Configuring Explorer for RasMol

Configuring your browser for RasMol

Internet Explorer

There are a number of problems running rasmol scripts through internet explorer. Our first suggestion is to go and use Netscape. However if you want to persist these are our hints.

Internet explorer is much more closely related to the windows operating system than Netscape. This means that there are more combinations to deal with. These instructions are based on Windows 2000 Pro and IE 5.5 and 6.0. They may give you ideas of what to try on other combinations, but copying them unthinkingly may not work. The first step is to set up the following two files. You might want to save them in the same directory as your raswin.exe (in our case c:\program files\rasmol\raswin.exe, but it does not matter as long as you know where they are. If you use several machines and have a folder that is loaded up whichever machine you are on it might be better to put them there.

In windows


"c:\Program Files\rasmol\raswin.exe" -pdb "%~1"


"c:\Program Files\rasmol\raswin.exe" -script "%~1"

Registering file types

You then have to tell the browser how to handle files of the relevant types. If you click on the 'My Computer' icon on your desktop, you start up Windows Explorer. Go to 'Tools' 'Folder options' and select the 'File Types' tag. Depending on the access permissions that you have on the system the New and Change boxes may or may not be clickable. If they are not clickable you cannot carry on, you will need to involve your system manager or use the hints below. If there are look to see if there is a PDB file extension already. If there is not do the following

  1. Click New
  2. Enter File type PDB
  3. Click Advanced to get 'Edit File Type'
  4. Click New to get 'New action'
  5. Enter 'open' in action
  6. In the 'application' box, browse to your raswin executable but before entering OK add %1 to the line so that it reads "C:\program files\rasmol\raswin.exe" %1
  7. Hit OK until you have closed all the dialogue windows.

You have now defined the .PDB extension. You should repeat it for .RAS and .PL files which are the extension on rasmol scripts except the application box should read "C:\program files\rasmol\raswin.exe" -script "%1"

If you have a PDB, PL or RAS file saved to disk you should now be able to click on them and they open up.

Trouble shooting or no permission to change file extensions

You may have notices the Change box on the 'Folder options' dialogue. The files will not work if you just put raswin there, it will start but not open the files. You can instead put rasscript.bat for PL and RAS files or rasstart.bat for PDB files. These should work here. If you click on an individual file and go to properties, it will tell you the type of file and what program opens with. Even if you do not have permission to change file extensions you can change the program here. In this case you should use rasstart or rasscript not raswin -if they do not come up on the menu browse to them using 'Other' button.

Further Problem

Internet explorer saves files to a place with a space in it. It is important to use a recent version of raswin (eg which will deal with this.

If you are still stuck

The ultimate fall back is to save the files to disk (to a folder without a space in the name) and start rasmol and use 'File' 'open' to open the PDB file or type 'script' filename to start a script.
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