Viewing the SURFNET surfaces

Viewing the maps in Rasmol

This file can be loaded into Rasmol like any other PDB file. If the data corresponds to a surface, or gap regions, of a given protein structure, you might want to view the protein together with the surfaces. As Rasmol allows only the input of a single PDB file, you can view both at the same time by concatenating surfnet.pdb with your original PDB file.

To view in Rasmol:-

1. Load the PDB file into Rasmol.

2. Type the following commands to view just view the protein structure:-

   RasMol> wireframe off
   RasMol> select not map
   RasMol> wireframe

   This displays just the protein in a wireframe representation. Alternatively, you can use one of the other display options for the protein (eg backbone, ball-and-stick, ribbon, etc)

3. Display the surface:-

   1. Surface as a wireframe grid. To show the surface as a red wireframe, enter:-

      RasMol> select map
      RasMol> wireframe
      RasMol> colour bonds red
      

      If more than one surface was written out to the surfnet.pdb file, you can define the one you're after by, say, select map2 to pick the second surface. This allows you to colour each surface in a different colour using the colour bonds command.

   2. Surface as dots. To represent the surface by blue dots, enter:-

      RasMol> select map
      RasMol> spacefill 0.2
      RasMol> colour atoms blue
      

      As above, if more than one surface was written out to the surfnet.pdb file, you can define the one you're after by, say, select map2 to pick the second surface. This allows you to colour each surface in a different colour using the colour atoms command.

4. Repeat step 3 for each surface to be displayed.

Example of SURFNET output displayed using RasMol. The yellow wire-cage surface is the surface generated by SURFNET, appended onto the end of the original PDB file (7hvp). The yellow surface is the binding site of HIV protease. The inhibitor is show as the capped-stick molecule inside the binding site (obtained using the RasMol command: wireframe 0.3). The sidechains of the protein are shown in the standard wireframe representation.

Viewing the SURFNET surfaces