WHAT IS RASMOL?

Available for Windows, Macintosh, and UNIX platforms, RasMol is a free, interactive molecular-graphics viewer. The program reads in the 3-D coordinates for a molecule using the pdb file format. It displays the molecule in various representations and allows one to rotate the molecule interactively. RasMol-ucb allows simultaneous viewing of multiple molecules.

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HOW TO OBTAIN RASMOL AND TO SETUP NETSCAPE TO USE IT.

The version of RasMol that we are using (RasMol-ucb) is the enhanced version developed by Marco Molinaro from the UC Regents/ModularCHEM Consortium. Be aware that this program is still in beta testing; thus, you may encounter bugs. It is based on the original RasMol that was developed by Roger Sayle at Glaxo, UK. (Reference: Roger A. Sayle and E. J. Milner-White, "RasMol: Biomolecular graphics for all", Trends in Biochemical Science (TIBS), September 1995, Vol. 20, No. 9, p.374.)

    1. Download the PC Windows version of RasMol-ucb. To install the PC windows version, double click on the Rasmol2.exe installer program. It is a self-extracting program and the executable is RasWin. This version runs under Windows 3.1, Windows 95, and Windows NT.
    2. Download the MAC version of RasMol-ucb. To install the MAC version*, double-click on the Rasmol-mac.sea program. It is a BinHex’ed, self-extracting archive for the Mac and PowerMac.

*NOTE TO MAC USERS: To download RasMol correctly from the internet, you need to have either "Stuffit" or "Binhex" on your Macintosh. These are free software programs and are available on the ACN (Academic Computing Network) Macintosh network or from Aladdin Systems. If you have any questions about this, please see R. Frey.

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INSTRUCTIONS TO USE RASMOL:

  1. Basic Instructions (using the menus):
    1. To open a file: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a .pdb file). (RasMol should automatically start and load in the molecule.)
    2. To open multiple files (i.e., can view up to 5 molecules simultaneously): File/Open (for each file, without closing the previous files) from within RasMol. From within Netscape, just click on another RasMol viewable molecule.
    3. To select a molecule: Click on molecule name in the Molecules window (the secondary window)
    4. To close a file (a molecule): File/Close when the molecule is selected.
    5. Moving the molecule(s):
      6.

      Action

      PC

      MAC

      Rotation

      Left-mouse
      button (Click & Hold)

      Mouse button (Click & Hold)

      Translation

      Right-mouse
      button (Click & Hold)

      <OpenApple> and
      mouse button

      Zoom

      <alt><SHIFT> and
      left-mouse button

      <SHIFT> and
      mouse button

      Z-Rotation
      <alt><SHIFT>and right-mouse button

      <option><SHIFT> and
      mouse button
    6. To change to different representations (i.e., CPK, stick, ribbon, etc.): Display/Stick
    7. To determine distances, angles, dihedral angles:
        1. Click on appropriate icon in the Molecules window (the secondary window)
        2. Click once on the appropriate number of individual atoms. (With angles, clicking on atoms must be in the appropriate order.)
    8. To rotate bond (Note: This changes the angle.):
        1. Click on rotate angle icon in the Molecules window (the secondary window)
        2. Click on 2 atoms
        3. Click on rotate angle icon in the Molecules window (the secondary window) again
        4. Click on 3rd atom
        5. Use mouse button to rotate
    9. To color molecule in different ways:
        1. To color by the protein-secondary structure: Colours/Structure
            • a -helices: magenta
            • b -sheets: yellow
            • turns: pale blue
            • all other residues: white
        2. To color by residue type (i.e., each type of residue is colored a specific color): Colours/Shapely
        3. To color by atom type (below are the default colors): Colours/CPK
            • Carbon: gray
            • Hydrogen: white
            • Oxygen: red
            • Nitrogen: blue
            • Sulfur: yellow
            • Iron: yellow
  2. Advanced RasMol Usage:

    3. The command line may also be used to perform more advanced commands. To find the commands, look in the RasMol manual under Help (PC) or ð /Basic Instructions. Other helps, such as reference manuals and tutorials, are available on the Internet:

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Revised July 29, 1999