On Mon, Aug 23, 2010 at 11:01 AM, Shore, Jay <jay.sh...@sdstate.edu> wrote:
>
> I really like jmol’s multiple bond representation – it is the only
> visualization tool that I know of that actually
> that actually does multiple bonds.
>
> The distance between the cylinders (that represent a double bond) changes
> when the molecule is rotated depending on the relative orientation of the
> bond and the axis of rotation. For example, if you spin a molecule with a
> double bond on an axis parallel to the double bond there is no change in
> distance between the cylinders representing the double bond. If you spin
> the same molecule on an axis perpendicular to the double bond, the distance
> between the cylinders change.
>
> correct
> If you spin benzene about an angle perpendicular to one of the double
> bonds, the distance between the cylinders for the different double bonds
> change differently. If you turn smartAromatic off, the distance between the
> dashed line and the solid line is different depending on the relative
> orientation of the spin axis and the bond axis.
>
> correct
> I would assume that the apperent distance between the two cylinders
> representing a double bond should always be the same no matter how the
> molecule was rotated. I would also assume that when a molecule is rotated
> the double bonds are rotated to keep their apparent distance the same. I
> just wonder if the angle between the the bond axis and the rotation axis was
> considered when rotating the double bonds.
>
>
Jay, that's not the algorithm. The algorithm sets the distance between the
lines of a double bond to be proportional to the distance between the bond
endpoints on the screen. This ensures smooth transition between vertical and
horizontal bonds and scales the bond to zoom appropriately.
Notice that multiple bond lines are not shown in perspective -- always
parallel. This is because they are calculated using 2D screen coordinates,
not 3D molecular coordinates (and, I guess, that was not desired).
So let's see, is there anything wrong with the first assumption? Given that
assumption:
1) What should looking straight down a double bond look like?
2) Starting with whatever your answer to (1) is, now rotate that model by a
slight amount around x:
rotate x 20
Now what should it look like?
2) Starting with whatever your answer to (1) is again, now rotate that model
by a slight amount around y:
rotate y 20
Now what should it look like?
3) How does one smoothly get from pictures (2) to (1) to (3)?
I think that's the problem solved by the algorithm used. But if you have any
example software that does this more to your liking, show it to us so we can
see. Maybe there's a better algorithm.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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