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 <[email protected]> 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 <[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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>>>>> tackle endpoint security challenges, access the full report.
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>>>>> Jmol-users mailing list
>>>>> [email protected]
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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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
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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:
>> http://p.sf.net/sfu/appdyn_d2d_mar
>> _______________________________________________
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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
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