Phil, Best Guess:
Bob gets the 2D molfile via jmol._getMol2D(). This appears to be getting the 2D file from Resolver, and you are consequently at the mercy of Resolver. JSME will read JSmol’s 3D molfile extraction and render it as 2D - i.e. ignores z coordinates. You may or may not like the resulting 2D “projection,” but it will be related to your orientation of the 3D model. This is how I handle 3D to 2D at: http://chemagic.com/molecules/mini.html <http://chemagic.com/molecules/mini.html> Click Draw button - then click Model > Draw button. Otis -- Otis Rothenberger [email protected] http://chemagic.com > On Aug 19, 2015, at 11:09 AM, Philip Bays <[email protected]> wrote: > > PS: I can’t decide whether this is a bug or a feature. > >> Begin forwarded message: >> >> From: Philip Bays <[email protected] <mailto:[email protected]>> >> Subject: jmol/jmse issue >> Date: August 19, 2015 at 11:06:29 AM EDT >> To: Jmol Jmol <[email protected] >> <mailto:[email protected]>> >> >> I have played with this. At first I thought it had do with symmetry, but >> now I think it is the presence of an aromatic ring. For example, if you >> load toluene in the dismal applet, then rotate it to look down the >> methyl-ring bond, send it to jsme and then return it to jmol, it will rotate >> the structure (or re-download it) so that the ring is face-on. I do not see >> the issue in molecules without an aromatic ring, even substituted >> cyclohexane seem to retain the new orientation in jmol. >> >> Phil >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> [email protected] <mailto:[email protected]> >> >> > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > [email protected] <mailto:[email protected]> > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > [email protected] <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-users > <https://lists.sourceforge.net/lists/listinfo/jmol-users>
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