Help File and Information

Dates and Features


Structure Input
There are several possibilities to input a structure. The upper input field accepts SMILES strings as structure specifications.If you are familiar with the syntax, you can type in simple queries manually. However, most of the time you will want to use some graphical structure editor. If your favorite desktop molecule editor supports Copy&Paste of SMILES strings, you can simply use this editor, put the structure on the clipboard as a SMILES string and paste it into the entry field. Editors which support this operation include ChemWindow and ChemDraw.

If you enter a structure file via the file selector box, it can be in any of the major formats, including MDL Molfile (or SD files), PDB, JCAMP/CS, CIF (Chiron interchange format, not Crystallographic formats), MDL RXN (Reaction file), RDF (Reaction Data File format), XYZ, SMD4, SMD5, CTX, CACTVS (binary, ascii, cbase), SMILES (including SMARTS subset), Compass, 441, Gaussian/Input, Gaussian/Archive, SCF, SHEL-X, XTEL (XTELPlot input format), Cerius (Ascii exchange format of CeriusII Toolkit), Sharc (SHift ARChives format), Alchemy, Hyperchem, Molconn-Z, Sybyl, Sybyl2, SLN (Sybyl line notation). The structure source (smiles string on the input field or data file) and the file format are automatically recognized.

As a third option, you can start a Java editor by clicking on the Start Editor button below the input field. You must use a WWW browser with Java support (Netscape, Internet Explorer) for this to work, and you must have Java enabled, which is an option in the browser configuration panel. A new window with a structure drawing application will open, or come to the top. Read the editor instructions on how to operate the program.

Take a look at our Example page.

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.

With this option you can choose the plot style - Ball&Stick, Capped, Wireframe, Spacefill and All Styles.
When All Styles is selected, you are able to switch between the four plot styles (Ball&Stick, Capped, Wireframe and Spacefill) within the VRML scene. To change the style you have to click the blue ball. (Example or take a look at our Example page)

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.

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.

Atom Labels
This option can be choose to mark the atoms with their Attom Labels. The Label size and Label color fields specify the size and the color of the labels. (Example or take a look at our Example page)

Atom Properties
If this flag is set, various Atom Properties will be add to the VRML scene. You can make a choice between the Atomic number, the Atom symbol, the Polarizability and the Sigma charge (by Gasteiger). The fields Value size and Value color specify the size and the color of the Property values. (Example or take a look at our Example page)

This option, which is active only when the plot style is Ball&Stick or All Styles (Ball&Stick), allows the calculation of the Atom distance, Bond angle and Torsional angle. You only have to click on the atoms of interest. The display shows the Atom coordinates, Atom distance between the to last atoms selected, the Bond angle of the three last atoms selected and the Torsional angle of the four last atoms selected. To set all values to zero click on the Reset button. (Example or take a look at our Example page)

Structure Code
This option allows the hidden inclusion of the structure code in the VRML file. Some molecule editors like CACTVS csed are able to extract this information from the VRML scene and thus can operate on the VRML file like it was a structure exchange file.

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.

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 very rapidly.

3D atomic coordinates are computed, if not contained in the input file, by the algorithm of the CORINA program, which is used here as a dynamically loaded module.

We thank Peter Ertl from Novartis Crop Protection AG for kindly allowing us to use the JME molecular editor. Novartis

Please contact Frank Oellien, if you have any questions or comments.

Last Change: 2001-04-02, F. Oellien