More problems than that -- turns out MSIE 10 has the same problem (at least
it does today!) see http://chemapps.stolaf.edu/jmol/jsmol.zip

Also includes optimization of molecular orbital calculations, and a cool
link called "make a nanotube"




On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

> (and other files in that directory)
>
>
> On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:
>
>> you haven't updated js/JSmolCore.js
>>
>>
>>
>>
>> On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
>> richard.ste...@ntlworld.com> wrote:
>>
>>>   Bob
>>>
>>> Many thanks for this. IE9 now works perfectly from files on my laptop,
>>> but not via the www from my server (still perfect with FF, Chrome, Safari).
>>>
>>> Actually your demo file shows the same symptoms: no blue outline seen,
>>> title tab still shows original wording not ‘jmolApplet0 is ready’.
>>>
>>> File URLs:
>>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>>> http://www.biotopics.co.uk/jsmol/jsmol.htm
>>>
>>> I hope it’s just something simple!
>>>
>>> Thanks for any help.
>>>
>>> Richard Steane
>>>   *From:* Robert Hanson 
>>> *Sent:* Friday, March 15, 2013 3:20 AM
>>> *To:* jmol-users@lists.sourceforge.net ; Zhou Renjian
>>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>>
>>>  The problem with MSIE 9 is fixed. A newly optimized version of JSmol
>>> is in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_mar
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

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

[Robert Hanson]

(and other files in that directory)


On Fri, Mar 15, 2013 at 9:52 AM, Robert Hanson  wrote:

> you haven't updated js/JSmolCore.js
>
>
>
>
> On Fri, Mar 15, 2013 at 8:11 AM, Richard Steane <
> richard.ste...@ntlworld.com> wrote:
>
>>   Bob
>>
>> Many thanks for this. IE9 now works perfectly from files on my laptop,
>> but not via the www from my server (still perfect with FF, Chrome, Safari).
>>
>> Actually your demo file shows the same symptoms: no blue outline seen,
>> title tab still shows original wording not ‘jmolApplet0 is ready’.
>>
>> File URLs:
>> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
>> http://www.biotopics.co.uk/jsmol/jsmol.htm
>>
>> I hope it’s just something simple!
>>
>> Thanks for any help.
>>
>> Richard Steane
>>   *From:* Robert Hanson 
>> *Sent:* Friday, March 15, 2013 3:20 AM
>> *To:* jmol-users@lists.sourceforge.net ; Zhou Renjian
>> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>>
>>  The problem with MSIE 9 is fixed. A newly optimized version of JSmol is
>> in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_mar
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

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

[Robert Hanson]

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 same symptoms: no blue outline seen,
> title tab still shows original wording not ‘jmolApplet0 is ready’.
>
> File URLs:
> http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
> http://www.biotopics.co.uk/jsmol/jsmol.htm
>
> I hope it’s just something simple!
>
> Thanks for any help.
>
> Richard Steane
>   *From:* Robert Hanson 
> *Sent:* Friday, March 15, 2013 3:20 AM
> *To:* jmol-users@lists.sourceforge.net ; Zhou Renjian
> *Subject:* Re: [Jmol-users] old Jmol, new JSmol
>
>  The problem with MSIE 9 is fixed. A newly optimized version of JSmol is
> in  http://chemapps.stolaf.edu/jmol/jsmol.zip
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

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

[Richard Steane]

Bob

Many thanks for this. IE9 now works perfectly from files on my laptop, but not 
via the www from my server (still perfect with FF, Chrome, Safari).

Actually your demo file shows the same symptoms: no blue outline seen, title 
tab still shows original wording not ‘jmolApplet0 is ready’.

File URLs:
http://www.biotopics.co.uk/jsmol/glucosetestcutdown.html
http://www.biotopics.co.uk/jsmol/jsmol.htm

I hope it’s just something simple!

Thanks for any help.

Richard Steane
From: Robert Hanson 
Sent: Friday, March 15, 2013 3:20 AM
To: jmol-users@lists.sourceforge.net ; Zhou Renjian 
Subject: Re: [Jmol-users] old Jmol, new JSmol

The problem with MSIE 9 is fixed. A newly optimized version of JSmol is in  
http://chemapps.stolaf.edu/jmol/jsmol.zip 
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users