Don't ask me to make sure the dotted line is on the inside. Just TOO
complicated.
On Fri, Sep 10, 2010 at 9:45 AM, Shore, Jay <[email protected]> wrote:
>
>
> Thank you Bob.
> I really really like it.
> I think that it looks great.
> I was happily surprised that when I “set smartARomatic false; reset
> aromatic” on your benzene it kept the bonds in the plane when I rotated the
> molecule. It did end up putting the dashed bond on the outside after
> rotating once though.
>
> Thank you again Bob.
> Jay
>
>
>
> On 9/10/10 8:19 AM, "Robert Hanson" <[email protected]> wrote:
>
> that can be experimented with at
> http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11
>
> I think this could be a new default. Let's talk about it.
>
> On Fri, Sep 10, 2010 at 7:31 AM, Robert Hanson <[email protected]> wrote:
>
> Uploading now a slight modification of this idea:
>
> # new feature: multipleBondSpacing
> # set multipleBondSpacing = -1 (default, varies with viewing angle)
> # set multipleBondSpacing = -0.5 (half that distance; varies with viewing
> angle)
> # set multipleBondSpacing = 0.35 (positive ==> fixed multiple bond
> spacing, Angstroms)
>
>
>
>
> On Fri, Sep 10, 2010 at 12:22 AM, Robert Hanson <[email protected]>
> wrote:
>
>
>
> On Thu, Sep 9, 2010 at 4:36 PM, Shore, Jay <[email protected]> wrote:
>
>
>
>
> I wonder if it would be easier to put it in the Sticks class – would that
> make it easier for use with external renderers (e.g. povray)?
>
>
> doesn't matter. The exporters use exactly the same rendering code. They
> just interpret the graphics commands a bit differently.
>
>
>
> For triple bonds, one could try to define a plane for each molecule so all
> triple bonds were oriented the same way. A vector, orthogonal to the triple
> bond, that goes through the three cylinders representing the triple bond,
> should be parallel to the plane defined for the molecule.
>
>
> Think about that.
>
>
> If the plane defined for the molecule corresponded to the plane with the
> maximum surface area (e.g., for benzene a plane perpendicular to the C6
> axis), most likely the planes of the double and triple bonds should be
> consistent.
>
>
> No way is that going to be efficient. Whatever it is, it has to be VERY
> simple.
>
> Let's try just double first, just to see what you think. Then tackle
> triple.
>
> version=12.1.11_dev
>
> # new feature: lockMultipleBonds (preliminary)
>
> set lockMultipleBonds 0.35 # set locked distance between cylinders for
> multiple bonds to be 0.35 Angstroms
> set lockMultipleBonds 0 # unlocks multiple bonds and lets them adjust
> distance between cylinders (Jmol default)
>
> Bob
>
>
>
>
>
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>
--
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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