Analysing an active site


Building Loops


Building a functionnal unit from a monomer


Crystal Symmetries


Electron Density Maps


Energy minimisation


Fitting Residues into Electron Density


Homology modelling


Making Phi/Psi statistics


Superposing Proteins





Last modified
31 March 98
by N.Guex


Analysing an Active Site

In this example, we will look at the active site of the lactate dehydrogenase (pdb entry 1ldm).

Step by Step

  • 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.

At this stage, you should be in this situation.


  • 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.