Thanks Bob. If you could keep me up to date on any more updates with showing
these lone pairs and orbitals, I would really appreciate it. Thanks again.
David
On 6/9/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
I guess for AX3E (ammonia) then lone pair is
lcaocartoon create "sp3"
but I still like the idea of
lcaocartoon create "lp"
and will create that as well now.
Bob
Bob Hanson wrote:
> actually, there's no bug (for H2O). The documentation was wrong. The
> command you want is
>
> select (atomno=3)
> lcaocartoon create "lpa"
> lcaocartoon create "lpb"
>
> for ammonia, it should be
>
> lcaocartoon create "lp", but I see that is not working and IS a bug.
> I'll look into it.
>
> If the smoothness of the lobe is not sufficient, use something like
> the following instead, with the isosurface command:
>
> isosurface resolution 15 lcaocartoon "sp3" (atomno=4)
>
> Bob
>
>
>
>
> David Kim wrote:
>
>> Idealy I would want them to be a tear-shaped lobe with two dots
>> within. If that is not possible then I think that a tear-shaped lobe
>> would be best for the purposes of visualizing molecular structure.
>> Thanks.
>>
>> On 6/9/07, *Bob Hanson* <[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]>> wrote:
>>
>> yes, so what do you want the lone pair to look like? two dots? a
>> tear-shaped lobe? etc.
>>
>>
>> David Kim wrote:
>>
>> > For example, in a molecule of H2O we know that the tetrahedral
>> > structure is caused by the interaction of the lone pairs and the
>> two
>> > hydrogen molecules. I would like to be able to view the lone
>> pairs so
>> > that I could visually show why water takes on the bent shape.
>> Is it
>> > kind of clear what I am going for? If not feel free to email me
>> again.
>> > Thanks for all your help.
>> >
>> > On 6/9/07, *Bob Hanson* <[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]>
>> > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
>> >
>> > What's your definition of a "lone pair" ?
>> >
>> > David Kim wrote:
>> >
>> > > I was wondering if it is possible to display lone pairs in
>> Jmol
>> > If so,
>> > > how would I switch between having them on and off? Thanks
in
>> > advance.
>> > >
>> > > David Kim
>> > >
>> >
>>
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>> > --
>> > Robert M. Hanson
>> > Professor of Chemistry
>> > 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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