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.
The special value Element-Specific for atoms colors the
atoms according to their element type (red for oxygen, blue
for nitrogen, etc). If you input file format encodes
atom color information, the read information will be used instead if
this option is selected. If you set any color except the default value for
hydrogen atoms, this color takes precedence over any other color source for
In the Bond Color field a special Split on Atoms
setting is included.
This option requests the splitting of the bond into two segments which
are colored in the color of the bonded atoms. Usually this option is combined
with a Element-Specific setting for the atom colors.||
|Normal coordinates||Pseudo-3D coordinates|
We thank Peter Ertl from Novartis Crop Protection AG for kindly allowing us to use the JME molecular editor.
The GIFs are plotted with a customized version of the GD GIF drawing library, which includes PNG output patches by Grep Roelofs. The 2D display coordinate generation (in case no 2D coordinates are passed in) is based on the algorithms of C. Shelley (J. Chem. Inf. Comput. Sci. 23 (1983), 61-65). It works nicely for most small and medium-sized organic compounds, but can sometimes fail in case of compounds with a cage structure.
Please contact Wolf-D. Ihlenfeldt, if you have any questions or comments. Commercial variants of this code are available.
Last Change: 2001-01-16 W. D. Ihlenfeldt