(The JME format usually does not include hydrogens). Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it then, it adjusts atoms into 3D, adds missing hydrogens and, using the built-in UFF force field minimization, generates a 3D model for the molecule. Its successor, JSME, needs no Java and runs in any browser using just JavaScript.Īmong their output formats there is a proprietary JME format, formed by a single line of text, specifying atom identities, coordinates and bonds. The JME Molecular Editor (by Peter Ertl) is a Java applet which allows to draw, edit and display molecules and reactions within a web page. To force the use of a certain server, you can do:Īnd put between the quotes the url in the proper request format use %FILE at the position where the SMILES string should be inserted into the url. Starting with Jmol 12.0.15 and 12.1.6, the NIH Cactus server is used instead. This ability was introduced in Jmol 12.0.RC15, using the web service at Indiana University.

(quotes may not be necessary, but are recommended for safety) Note that the unsigned applet is not allowed connection to external servers ad so does not support this method. To do this, you put a dollar sign before the SMILES string, or you use the smiles parameter. Jmol can read this format (not from file, just from a text string) as long as it can connect to a server that will do the conversion to a 2D or 3D format. the order in which atoms and bonds were added). That is, the same chemical compund can be assigned different SMILES depending on the software used to generate the SMILES string or how the structure was drawn (e.g. Note that there is more than one variant of SMILES strings. It can be thought of as a 1D format, specifying just atoms and their connections, no coordinates. This ( Simplified Molecular Input Line Entry Specification) is a standard format used for plain-text, single-line description of a chemical structure.

They can be put into text files or be just a text string fed into Jmol (inline loading). Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.

3ds file structure