Helix and bending analysis of nucleic acid double helix structures

Configuring your WWW browser for RASMOL

RASMOL is a viewer for 3-dimensional structures of biomolecules. Molecules are displayed as 3-dimensional objects which can be moved and rotated by the user. RASMOL can visualize molecules from standard molecular coordinate files (PDB coordinate files, TRIPOS mol2 files) or from RASMOL script files. RASMOL script files contain not only the coordinates but also instructions for coloring and rendering the model. RASMOL 2.6 or newer is required for using script files. RASMOL 2.6 is available on all UNIX workstations within the IMB Jena. To gain advantage from hyperlinks to RASMOL script files or PDB coordinate files, you should configure your WWW browser to launch RASMOL automatically if one of these files is received.

Contents of this page

1. Configuring your WWW browser: The principles

2. A recipe for SGI workstation users

3. More about RASMOL and chemical MIME types

4. Some basic RASMOL commands

5. Why using the script rasmol?

1. Configuring your WWW browser: The principles

The IMB Jena WWW server makes use of the chemical MIME types chemical/x-pdb and chemical/x-ras. If you click on a hyperlink to a RASMOL script or to a PDB file, then these files are sent to your WWW browser attached with an information about the MIME type of this file. Now it depends on your browser to start an appropriate helper program or plug-in. The dependency between MIME types and helper applications is defined in the file $HOME/.mailcap. To configure your WWW browser for using RASMOL as a helper application, you should copy the following five entries into your $HOME/.mailcap file. Note, that some WWW servers use different MIME types for the same type of data file.

   chemical/pdb;xterm -e rasmol -pdb %s;\
        description="PDB file, ExPASY Server"
   chemical/x-pdb;xterm -e rasmol -pdb %s;\
        description="PDB file, Birkbeck Server"
   chemical/x-xyz;xterm -e rasmol -xyz %s;\
        description="XYZ coordinate file"
   chemical/x-ras;xterm -e rasmol -script %s;\
        description="RASMOL Script, Birkbeck Server"
   application/x-rasmol;xterm -e rasmol -script %s;\
        description="RASMOL Script, Brookhaven Server"

2. A recipe for SGI workstation users

As I am working on a SGI workstation the following recipe for configuring your WWW browser is mostly intended for SGI Irix and the C shell.

• If you do not have a directory named $HOME/bin, create it (mkdir $HOME/bin) and add the name of this directory to the environment variable $PATH:

     set path = ( . $HOME/bin $path )

• To make this setting permanent, you have to copy that command into your $HOME/.cshrc file.
   
• Copy the shell script rasmol into your $HOME/bin directory. Use this script as your personal UNIX command to start RASMOL. See section 5. 'Why using the script rasmol for starting RASMOL?' for more information about this script.
   
• You maybe have to modify the header of rasmol. Assign the path names and file names, which are appropriate for your local RASMOL installation, to the variables in the header of the script. This is not neccessary for users at the IMB Jena.
   
• Make the shell script executable with the command:

     chmod 744 $HOME/bin/rasmol

• Copy the following lines into your $HOME/.mailcap file. If you do not have a $HOME/.mailcap file, create a new one.

     chemical/pdb;rasmol -nofork -pdb %s;\
          description="PDB file, ExPASY Server"
     chemical/x-pdb;rasmol -nofork -pdb %s;\
          description="PDB file, Birkbeck Server"
     chemical/x-xyz;rasmol -nofork -xyz %s;\
          description="XYZ coordinate file"
     chemical/x-ras;rasmol -nofork -script %s;\
          description="RASMOL Script, Birkbeck Server"
     application/x-rasmol;rasmol -nofork -script %s;\
          description="RASMOL Script, Brookhaven Server"
  

• Restart your WWW browser and try out the following links. For every link you should get a RASMOL window displaying 56 residues of the ovomucoid proteinase inhibitor.
   

  PDB file with MIME type chemical/pdb

  PDB file with MIME type chemical/x-pdb

  RASMOL script with MIME type chemical/x-ras

  
   
• If you want to start RASMOL from your command shell, just type one of the following commands:

     rasmol
     rasmol pdb_file_name
     rasmol -script script_file_name
  

3. More about RASMOL and chemical MIME types

If you are using computers other than SGI you may find some useful information about RASMOL and how to configure your WWW browser in Section 6 of Birkbeck colleg's course Principles of Protein Structure Using the Internet. Also the RASMOL Home Page may be of interest. The documents MIME types for Chemistry and the The Chemical MIME Home Page provide some general information about chemical MIME types.

4. Some basic RASMOL commands

• A molecules is translated by moving the mouse pointer with the right mouse button pressed.
• A molecule is rotated about the x and y axes by moving the mouse pointer with the left mouse button pressed.
• A molecule is rotated about the z axes by moving the mouse pointer to right or the the left side and having the Shift key and the right mouse button pressed.
• The size of a molecule is scaled by moving the mouse pointer up or down and having the Shift key and the left mouse button pressed.
• The performance is drastically increased when the specular and shadow options are turned off.

For a detailed description of all commands have a look at the RASMOL manual.

5. Why using the shell script 'rasmol'?

The shell script rasmol is intended for starting RASMOL on SGI UNIX machines in the most comfortable way. Two windows are needed for a RASMOL session, the command window and the viewer window. Usually, the command window is just the window of the command shell from which RASMOL was started. But with rasmol a new command window is opened each time, RASMOL is started. This window is started as a background process. This keeps your current shell window free for other purposes.

RASMOL always requires a command window. When RASMOL is started from a WWW browser, the browser should first start a new xterm or shell window and then launch the RASMOL executable within this new window. Exactly this is done by the script rasmol. Helper applications started by a WWW browser must be run as foreground processes. By default rasmol runs RASMOL in background, but if the optional command line argument "-nofork" is given, RASMOL is started as a foreground process. This is the same syntax as used with other X-programs like imgview.