Thanks all! I thought based on the CDK demo web page that the
jchempaint and jmol would talk to each other, but it looks like there
is more going on than I thought. I'll look in to the suggestions that
I've got. Cheers.
Aaron Glimme
Berkeley High School
On 19-Nov, 2005, at 05:46, Miguel wrote:
Aaron wrote:
The first is the bond length seems really large in Jmol I'm having
trouble getting the files to look like a ball and stick model.
I may be mistaken, but I believe that jchempaint is saving the atom
positions in the incorrect units.
I believe that jchempaint stores the atom coordinates in pixels. Jmol
(and, I believe, the .mol format) expect the coordinates in angstroms.
The second is the geometry isn't working, the models
come out in a 2d plane,
jchempaint is a 2d drawing package.
is there some trick or script I need to run to get the
geometry right. I haven't been able to figure it out
yet, any help would be much appreciated.
Calculating 3D molecular structure from a 2D representation is a
non-trivial problem.
Miguel
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