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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>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
>>>>
>>>>
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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
>>>
>>>
>>>
>>> _______________________________________________
>>> Jmol-users mailing
>>> [email protected]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
>>> [email protected]
>>> 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
>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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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
>
>
>
> ------------------------------------------------------------------------------
> 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
> [email protected]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:
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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
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