1. Getting Started

NOTE: Plan to work at least through section 4 of this tutorial without stopping. Thereafter, the end of any section is a convenient stopping point. See the end of section 4 for instructions on how to resume the tutorial after stopping.

RasMol works best if it is located in the same directory or folder as the PDB files you will be opening, and the script and graphic files you will be writing. Transfer a copy of raswin.exe (for PC) or RasMac (for Macintosh) to the directory or folder you will be working from, along with copy of the rasmol.hlp file. Start this copy of the RasMol program (double-click its icon) before downloading a PDB file. (If the RasMol program is already open and displaying a structure, select Close from the File menu, or type zap afer the RasMol > prompt in the command window, to clear the structrure from the display.)

Use your web browser to obtain the atomic coordinate file (or PDB file) with code 1cyo from the Protein Data Bank by following these instructions:

  1. Click here to open a new window for the PDB Home Page. Immediately add a Netscape bookmark for the PDB Home Page with the menu command Bookmarks: Add Bookmark. In the future, you can use this bookmark to go directly to the Protein Data Bank.
  2. Slide the PDB window aside so that you can read these instructions and carry them out in the PDB window.
  3. Find the Search tool that says Enter a PDB ID or keyword:. Click to place the cursor in that box and type in 1cyo. Click on the check box that is labeled "query by PDB ID only", Then click the Find the Structure button or press <return>. The Structure Explorer Summary Information page for 1cyo should appear.
  4. At the left side of the page, click View Structure. The View Structure page appears.
  5. Under Interactive 3D Display, click RasMol. The file will be downloaded, and it my automatically be opened by RasMol. Alternatively, you may see a message that begins, "You have started to download the file "1cyo.pbd"...". If you get this message, click the button labeled Pick app. In the dialog that appears, navigate to your working copy of RasMol, select the program, and click Open.
  6. The file 1cyo.pdb should open in RasMol AND its icon should appear in the location where Netscape puts your downloaded files (on a Macintosh, the location is usually the desktop).
  7. Before exploring the structure, find the downloaded file and move it to your working directory or folder. If you do not move or copy the file, it may be discarded when you quit Netscape.
  8. Close the PDB window in Netscape.
  9. In the future, when you follow this procedure to obtain a PDB file, the file should open immediately in RasMol without the need for the Pick app operation.

The web page PDB File Contents provides a complete description of the contents of a PDB file, allowing you to learn what information RasMol uses to create molecular graphics displays. But first, get started with viewing. After you have learned some basics, the contents of the PDB file will mean more to you.

2. Windows and Help