Yes, and Jmol will read those mol files and convert them to 3D just like theyif you use

load "xxx.mol" filter "2D"

(although in the latest prerelease version of Jmol there could be a bug there. )


On Sun, Jun 27, 2010 at 9:03 AM, Otis Rothenberger <> wrote:

This is a point of information that you may already know. I just
discovered it, so I'll point it out just in case it's new information to
you or other JME users.

When the JME editor creates a molfile with JME.molFile(), it saves the
same stereo information contained in the SMILES and the proprietary JME
file. Where the JME file uses -1(up) and -2(down), the JME created
molfile puts a 1(up) and 6(down, go figure) in the connection table's
first extra info column, next to the bond in question.

JME uses this information when it reconstructs a 2D drawing with the
JME.readMolFile(str) function. In all of my playing, I simply missed
this point until now.


Otis Rothenberger

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