1. Analysing an active site
2. Building Loops
3. Building a functionnal unit from a monomer
4. Crystal Symmetries
5. Electron Density Maps
6. Energy minimisation
7. Fitting Residues into Electron Density
8. Homology modelling
9. SWISS-MODEL Workspace
10. Making Phi/Psi statistics
11. Superposing Proteins

 

Analysing an Active Site

• First of all, open the pdb file 1LDM (it is included in the tutorial package).

   

• Select the "Compute H-bonds" item of the "Tools" menu.

   

• Click on the control panel window, scroll to the bottom (or hit the page down key), and select the groups "NAD1" and "OXM2". They should become red in the control panel. If they don't, it is a good idea to read the "Control Panel Selection" section).

   

• Now, choose the item "Show Only H-bonds from selection" of the "Display Menu". Then choose the item "Show only groups with visible H-bond" of the same menu. Finally hit the "=" key of the numerical keypad (right mouse button for PC) to rescale and recenter the view.

• Now you can measure distances using the tools located at the top of the display window, or show the H-bonds distances with the appropriate item of the "Display" menu.

[last modified: 16 Jan. 2001 by T.S.]