Necessary Configuration Details for WWW Browsers Implementing Chemical MIME
Chemical MIME types are a mechanism that has been proposed to enable
intelligent handling of molecular information using "helper" programs invoked from
To make full use of some of the html documents available, a WWW browser capable of
supporting FORMS, such as NCSA Mosaic Version 2 onwards, Netscape 1.1N or 2.0, Microsoft Internet Explorer.
To be able to display co-ordinate files referred to on this page, you will need to
acquire a visualiser (helper) program and to configure your system appropriately.
These programs tend to differ according to the system you are working on.
The choice of helper is up to you! The only criterion is that
it must be capable of reading the particular data type define by the MIME label.
We have indicated below some programs freely available by ftp transfer, but if you
have commercial programs, it should be possible to use those instead. We would be
happy to hear from anyone who has successfully used programs not mentioned here.
Delaying Image Loads: If you are experiencing difficulties with
network bandwidth in downloading some of the larger images, you may wish to add the
following line to the Mosaic configuration file stored as
Another recommended route is to specify a so called "proxy" server. If
this server implements local caching (ie the CERN http server), then all requests
for large files can be redirected to this local server, reducing the download
time. On Unix Mosaic servers, you have to define a local environment variable;
http_proxy = http://your_local_caching_server/
and then appropriately export this variable.
On Mosaic for Windows, a similar line has to be inserted into the Mosaic.ini
file. On Macintosh NCSA Mosaic 2.0, this can be achieved via the preferences
There are several free molecular visualisation and utility programs available from ftp sites, including
We currently recommend RasMol for the visualisation of "pdb" and "xyz"
files, although XMol, EyeChem and others can also be used.
You will need to edit/create your .mailcap file located in your home directory and
add the lines:
chemical/x-pdb; rasmol %s
chemical/x-xyz; rasmol xyz %s chemical/x-xyz; xmol -readFormat xyz %s
chemical/x-csml; csml %s
chemical/x-kinemage; mage %s
chemical/x-pdb-ribbon; eyeribbons %s
chemical/x-mopac; xmol -readFormat mopii %s
chemical/x-mopac-out; eyemopac %s
chemical/x-mopac-out; xmol -readFormat mopo %s
chemical/x-mopac-den; eyemopacview %s
chemical/x-mopac-esp; eyemopacesp %s
chemical/x-mopac-vib; eyemopacvib %s
chemical/x-gaussian; xmol -readFormat gaussin %s
chemical/x-gaussian-log; eyeg92 %s
chemical/x-eye2eye; eye2eye %s
application/x-mathematica; math %s
These suggested entries assume that you have a path defined to the relevant programs.
If you are using your own helpers in a non-standard path, enter the following;
chemical/x-pdb; /usr/local/bin/rasmol %s
There are also occasions when you may wish to open up a command line interface
to the helper program (ie Rasmol uses this extensively). Replace the mailcap
entry with the following;
chemical/x-pdb; xterm -T title -e rasmol %s
Two windows will then appear on your screen rather than the usual one.
The mailcap file defines the chemical MIME type with a secondary characteristic of
e.g. /pdb, and associates it
with whichever program you have implemented on your own system. This is in accord
with our proposal
to implement a direct chemical mime type. You should also be aware that a global mailcap file is installed when
the utility metamail (currently V2.7) is installed on your system. Normally
located in /usr/local/etc/mailcap you may wish to ask the system
administrator to update this file with the entries above so that users do
not have to create their own mailcap file.
If you encounter a hyperlink that downloads a file ending with the suffix
.csml, you have encountered what we term our chemical structure markup language.
This is a way of sending to the RasMol molecular visualiser explicit instructions
to highlight or mark in some way the molecular structure it is already displaying.
Note that CSML will not work unless you already have such a molecular structure on
display with RasMol. To ensure that this markup works, go through the following
- There are two implementations available. For Unix workstations,
follow the instructions below. For Windows 3.1 and 95, acquire
a product called Chemscape Chime from MDLI as a Netscape plug-in.
- Ensure that the following is in your .mailcap file; chemical/x-csml; csml %s
- You must also have the Tk/Tcl environment installed on your workstation. Most
modern workstations have this pre-installed. If not, acquire it from
- Next, acquire a script called
csml. This has to be placed
in an executable path on your workstations (i.e. /usr/local/bin).
- A typical example of CSML is shown below;
SELECTION COLOUR REPRESENTATION REPRESENTATION_BOOLEAN ATOMLABEL LABELCOLOUR
- SELECTION is of the type gly39 or atomno=410
- COLOUR is of the type e.g.red, green etc. It can also have the
value CPK for the "natural" atom colours
- REPRESENTATION is spacefill, Wireframe, ribbon, dot etc
- REPRESENTATION_BOOLEAN is on or off to make the represenation visible or invisible
- ATOMLABEL is any single word (no spaces but underscore should work) to label the representation
- LABELCOLOUR similar to COLOUR, just applies to the ATOMLABEL
- For further details on CSML, see here
- For further details on Rasmol and other attributes not indicated here, consult the RasMol manual
- If everything is installed correctly, activating a hyperlink to a CSML
file will induce the instructions contained within it to be executed
by RasMol. In theory, hundreds of such instructions could be executed, resulting
in very complex markup. In practice, most CSML scripts just highlight a few
atoms to clarify the points being made in the original document.
On a Macintosh system the following programs are worth a look;
Kinemage consists of a pdb pre-processor to convert the
file to "Kin" format, and a Kin viewer. "Kin" type files can be introduced
as a chemical MIME type in their own right as part of a project by the
Journal Protein Science.
for further details.
Netscape users should click here.
To use MacWeb, add the following MIME types to the configuration;
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)
MS Windows version of both Kinemage and Rasmol are available.
A Sample Mosaic.ini file
in which the MIME types and Helpers are defined is available
here. This should be placed in the Windows directory.
Configuring Netscape is done within the program.
Updated 2 April, 1996 by firstname.lastname@example.org