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.
In the moment we only support xyz file formats.
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.
The period of one animation cycle in seconds.
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
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.
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
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
This factor controls the appearance of the material used
for atoms spheres and bond sticks. 75% is a kind of shiny plastic.
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
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
Last Change: 2000-06-19, F. Oellien