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     by N.Guex & T.Schwede

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