Setup - Viewing Molecular Data on the Web
With RasMol properly
installed on your local computer you can view the protein data
presented herein. The studied domain is shown in white using a
cartoon representation, the rest of the molecule is shown in
wireframe. If a rule involves a secondary structure, this is shown in
red. Negative examples are preceded by ':-'. We describe an installation for running under Netscape Communicator and Unix,
however the installation for a different browser/architecture should
be similar.
Installation
On most platform, RasMol compiles out of the box; download and follow the
instructions. However, if you need further information consult SCOP RasMol
installation page.
Configuration
Your need tell your browser how to handle the scripts that our server
will send to you. Rasmol scripts are often generated dynamically, but
because our data-set is static and relatively small, all scripts have
been pre-computed. Rasmol scripts will be pushed to you as
application/x-rasmol objects. Rasmol scripts have an
extension .rasmol. You need to tell that to your browser,
add the following line to your ~/.mime.types file:
application/x-rasmol rasmol
It defines a new type and associated file extension. Now you need to
tell your browser what to do with objects of this type. If you have a
local copy of the PDB database
(some 3.2 GBytes) then simply add the following to your
~/.mailcap file:
application/x-rasmol;xterm -e rasmol -script %s
It says that an object of type application/x-rasmol is
handled with the command xterm -e rasmol -script %s, and
%s will be substituted by the name of the script
(generally saved in your tmp area). We could have simply said
rasmol -script %s but there would be no console for you
to interact with.
If you don't have a local copy of PDB, the authors of SCOP are
providing the following script
that will transfer the coordinate files automatically for you, see instructions.
Alternatively, you can use the following script which does the same, but it keeps the
files (caching). That way, you can build your own PDB subset as you
need it. Add the following instead to your ~/.mailcap
file: ~/.mailcap file:
application/x-rasmol;rasmol.csh %s
If you have several structures to view and are running under Unix, you
can use the following Perl script which keeps
a RasMol session open. The script relies on Unix named pipe
mechanism. I use the same approach to communicate data to RasMol from
Prolog, contact me if interested.
Links
Marcel Turcotte (M.Turcotte@icrf.icnet.uk)