Thanks for the help everyone. Angel, the vrml output does "freeze" cylinders, so for simple situations with only one double bond I can position the molecule appropriately and get the structure I want. But when double bonds exist in different planes, I get a 3D snapshot as a vrml file with inconsistent planes.
Since posting the original question, I did discover that pymol can display bond order and export as vrml. I second the feature request for jmol! Dan ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: [email protected] >>> Angel Herráez <[email protected]> 09/22/09 4:03 PM >>> Hi Daniel Adding to what Bob has already replied, > from the Jmol application or signed applet: > write "XXX.vrml" > or > write VRML "XXX.xxx" In addition, Daniel, you have "export to VRML" in the pop-up menu (depending on the version of Jmol, in "Save" or in "File"). It will eventually be in the topbar application menu, but not yet. > multiple bonds -- I guess this depends upon your definition of "ideally." Others feel that "ideally" > the bonds should rotate so that there is never a question as to their order. In addition, this > introduces the ambiguity in cases such as H2SO4 where no reference plane exists. Definitely not > easy. If I remember correctly, VRML output by Jmol displays the two cylinders in some (random?) orientation that does not rotate as the Jmol view does. Just try it. Make sure to use v. 11.8 at least. ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
