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
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.
Rasmol/Rastop
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.
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
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.