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 better with Netscape if it is located on the desktop. Transfer a copy of RasMol (for PC) or RasMac (for Macintosh) and the file rasmol.hlp to your desktop. Start the desktop copy of the RasMol program (double-click its icon) before you download a PDB file.

Use your web browser to obtain the atomic coordinate file (or PDB file) with code 3b5c from the Protein Data Bank by following these instructions:

 

(USM students can find the file on a USM Macintosh computer in the folder PMLMAC.MACAPPS/Course_Materials/BIOCHEM/RasMol.)

  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 PDB.
  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:. Click to place the cursor in that box and type in 3b5c. Then click the Explore button or press <return>. The Structure Explorer Summary Information page appears. NOTE: PDB file 3B5C has now been replaced with a newer version, 1CYO. The search tool should redirect you to 1CYO. If not, search for 1CYO instead.
  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 "3B5C.pbd"...". If you get this message, click the button labeled Pick app. In the dialog that appears, navigate to the desktop copy of RasMol, elect the program, and click Open.
  6. The file 3B5C.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 either move it to a safe location or make a copy of it. 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 SPdbV 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, thus 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