Nevertheless, I would like to note the problem that happens when a Transition
State (TS) molecule is sent to the molecular hyperglossary.
A TS is caracterized by a distance/s greater than the normal one/s between two
(or more) atoms. This fact makes that there is not a connection between those
atoms in a pdb form (because the distance is greater than the sum of the
covalent radius) and therefore the bond/s are not displayed when the TS is
visualized (eg. with RasMol). In adddition, the scripts for converting 3D into
2D are not able to cope with this limitation, and the final result is an
unsuitable 2D visualization.
We have done a simple test: see the molecule called "Thiele's Ester" in the
ECTOC Hyperglossary Tester:
This molecule is the TS of the Diels-Alder reaction between two substituted
ciclopentadienes. As a result of the "missing" bonds, the 2D picture shows
two issolated molecules.
Now the question is: how can we improve the scripts in order to "recognize"
transition state molecules?