Something else to consider is the intent of the display. Sitting at the screen rotating a molecule by hand to get to a particular view of the molecule is one thing. Creating a movie which is is presumably intended to illustrate something about the molecule is another.
In the former having things jump around a bit in order to always show the imposed bond orders is acceptable. In the latter this is often just distracting to the eye and could be dispensed with. Our brains are good at managing the loss of a particular visual cue yet still retaining the information so having what was a double-bond gradually (key word) morph into single for a moment as it rotates is not a real problem. I'd like to see a switch which I could set to have the sticks of multiple bonds remain in a single plane for movies. Rich On Wed, September 8, 2010 11:17 pm, Robert Hanson wrote: > [should move this to Jmol-Developers list...] > > Jay, before you go after this, I'd like to hear what you expect to observe > under various conditions -- > > A --- bond is vertical and is rotated along its axis. > B --- bond is vertical and is rotated perpendicular to its axis until it > is > pointing into the plane. > C --- bond is horizontal and is rotated around the y axis until it is > pointing into the plane. > > B then reverse of C. > > I'm just interested in what you are expecting. > > If you are interested in playing, the algorithm is in > org.jmol.shape.SticksRenderer.java, method drawBond(int). Notice that it > is > working entirely in 2D, not 3D. > > Bob > > On Wed, Sep 8, 2010 at 9:42 PM, Shore, Jay <jay.sh...@sdstate.edu> wrote: > >> >> >> Thank you Bob for your thorough explanation. I think that I finally >> understand. >> >> While jmols biggest advantage may be with its ability to let users >> interact with structures, it is also an excellent tool for making movie, >> especially with the povray export. If I wanted to make a movie of a >> molecule rotating about the y-axis, the distance between the two >> cylinders >> would not have to change, because I would not have to worry about >> rotation >> about any other axis. Do you think that it would be simple for me to >> make >> this modification? I have looked at the code, but I have not found >> where >> the distance between the two cylinders is defined and the algorithm you >> mentioned is implemented. I would very much appreciate if you could >> give me >> some hints as to how I can disable the changing of the distance between >> the >> two cylinders representing a double bond. >> >> Thank you very much. >> Jay >> >> >> >> >> On 8/24/10 3:16 PM, "Robert Hanson" <hans...@stolaf.edu> wrote: >> >> >> >> On Mon, Aug 23, 2010 at 11:01 AM, Shore, Jay <jay.sh...@sdstate.edu> >> wrote: >> >> >> I really like jmols 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 >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net Dev2Dev email is sponsored by: >> >> Show off your parallel programming skills. >> Enter the Intel(R) Threading Challenge 2010. >> http://p.sf.net/sfu/intel-thread-sfd >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > ------------------------------------------------------------------------------ > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd_______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. 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