VRML Plot of a
"Brian's" PDB Structure

Brian T. Luke, Ph.D.

[email protected]
To generate a VRML plot of a PDB-like structure generated by one of the other programs I've written, you need to type in the name of the PDB file in the top box and make sure that Brian's PDB is selected as the Format. In this example, the supplied PDB file PDBOUT (written as output by the program SimVol) 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

In this example we will construct a Ball and Stick 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 PDBOUT.B-S.wrl to disk. If you had selected a CPK or Rods plot, VRMol would have created PDBOUT.CPK.wrl, or PDBOUT.Rods.wrl, respectively.

To see this VRML image from a browser that supports a VRML Plug-in, simply click on PDBOUT.B-S.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. This structure file actually contains two polypeptides, but only the first is displayed. If you want to display multiple chains, you need to edit the PDB file and remove the "TER" card between chains.

� 1999 Brian T. Luke, Ph.D.