Visualisation

  • PISA supports two viewers:
    1. Jmol and
    2. Rasmol / Rastop.

    Each page, which contains visualisation buttons, also contains a drop-down switch between Jmol and Rasmol/Rastop.
  • Jmol 

    Jmol is a platform-independent server-side java viewer, which is the default in PISA. It should work on any browser which has java plug-ins enabled. Starting Jmol for the first time will take some additional "dead" time for the Jmol applet to download from our server. Repeated use of Jmol will be normally much quicker, even quicker than using Rasmol/Rastop because PISA compresses the structural data before sending it to Jmol. There will always be a natural delay after starting the applet and displaying the structure, which depends on the structure size and your internet connection speed. If Jmol does not work, please consult Jmol documentation pages. Jmol has a limitation on the number of atoms it can display in the screen. Large protein assemblies may go over this limit, in which case only backbone atoms will be sent for visualisation and a warning will be displayed in Jmol window. In order to see all atoms, use Rasmol/Rastop for visualisation.

  • Rasmol/Rastop  PISA sends an ordinary PDB file, preceeded by Rasmol script, when you click view a button or link in a PISA page. If your browser was not previously configured for working with such data, you will be asked if you want to open the data with an application or to download them into a file. Choose "Open with application" and then specify the application details. Those are platform-dependent; we describe the options below. All visualisation tools recommended here are freely available and may be redaily found internet search. Having properly configured your browser once, you should be able to view structures from PISA as smoothly as you would do that from a standalone application, without any intervention from the browser.
  • APPLICATION (Unix/Linux) The server assumes using the Rasmol as the visualisation tool. Netscape users should include it into the browser's helper application list.
  • APPLICATION (Windows) For MS Windows machines, we normally recommend using Rastop as a more functional tool. However, there are reports on problems with launching Rastop from browsers in MS Windows 2000 and may be in other MS Windows platforms; should you encounter any of those, consider using Raswin instead. Raswin may be found in Rasmol distributions. In our experience, Raswin 2.6 beta-2a, available from the following link, works just as well as a UNIX-based Rasmol.
  • VISUALISATION DATA The server sends the visualisation data as a file named send.rasmol, mime type application/x-rasmol. The data is suitable for both Rasmol/Raswin and Rastop.
  • USING Rasmol The server's data should be passed to Rasmol as second parameter, the first one being -script (older versions) or -s (newer versions of Rasmol).
  • Rasmol in Netscape 6 Netscape 6+ has an apparent bug that does not allow the specification of -script or -s as a first parameter when Rasmol is included into the browser's helper application list. The following C program allows the option to be hidden (use it as you would use Rasmol but without -script or -s parameter; Rasmol should be installed and accessible to the program): 
    #include <string.h>
#include <stdlib.h>

int main ( int argc, char ** argv, char ** env )  {
char S[1000];
  strcpy ( S,"rasmol -script" );
  for (int i=1;i<argc;i++)  {
    strcat ( S," "     );
    strcat ( S,argv[i] );
  }
  system ( S );
  return 0;
}
  • USING Rastop The server's data should be passed to Rastop as the only parameter.
  • USING Raswin The server's data should be passed to Raswin as second parameter, the first one being -script.  Raswin in Internet Explorer Internet Explorer picks the application according to the file type (file extension) of the document to be opened. There are difficulties in specifying -script as a first parameter and, sometimes, in getting a data stream from the browser. The following script 
    
 copy %1 c:\temp.pdb
 start drive:\path\rw32b2a.exe -script c:\temp.pdb
    buffers the browser's output stream and then calls Raswin. Sometimes the following: 
    
 start drive:\path\rw32b2a.exe -script %1
    works just fine. Locate the script when IE asks you to specify an application for displaying (opening) rasmol data, and check "Always open with this application" if you are happy with the results. To remove the script from the list of associated applications, open any folder in Windows Explorer and then go to View/Options/File Types.