User Guide

  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. Making Phi/Psi statistics
  10. Superposing Proteins
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These examples presuppose that you know the basic manipulation of the program; i.e. that you have already read the user guide and completed the Basic Tutorial prepared by Prof. Gale Rhodes (cf. below). If you are interested, you are also invited to join the "Deep View Discussion List" moderated by Gale Rhodes.

The best way to learn is by practising. Therefore, I have provided some practical examples that you should read, not only because I have spent so much time making them, but because they illustrate many operations that you will probably have to use during your research.

You will need some PDB files to complete the tutorial. You can download them all (except some electron density maps that are available from their specific tutorial) in one operation:

If you wish to learn the basic manipulation of Swiss-PdbViewer through a tutorial, I recommend that you have a look at the one prepared by Prof. Gale Rhodes from the University of Southern Maine Portland. This tutorial has been prepared specifically for students and gives a lot of useful information not only on Swiss-PdbViewer manipulation, but also on general protein structure. As Prof. Gale Rhodes has spent a lot of time playing with the program, some interesting tips and details missing from my main documentation are unveiled.