VRML Plot of a
Brookhaven PDB Structure

Brian T. Luke, Ph.D.

[email protected]
To generate a VRML plot of a Brookhaven PDB structure, you need to type in the name of the PDB file in the top box and make sure that Brookhaven PDB is selected as the Format. In this example, the supplied PDB file 1aan.pdb is used. Therefore, the initial VRMol window will look like this.

Once this is entered, you should click on the [Apply] button. Another dialog window appears asking you for the type of plot you want. Your choices are

  1. Ball and Stick
  2. CPK
  3. Rods
  4. Ca Trace

Since PDB structures can be very large, this example generates a Ca Trace plot. This option should be selected from the pull-down menu so that the window looks like the following:

When you click the [Apply] button, VRMol writes the file 1aan.pdb.Ca.wrl to disk. If you had selected Ball and Stick, CPK, or Rods plot, VRMol would have created 1aan.pdb.B-S.wrl, 1aan.pdb.CPK.wrl, or 1aan.pdb.Rods.wrl, respectively.

To see this VRML image from a browser that supports a VRML Plug-in, simply click on 1aan.pdb.Ca.wrl.

Unfortunately, browsers under AIX do not support such a plug-in, and you will have to examine this structure using another product. A few are available, and for ease of use I would recommend an older viewer called VRWeb. For further information, please consult Installing and Using VRWeb.

Program Limitation
The current version of VRMol only plots a single polypeptide chain. This means that if the PDB structure contains two or more chains, only the first will be displayed. If you want to display multiple chains, you need to edit the PDB file and remove the "TER" card between chains. For this Ca Trace, an erroneous bond will be drawn connecting the last alpha-carbon of the preceeding chain to the first alhpa-carbon of the following chain.

� 1999 Brian T. Luke, Ph.D.