My strong preference would be to move the default to fixed (eg, "set multipleBondSpacing = 0.35"). My opinion is that the double bonds always rotating to face the viewer is a little creepy -- sort of like Mona Lisa's eyes following you around the room! :) I very much feel that the double bonds should remain in the plane of the aromatic system to which they belong -- ie orthogonal to the pi-cloud.
-Tom On Fri, Sep 10, 2010 at 6:19 AM, Robert Hanson <hans...@stolaf.edu> 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 <hans...@stolaf.edu> 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 <hans...@stolaf.edu>wrote: >> >>> >>> >>> On Thu, Sep 9, 2010 at 4:36 PM, Shore, Jay <jay.sh...@sdstate.edu>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 >>> >>> >> >> >> -- >> 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 >> > > > > -- > 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 > > > ------------------------------------------------------------------------------ > Automate Storage Tiering Simply > Optimize IT performance and efficiency through flexible, powerful, > automated storage tiering capabilities. View this brief to learn how > you can reduce costs and improve performance. > http://p.sf.net/sfu/dell-sfdev2dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > >
------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
