Swiss PDB Viewer

The Swiss PDB Viewer is a powerful modeling tool. In addition to the examples I illustrate, it has the capability to do:

Several problems in our problem sets are best done with the Swiss PDB Viewer, which is available for free (link on our Useful Web Sites page). Here I provide some simple directions, and a link to a Deep View tutorial created by Gayle Rhodes at USM.

  1. Ramachandran diagrams

    • Use File/Open to load your protein structure (Download your choice from the Protein DataBank)

    • If the Control Panel window doesn't open automatically, use the Window menu to open it

    • Clean up the graphic a bit:

      • Choose: Display/Render in Solid 3D to get higher quality graphics

    • Choose All from the Select menu

    • Choose Ramachandran Plot from the Window menu

    • A Ramachandran plot appears

      Passing the cursor over any point in the diagram identifies the amino acid

    • A list of the parameters for the diagram can be saved by choosing File/Save/Ramachandran.

      • To save the graphic, click in the window to make it active

      • Then hold down Alt and press the PrintScreen key

      • An image of the window will be saved to the clipboard and can be pasted into any Windows application

    • Backbone angles can be altered interactively by clicking and dragging the points on the Ramachandran diagram

  2. Solvent Accessible Surface (SAS)

    The SAS is defined by rolling a sphere of the approximate radius of a water molecule over the protein, and summing the points that it touches.

    Deep View also finds any cavities in the interior of the protein large enough to hold a water molecule

    • Load the protein. Set Render Solid 3D as before. Turn off side chains.

    • Choose Preferences/Surfaces

      • Set Quality to 6

      • Click the Cavity radio button

    • Choose Tools/Compute Molecular Surface

      The overall surface of the molecule will appear, colored yellow. A check box labeled Surfaces and Cavities also appears

      • Click in the Vis column to turn on/off displays of the surface and cavities

      • Areas are given in Å2, volumes in Å3

    • The graphic may be saved by choosing File/Save/Image

  3. Structure Alignment

    Deep View does what it calls a "magic fit". This involves:

    • Look for the largest block of identity in the sequence alignment

    • Translate the proteins so that these residues are structurally aligned

    • Calculate the rmsd (root mean square distance) between the the selected atoms in the two structures

    • Adjust the alignment and recalculate the rmsd

    • Continue to the minimum rmsd

    To carry out an alignment:

    • Load the two proteins, and turn off display of the side chains;set solid 3D graphics

    • Right click on the box at the right of the control panel and choose a color for the protein

    • At the top of the controll panel click on the box where the protein identity is display, and choose the other protein

    • Repeat the selection of a color for that protein

    • Choose Fit/Iterative Magic Fit

      • I recommend aligning only backbone atoms; side chains often are significantly disordered

    • The rmsd will be displayed below the toolbar and the structures displayed in the best alignment
    Here is an alignment between two fungal laccases, one from T. versicolor and one from M. albomyces:

    The rmsd is 1.16 Å although the two have only 26% sequence identity (PAM250).

    If the PDB files you are aligning contain different numbers of chains, your alignment will either fail, or give a high rmsd. You can select a single chain from a multi-chain file as follows:

    • Load the multi-chain structure

    • Hold down Control and left-click on the "A" at the top of the lefthandmost column. This selects the A chain.

    • Use File-->Save-->Selected Residues of Current Layer to write the A chain to its own PDB file, giving it a name to indicate that only one chain is present. I usually use something like 1gyc-A.pdb.

    • Close the multichain file (File-->Close) and open the one-hcain file use just made.

    • Proceed with your structure alignment

    This page last modified 9:37 AM on Thursday March 29th, 2012.
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