I see. You must be using JME format to pass the data. Jmol has indeed a reader
for JME,
though is is declared as "not fully supported".
If I request Show > File Contents from Jmol, I see it as e.g.
8 8 C 9.44 -7.81 C 9.44 -6.41 C 8.23 -5.71 C 7.02 -6.41 C 7.02 -7.81 C 8.23
-8.51 C 8.23 -
4.31 C 8.23 -9.91 1 2 1 2 3 1 3 4 1 4 5 1 5 6 1 6 1 1 3 7 -1 6 8 -1
What I see is that the wedge-drawn bonds are specified as -1 bond order, and
for some
arcane reason Jmol is drawing them as wedge shaped bonds.
They can be redefined using
connect {C3} {C7} single
but by far the best solution is that you use MOL format for transferring the
structure between
JME and Jmol.
Also, I think you are really not retaining any stereo info, the model arrives
flat, so whether
you get the chair or boat is purely coincidential.
A separate question:
> As you may already know, the
> JME hydrogens must be explicitly inserted.
Does that mean you draw them manually? Or do you have some way of doing that in
one
go?
I've worked on my own 2D to 3D tool and faced that limitation.
------------------------------------------------------------------------------
Return on Information:
Google Enterprise Search pays you back
Get the facts.
http://p.sf.net/sfu/google-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
