The chemical/x-pdb, chemical/x-kinemage and other chemical-MIME types can be used to good effect in your documents, so long as whoever is reading them has the appropriate software installed and their WWW browser correctly configured.
(N.B. before reading the following section, make sure you have RasMol installed as a helper application for your WWW client, configured for the chemical/x-pdb MIME-type. Refer to "Chemical MIME on the course technology page if necessary.
If you wish to include a structure which is included in the PDB, you can give the absolute URL of the PDB file at Birkbeck:
where **** is the 4-letter code. For example: http://www.cryst.bbk.ac.uk/PDB/pdb2ovo.pdb (a 57 Kb file)
When someone clicks on a link to such a URL, the PDB file will be served by the Birkbeck Crystallography WWW Server, stamped with the appropriate chemical-MIME type.
This is because the Crystallography server is configured to stamp all files which have the .pdb extension with the MIME-type chemical/x-pdb.
At the Brookhaven National Laboratories Protein Data Bank itself, you can obtain a PDB file from their WWW Server with a slightly more complex URL, because it involves sending a query to cgi-bin software (refer to the notes on WWW Server configuration). This is very useful because you can request the server to deliver the file either as plain text, or stamped with chemical-MIME.
The URL for the chemical-MIME file is:
For plain text, replace &type=view with &type=text. E.g. http://www.pdb.bnl.gov/cgi-bin/get-pdb-entry?id=2ovo&type=view&encoding=none fires up RasMol, while http://www.pdb.bnl.gov/cgi-bin/get-pdb-entry?id=2ovo&type=text&encoding=none gives the file as text.
A similar principle operates at ExPASy, where
chemical-MIME stamps the file, and
delivers the text.
If you want to serve a chemical-MIME stamped copy of a .pdb file stored locally on your own server (you would have to do this for any PDB-format files you might make yourself, for example), then your server must be configured to do so- otherwise it will be served as plain text. Therefore, ask your 'Web-Person' about this.
You can do much more than simply reference the MIME-stamped PDB file, however. You can write RasMol scripts which are equivalent to typing in commands at the RasMol command line prompt. As long as you are familiar with RasMol commands, producing scripts is very easy. You can even type write script <filename>, which will write a script to generate the current view in the RasMol display window. RasMol scripts are very useful as they enable you to deliver a structure to the reader, with particular elements highlighted in the manner you wish.
Getting these scripts delivered in the appropriate manner to whoever is browsing your hyperdocument is more difficult.
For example, the Birkbeck Crystallography server stamps files with the extension '.ras' with the MIME type chemical/x-ras, which means 'rasmol script file'. If the reader has his or her client configured correctly, i.e. to start RasMol and automatically read in the contents of the script, then they will get the desired result.
For example, for Unixsystems, the required line in .mailcap would be something like
chemical/x-ras; xterm -e /local/IRIX52/bin/rasmol8 -script %s
The important thing here is the '-script' parameter.
load pdb "pdb2ovo.pdb"
RasMol will therefore look for the file on the client's local filesystem.
This is a slightly unwieldy method.
For example: click here to download the structure 2ovo from your nearest WWW server: Birkbeck, Brookhaven, ExPASy. Then click on and save this script file, 2ovo_2.txt (N.B. this file has not been given the .ras extension; otherwise it would start up a second RasMol which would just read the script, assuming you had configured your Web client as indicated above.) If all goes well, the initial view should look something like this.
A disadvantage of this is that the author must have a copy of the PDB file (with added script) on his or her local server, rather than using an existing copy at Brookhaven, Birkbeck, etc.
If you do not have RasMol 2.6, then you should configure your browser to read the above type of .ras file (i.e. PDB file + script) as a normal .pdb file (the script portion will be ignored). I.e. don't use the -script parameter, otherwise RasMol will just read the script and not display the structure.
Kinemages are created using the program PREKIN (the program which displays them is called MAGE). PREKIN is currently available for MS-Windows and Macs.
Kinemages allow the inclusion of text, and predefined elements of a structure can be switched on and off in different ways in a very user-friendly interface. The reader can also even change the conformation of the structure being displayed, e.g. this kinemage displays torsion angles. Objects in a Kinemage need not be only atoms and bonds; for example this kinemage illustrates the dimensions of an ion-channel (more information on this structure).
Further information is to be found on the course Kinemage page.
Last updated 15th Jan '97