Help File and Information


Dates and Features


Options

Structure Input
Our service supports three methods of input chemical structure data:
  • Molecular editor,
  • SMILES String,
  • direct loading of structure files (with surface information).
The most easiest way to create a new structure is to use the JME Molecular Editor (courtesy of Peter Ertl, Novartis).
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.

Surface Style
With this option you can choose the surface plot style - Surface, Mesh(Grid) and Dot Cloud.

Structure Style
With this option you can choose the plot style - Ball&Stick, Capped and Spacefill.

Bond Order
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 alpha-position to these, which typically corresponds nicely to the pi-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.

HUD Menu
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.
pi

Surface Color Coding
This control allows the selection of several color schemes for surface color coding (e.g. rainbow colors, red-white-blue, asa).

Scaling
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!
pi pi pi
originale relative user-defined


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) general-purpose 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 from Novartis Crop Protection AG for kindly allowing us to use the JME molecular editor. Novartis

We thank Tim Clark from the University of Erlangen for kindly allowing us to use the VAMP program.

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