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. 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. 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. Hopefully with my assumptions, I have not made too big of a$$ of myself. Jay On 8/20/10 11:47 PM, "Robert Hanson" <hans...@stolaf.edu> wrote: On Tue, Jul 13, 2010 at 1:34 PM, Shore, Jay <jay.sh...@sdstate.edu> wrote: Any suggestions as to where I should look in the code to try to remove this effect? no idea. It's important it does it this way, actually. What were you thinking would be better? Thanks, Jay On 7/12/10 11:33 PM, "Robert Hanson" <hans...@stolaf.edu <http://hans...@stolaf.edu> > wrote: Nice movie -- how do you do that? Enjoy the effect. Actually, the two lines are passing THROUGH each other, hidden by the spacefill. More dramatic with wireframe only :) Bob On Mon, Jul 12, 2010 at 9:31 PM, Shore, Jay <jay.sh...@sdstate.edu <http://jay.sh...@sdstate.edu> > wrote: Hello All, I think that there might be a possible problem with the representation of a double bond. It seems that when a molecule with a double bond is rotated about an axis orthogonal to the double bond and in the plane of the screen, the distance between the two cylinders that represent the double bond changes. This happens with perspective on and off. Below is a link to a movie I made using jmol, where you can see the effect. http://www.vchem.org/Movies/E-but-2-ene.html Jay ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first <http://sprint.com/first> <http://sprint.com/first> -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net <http://Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first <http://sprint.com/first> -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
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