Help File and Information
Dates and Features
- 2002-11-09: COSMO files can be uploaded.
- 2002-11-09: Background color option.
- 2001-01-30: Start of the service.
Our service supports three methods of input chemical structure data:
The most easiest way to create a new structure is to use the
JME Molecular Editor (courtesy of Peter Ertl, Novartis).
- Molecular editor,
- SMILES String,
- direct loading of structure files (with surface information).
After drawing a structure, press the 'Submit Molecule' button in the editor
window and the corresponding SMILES String will be transfered to the main form.
Users who are familiar with the SMILES format can also input the SMILES String by hand.
The third input possibility is useful for people with structure files on their
disk. They can select their structure file by clicking the 'Browse...' button in the main frame. In the moment we only support the VAMP and COSMO file format.
With this option you can choose the surface plot style - Surface, Mesh(Grid) and Dot Cloud.
With this option you can choose the plot style - Ball&Stick, Capped and
If this flag is set, multiple bonds are plotted by an equivalent number of distinct
lines or (downsized) bond cylinders. The bonds are positioned below and above
the averaged plane constructed from the atoms of the bond
and all atoms in -position to
these, which typically corresponds nicely to the
-Orbitals. Note that in some
file formats (PDB, XYZ) the bond order must be determined algorithmically, which is
especially difficult if hydrogen atoms are lacking.
If this flag is set, a menu will be added to the VRML scene. The menu includes a
legend for the value range, a slider for the surface transparency and several buttons. The Surface buttons allow a interactive switching between the surface plot styles. The Structure buttons are usefull to switch the structure on or off.
Surface Color Coding
This control allows the selection of several color schemes for surface color coding (e.g. rainbow colors, red-white-blue, asa).
This control, allows different values for the Max/Min scale.
Original: Original Max/Min values.
Relative: Max/Min have the same absolute value and depend on the biggest absolute value from the computation. The value 0 is in the middle of the colorscheme.
User-defined: The user can choose Max/Min. Max/Min (absolute values) must be bigger or the same as the original values!
Technology and Acknowledgments
The CGI script connected to the form
runs on a non-GUI version of a class of progammable (in
Tcl/Tk and Extensions)
chemical structure handling programs of the
CACTVS system. Using the
powerful scripting language interface of these programs,
it is possible to implement nearly every graphical or
structure handling application very rapidly.
We thank Peter Ertl
Novartis Crop Protection AG for kindly allowing us to use the
JME molecular editor.
We thank Tim Clark
University of Erlangen for kindly allowing us to use the
We also thank Johann Gasteiger
from the University of Erlangen
for kindly allowing us to use the CORINA program.
Last Change: 2001-01-30, Frank Oellien