Help File and Information

Dates and Features

• 2000-06-19: Add Play/Stop/Step Menue style
• 2000-06-19: Add Capped style
• 2000-06-05: Start of the service.

Examples

Options

Structure Input

In the moment we only support xyz file formats.

Hydrogen Addition

One of the curses of many of the more popular structure file formats is their lack to specify hydrogen atoms explicitly. It is often unclear whether an atom is a radical center, carbene or saturated. Since most compounds presumably are not exotic structures, we by default add hydrogen atoms (depending on the file format, this may involve heuristics). If you are sure your file specifies all hydrogen atoms there are, you may wish to suppress the hydrogen addition. The hydrogen addition takes place only if the compound is read from file. Smiles strings contain full hydrogen information.

Cycle Time

The period of one animation cycle in seconds.

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 -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.

Play/Stop Menu

If this flag is set, a menu will be added to the VRML scene. The menu includes a Play and a Stop button to start or stop the animation at any time. There is also a Step button which allows a stepwise animation through useraction.

Bond Color

This is the color of the bonds if they are plotted, i.e. the display style is not Spacefill, and the type of plot does not force a color split of the bond, i.e. both halve assume the color of the closer atom. This is the case with the Wireframe and Capped style. You can force a color split even in Ball&Stick mode when you select Split Atoms as special color. If your input data contains individual color information for the bonds, these color values are used if you select Specified.

Bond radius

This field specify the size of the bond radius.

Van der Waals Scale Factor

This control, which is active only when the plot style is Ball&Stick, controls the scaling of the atom spheres relative to their Van der Waals radii. If the display style is Spacefill, it is always 100%. If the display style is Capped, the size of the atom spheres is the selected bond radius.

Glossiness

This factor controls the appearance of the material used for atoms spheres and bond sticks. 75% is a kind of shiny plastic.

Transparency

If this value is not 0%, the atoms and bonds become gradually transparent. This can be especially useful if you want to integrate the VRML scene into another scene with auxiliary information. Note that not all VRML viewers are actually capable of rendering transparent objects, and in any case it is an expensive attribute for the graphics library.

Technology and Acknowledgments

Last Change: 2000-06-19, F. Oellien