
README 

Installation of Relibase 3D Visualization Software (UNIX systems)

For visualization of query results, Relibase uses 
Roger Sayle's Rasmol (version 2.6.4), see  
http://klaatu.oit.umass.edu/microbio/rasmol/ .
Rasmol needs to be installed on all client sides accessing
the Relibase server, together with a Perl script. Client-Server 
communication is established via a web browser helper application, 
which make use of a special MIME type 'chemical/x-relibase'.
Before you can use the 3D visualization tools in Relibase,
you need to set up this mime type in your web browser (see below). 


To install the Relibase visualization software, follow
instructions below:

1) After gunzipping and untarring the file 'relibase_client.tar.gz',
   you should find the following files in the directory containing
   your Relibase client side installation:

   README
   rasmol.2.6.4.exe_{your_operation_system}
   rasmol.pl

2) Usually, it should be sufficient just to the define a new
   helper application in your Web-browser. This can be
   done be defining a new MIME-type, which will call
   the 'rasmol.pl'-script.
   
   1.Start Netscape 

   2.Select Edit 

   3.Select Preferences.... A pop-up should appear.
     (Note: if there is not a Preferences... option in your Edit menu then 
     you may be running Netscape 2 or Netscape 3 and not Netscape 4.) 

   4.Select the right-pointing arrow-head next to Navigator in the 
     Category list of the pop-up. Two sub-categories should be displayed: one of
     these will be Applications.

   5.Select Applications 

   6.You should see a list of MIME types recognised by your browser. 
     If 'chemical/x-relibase' is listed then select this and then the Edit...
     button (below the list). If chemical/x-relibase is not listed, select New... 

   7.You will need to fill in the following fields: 

         Type: chemical/x-relibase 
         Suffix: rlbcoord 
         Select Application and enter 

            #path#/rasmol.pl %s   

         where #path# is the location of your Relibase client side software directory,
         e.g.: '/usr/people/relibase/rasmol.pl %s' 

   8.Select the OK button on the Edit or New window, the OK button on 
   the Preferences window and Netscape will then be configured. 


3) Restart your browser. You should be able now to launch rasmol
   using the launch button in the Relibase visualizer toolbox.

4) Problems:
   If the mechanism does not work, check for following possible problems:

   a) Currently, only one rasmol process is allowed on your machine.
      Ensure that there is no hidden rasmol running on your host.

   b) Check whether the path of your helper application is defined
      correctly, and whether you parse one parameter to the script.
      The application must be something like:
      "/usr/people/relibase/rasmol.pl %s" 

   c) Is perl5 properly installed? If necessary, install perl5 on
      your platform, and/or change the perl-call in the first line
      of rasmol.pl (e.g. '#!/usr/bin/perl5').

   d) Is the rasmol executable valid on your machine? Try
      running the executable from a shell. If this does not
      work, you need to compile a proper executable yourself.
      Download the source code from 
      http://klaatu.oit.umass.edu/microbio/rasmol/getras.htm
      Ensure, you are using version 2.6.4.
      Failing of rasmol may have to do with your screen. Choose
      the correct BIT size before compiling rasmol.


   e) Please report any problems to CCDC:

      Cambridge Crystallographic Data Centre
      12 Union Road
      Cambridge CB2 1EZ
      United Kingdom
      tel: (44)(1223)336022
      email: support@ccdc.cam.ac.uk



