Chemical MIME types are the currently favoured mechanism for delivering such information via the Internet. Although MIME can be used within the Gopher and Mail Internet protocols, it is best implemented within the World-Wide Web infra structure. This enables hyperlinks to be inserted into e.g. the text or image of a paper which points to molecular data stored in a standard format. When the hyperlink is activated, the molecular data will be automatically transferred to your computer and can be processed using a pre-defined "helper" program. Such "Internet modelling kits" have also been referred to as "hyperactive molecules".
These notes set out how to insert such molecular hyperlinks into HTML documents, how to acquire and specify molecular "helpers", and how to set up the mechanism on your own World-Wide Web server if you wish. The specific details have been organised according to the three principal types of computer most commonly used for WWW browsing. This document is NOT a HTML primer, on which you can get much more information here which contains a comprehensive FAQ list, or here which is the NCSA guide.
The following list indicates the filename suffixes you will have to assign in
order to add other types of document;
.mol MDL Molfiles .xyz Files saved in the XMol format (highly concise and shorter than e.g. .gal) .pdb The Brookhaven FormatYou can use other formats, but you will have to define the appropriate MIME types.
If you want to use the ECTOC server to save your HTML and
coordinate files, enter a <A HREF="1prc.pdb">local file reference</A>
and send both the HTML file and the molecular data file to the ECTOC conference. Note also that local
references can be globally converted to absolute references by the addition
of a line of the following type to the header field at the top of the HTML
<HEAD> <BASE HREF="http://www.ch.ic.ac.uk/"> </HEAD>
Whilst X-Mosaic appears to support this syntax, other browsers may not.
XMol is best suited for the visualisation of data derived from e.g. programs such as Gaussian 92, MOPAC etc, and can also be used for generating animations of reaction paths, IRCs, normal vibrational modes and dynamics runs. Installation is via a Makefile, althoug be warned that this generates quite a number of directories and files, and is best done as Superuser. A new release of XMol is expected shortly.
RasMol consists of just one single executable file which should be installed either in your own directory, or in a generic directory such as /usr/local/bin (as Superuser). and is the program of choice for the visualisation of large molecules. It also supports a highly flexible "markup" syntax, which can be used via a script such as CSML to annotate the structure in order to highlight particular aspects.
The Iris Explorer EyeChem suite offers the capability for display of a number of molecular properties, but currently only runs on SGI systems with Version 2.2 of Explorer.
chemical/x-pdb; rasmol %s chemical/x-xyz; rasmol xyz %s chemical/x-pdb; xmol -readFormat pdb %s chemical/x-mopac; xmol -readFormat mopii %s chemical/x-mopac-out; xmol -readFormat mopo %s chemical/x-gaussian; xmol -readFormat gaussin %s chemical/x-gaussian-log; xmol -readformat gausso %s chemical/x-xyz; xmol -readFormat xyz %s chemical/x-mopac-out; eyemopac %s chemical/x-gaussian-log; eyeg92 %s chemical/x-csml; csml %s application/x-mathematica; math %sYou must have a path defined to the relevant programs. If these are stored in other locations, you can specify the path as e.g.;
chemical/x-pdb; /usr/local/bin/rasmol %sThere are also occasions when you may wish to open up a command line interface to the helper program (i.e. Rasmol uses this extensively);
chemical/x-pdb; xterm -T title -e rasmol %sTwo windows will then appear on your screen rather than the usual one.
chemical/x-pdb pdb chemical/x-xyz xyz chemical/x-mopac mop chemical/x-mopac-out moo chemical/x-mopac-vib mvb chemical/x-gaussian gau chemical/x-gaussian-log gal chemical/x-csml csml application/x-mathematica maAfter these modifications, you will have to kill the httpd process and restart it by typing /usr/local/etc/httpd/httpd
Kinemage consists of two programs, a pre-processor to convert pdb files to "Kin" format, and the Kin viewer MAGE. "Kinemage" type files have been proposed as a chemical MIME type in their own right. Mail firstname.lastname@example.org for further details.
Ball & Stick supports a wide variety of file types, including MOPAC, SHELX, MOLDAT etc, but the files have to be opened manually using the Import Menu item and are limited to the display of 40 atoms in the demo version.
Chem3D Viewer only reads files in CSC format, although the full version of the program can read MOPAC, PDB and a large variety of other files.
MicroWorld is an impressive display package, but does not read most file formats directly and requires that you use Babel to convert from the standard formats first.
RasMac for the Macintosh was released in October 1994. If you know of other freely distributable Macintosh Molecular visalisers, and in particular ones which do not require user intervention on startup (i.e. the ones above all throw up a user dialog before displaying an image), then Henry Rzepa would be delighted to hear from you.
To use MacWeb, add the following MIME types to the configuration;
chemical/x-mopac (suffix mapping .mop, 7-bit EOL translations) chemical/x-pdb (suffix mapping .pdb, 7-bit EOL translations) chemical/x-kinemage (suffix mapping .kin, 7-bit EOL translations) application/x-mathematica (suffix mapping .ma, 7-bit EOL translations)
We have implemented a simple such mechanism for annotating a Rasmol display, which we have found particularly useful for enhancing navigation through a complex biomolecule via the WWW mechanism.
To implement this mechanism on an X-Window workstation,
you will need to first acquire
if it is not already installed on your system (most do nowadays).
In the spirit of the html markup language, we have defined a simple
chemical structure markup language
which is interpreted by a short
script resident on the local machine.
The way it all works is as follows. Ensure that your .mailcap file
has an entry of the following type
If you are running a HTTPD server, the mime.types file has an entry of the type;
Place the CSML script in a suitable directory such as /usr/local/bin. A typical set of CSML instructions might take the form;
gly39 red spacefill atomno=410 blue dot chain yellow ribbon etcand would be saved on the HTTP server with the suffix .csml in the filename. A hyperlink is then made to this file from a suitable point in a document. When activated, the file is copied to the local system, and run as the input to the CSML script. This script ensures that the instructions contained in the file are passed to a running Rasmol process which ensures that the selected residues or atoms are suitably highlighted. To see an example of this process in action, click here.
If you wish to print a document, all WWW browsers support printing. However, the results can be highly variable. X-Mosaic supports postscript printing, but appears to handle the color map of in-lined images rather oddly. Mosaic for Windows does rather a good job of rescaling in-lined images, although beware that page throws may not be handled particularly intelligently.