Chemical MIME

Molden can display molecular geometries in a variety of formats, including lines, tubes, ball and stick, ribbons, and CPK. The user has some control over colors and sizes. Molden also has features designed for the display of proteins and crystal structures. The display can be exported as postscript, VRML, Povray, and image files. It can also be configured as a chemical mime viewer. 

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

Rzepa, H.S., Murray-Rust, R, Whitaker, B.J. The application of chemical multipurpose Internet mail extensions (Chemical MIME) Internet standards to electronic mail and World-Wide Web information exchange, J. Chem. Inf. Comp. Sci. 1998,38, 976-82. D01 10.1021/ci9803233. 

Chemical/MIME They are provided by the server, chemically-aware. ... 

Efforts are currently being undertaken to standardize the MIME types of a number of popular structure and spectral information exchange file formats. Even without the official blessing of the standardization organizations, the proposed chemical MIME data types are already used in a consensual fashion. This topic is continued in Internet-based Computational Chemistry Tools. The article includes an extensive table of the important chemical MIME format identifiers and their corresponding file formats and typical extensions. 

There are two basic mechanisms for transporting a three-dimensional chemical visualization as Internet data as a file with geometric objects or as a chemical MIME structure file. MIME files have been discussed in the previous paragraphs. They offer full chemical information, but only severely limited display choices, restricted to what is available to the local helper application and which, furthermore, cannot be controlled by the author. The transport of information such as orbital shapes, other than atomic coordinates, is not possible with the standard chemical MIME formats. 

A notable hybrid between representation by geometrical objects and structure data is the Molecular Inventor (MI) system from Silicon Graphics. MI is based on the standard Inventor file format, which is very similar to VRML 1,0, In addition to normal Inventor nodes, a MI file contains additional nodes which describe a chemical structure and attached physicochemical data. Because both arbitrary visualizations and structure-oriented data for potential extraction and further processing are stored together in one file, the best features from both approaches are combined. The major problem is portability MI viewers are available for free, only for Silicon Graphics platforms. Commercial versions for PCs can now be purchased. Compared to the much easier and generally free availability of viewers both for pure VRML and for chemical MIME data, this severely reduces the general acceptance of this product. 

D coordinates for a small set of molecules are defined using standard modeling techniques, saved in one of the chemical MIME formats, associated with the appropriate MIME type (e.g., chemical/x-mdl-molfile, chemical/x-pdb, chemical/x-xyz) and placed on a Web server. The molfile format in particular carries an atom connection table, which will allow structures encoded in this format to serve as a substructure search query in an appropriate database if necessary. 

At this point, a molecule coordinate file selected by the user needs to be displayed within a frame of the browser window. Generic browsers are capable of displaying only HTML documents, and some image formats, and at this point the MIME mechanism must be invoked for handling other types of media content. If the user has defined a so-called helper program associated with the three possible chemical MIME types represented in the selection list, then this program will be activated and the coordinate files passed to it as data. 

The approach above enables a document to reference chemical data in terms of a small set of chemical MIME types. 

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