Displaying protein chains with VMD

VMD is a molecular visualization program that can display static or animated systems. It has a built-in programming language called Tk. The version used in this post is 1.8.7.

We are going to show some common operations on the protein Triosephosphate Isomerase in Complex with DHAP using this modified PDB file.

We start by displaying the protein chains using different colors.

1. start VMD program
2. menu File > New Molecule, browse to the downloaded file 1NEY.pdb, then click Load button. You should see something like this:
   
   
   
3. menu Graphics > Representations
4. select the line in the list of representations and delete it by clicking Delete Rep button,
5. click twice the Create Rep button to create one graphical representation for each chain,
6. select the first graphical representation line,
   - for Drawing Method choose for instance NewRibbons
   - for Coloring Method choose ColorID and then choose a color in the list of IDs
   - in the Selected Atoms field enter chain A
   - then click the button Apply
7. select the second graphical representation line,
   - for Drawing Method choose for instance NewRibbons
   - for Coloring Method choose ColorID and then choose another color in the list of IDs
   - in the Selected Atoms field enter chain B
   - then click the button Apply

You should get this output:

Remember the keyboard shortcuts to toggle the mouse pointer mode:

• r for rotating
• t for translating
• s for scaling