Structure visualisation in PDBeFold

Starting from version 1.26 of 07/10/2005, PDBeFold supports two viewers: Jmol and Rasmol / Rastop. Each page, which contains visualisation buttons, also contains a drop-down switch between Jmol and Rasmol/Rastop.

Jmol is a platform-independent server-side java viewer, which is made default in PDBeFold. It should work on any system where browser uses java plug-in. This comes as a standard nowadays. Most probably you already have a properly configured system if it is not older than 4-5 years. This means that you should be able to use Jmol right away, no additional adjustments are required. 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 PDBeFold 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 for you, please consult Jmol documentation pages.

PDBeFold sends an ordinary PDB file, preceeded by Rasmol script, when you click view buttons or links in the PDBeFold pages. If your browser was not previously configured for working with such data, it should ask you if you want to open these 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. Rasmol and Rastop are freely available and may be easily found in the net. Having properly configured your browser once, you should be able to view structures from PDBeFold as smoothly as you would do that from a standalone application, without any intervening from the browser.

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 the problems with launching Rastop from browsers on MS Windows 2000 and XP; should you encounter any of those, consider using Raswin instead. Raswin may be found in Rasmol distributions. To 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 good 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 to specify -script or -s as a first parameter when Rasmol is included into the browser's helper application list. The following C program allows one to make around that (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 )  {
int  i;
char S[1000];
  strcpy ( S,"rasmol -script" );
  for (i=1;i<argc;i++)  {
    strcat ( S," "     );
    strcat ( S,argv[i] );
  system ( S );
  return 0;

font color="blue">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 aplication" 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.