[Jmol-developers] [ jmol-Bugs-964835 ] deal with lone pairs

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Bugs item #964835, was opened at 2004-06-02 03:26
Message generated for change (Comment added) made by hansonr
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Miguel (migueljmol)
Assigned to: Bob Hanson (hansonr)
Summary: deal with lone pairs

Initial Comment:
need to come up with some strategy/approach for dealing
with lone pairs of electrons ... as in
samples/xyz/met-enkaphalin_movie.xyz

---------------------------- Original Message
---------------------------- Subject: Re:
[Jmol-developers] element symbol LP
From:    "Bob Hanson" <ha...@st...>
Date:    Tue, June 1, 2004 18:52
To:      jmo...@li...
--------------------------------------------------------------------------

Rendering of a lone pair would be nice. I suppose
someone out there has a  program that wants to "fake" a
display of a lone pair of electrons. This could take
the shape of anything from a teardrop (point on closest
atom; center  of tear on xyz coordinate) or, more
likely, just a pair of dots like this:


     X :

whose imaginary connecting line is perpendicular to the
line connecting the xyz  coordinate to that of the
nearest atom.

Chime ignores these.


Miguel wrote:

>>>The file samples/xyz/met-enkaphalin_movie.xyz
contains the element symbol
>>>'LP'
>>>...
>>>H    2.056   2.462  -4.930
>>>S    3.057   4.570  -4.353
>>>LP   3.502   4.170  -4.030
>>>LP   2.652   5.106  -4.475
>>>C    3.658   4.243  -6.025
>>>H    4.409   3.452  -5.958
>>>...
>>>
>>>Do you know what this is supposed to be?
>>
>>Lone pair.

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>Comment By: Bob Hanson (hansonr)
Date: 2004-07-15 09:13

Message:
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Miguel,

Rendering: Yes, there should be a VERY close atom. In the
case sited, it's 68 pm--a very short distance. Shouldn't be
any problem at all. I think it's important to identify that
atom and to place the two dots on a perpendicular to the
line connecting the "LP" and atom X.

Default Color: white 

I would stay far away from the "tear-drop" idea. While some
lone pairs have that nature, many do not. (Some are more
p-orbital shaped, for example, and some are spherical.)
Applying that model to all seems inappropriate to me. Of
course, I suppose if someone has PLACED the LP in the file,
maybe they do want them rendered as tear drops. Hmm. Later
on that.

Bob


----------------------------------------------------------------------

Comment By: Miguel (migueljmol)
Date: 2004-07-15 04:50

Message:
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user_id=1050060

Bob,

Within Jmol we will represent a Lone Pair as an atom with
some high element number (110 or something like that). 

Internally, its element symbol will be Lp. The 'p' needs to
be lower case because all elements have a lower case second
letter. We probably will be able to render it as ALLCAPS LP
for display purposes. 

The easiest way to render a lone pair would be as two small
spheres. 

The Lp *atom* would have a size just like all atoms. But we
would scale this size by a factor of 8 (or something). 

The simplest thing would be to always display the Lp in the
vertical vertical orientation or horizontal if you prefer).
That way, we don't have to make the rendering a function of
the orientation. 

If we *do* want to change the orientation of the Lp during
rendering, then we need to associate the Lp with an atom.
This means making a bond in the internal data structures
between the Lp and its associated atom. If we did this, then
we could orient the dots so that they were always
perpedicular to their associated atom. 

But, this means that we need to have some way to identify
which atom the Lp is bonded to. The only place I have ever
seen an Lp is in a .xyz file ... where there is no
connectivity information. 

Q: How does one determine which atom an Lp is associated
with? Is it the closest one. 

Q: By default, what color should an Lp be? 

After we do all of this, then we can think about changing
the shape to a teardrop (or whatever). 


----------------------------------------------------------------------

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