I, too, have always thought that it was a bit weird to see the double bond lines move around, and I think perhaps it really was just because nobody had devised a simple way of defining the bond plane, finding the normal, and working with that. One thing to realize is that prior to my implementing the code for hybridization and lcaoCartoons and such, none of this was possible. As it is, this multipleBondSpacing parameter business was actually almost trivial to implement, since I had all that infrastructure already. So it's reasonable to reassess the default visualization. If we do that, I'd like to go back and implement it in both 12.0 and 12.1 and call it a "Version 12" feature. It's the sort of thing that is at that level, I think.
I seriously doubt anybody is particularly enamored by the current method of twisting around multiple bonds to always be visible. Might be interesting to have Miguel's input here, as he probably devised this in the first place. What I'm a bit worried about is that it will escalate. Ideas like this tend to do that. getting the dotted bond, for example, on the "correct" side might seem like a bug rather than just an unimplemented feature. That's a MAJOR challenge if you want to do it right. As it is, I suppose we still have that issue, but it doesn't seem quite as "bug-like" because the "side" keeps changing. One good argument for doing this, I think, is that the "cartesian" exporters (VRML, in particular) would have a better representation. I can't remember at this moment how those work now.... The nice thing is that now at least we can very simply set the default to something other than what it has been for so many years. Bob On Fri, Sep 10, 2010 at 12:36 PM, Thomas Stout <[email protected]>wrote: > > > 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 <[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 >>>> >>>> >>> >>> >>> -- >>> 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 >> [email protected] >> 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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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