Please read the instructions on this page carefully. Don't rush through this practical - it's not a race! If you don't finish the practical, or wish to look up something later on, it will continue to be available on-line, so you can do this at any time from the comfort of your own lab or home.

This practical is intended to introduce a number of publicly available tools that help you assess the reliability of structural models. Assessing the quality of a model is called validation. Validation is something that needs to be done both by producers (crystallographers, NMR spectroscopists, electron microscopists, etc.) and users (biologists, enzymologists, medicinal chemists, etc.) of models. Note that we talk of models rather than structures, since a model is just a simplified representation of a human being's hypothesis of what a molecule looks like (a collection of point atoms, often even ignoring hydrogen atoms).

In this practical, we will focus mainly on validation of protein models determined using crystallographic data. This does not mean that NMR or EM models are more reliable a priori (au contraire), or that nucleic acid models need no validation (au contraire). Fortunately, many coordinate-based quality checks can be applied equally well to NMR or EM as to X-ray models, and some apply just as much to nucleic acid models as they do to protein models.

Upon successful completion of this practical, you should be able to:

Attention CSHL students (October, 2013)!

We will not be using RASMOL, so whenever this program is mentioned ignore it. To inspect maps and models from the Uppsala Electron Density Server you can use O or Coot.

To do this practical you will need a molecular graphics program or plug-in that allows you to look at protein structures, identify atoms and residues, etc. A simple program such as RasMol is fine (check here if you have Rasmol installed and if your browser is configured appropriately), but O, Coot, SwissPDBViewer, PyMol, Jmol, etc. will also do fine. Check which graphics programs are installed on the computer you are using and pick the one that you are most familiar with.

Also, if you want to make full use of the Uppsala Electron Density Server (EDS) during this practical, you will need to have access to (and some experience with) the program O (this only applies to [aspiring] crystallographers). (Note that some other programs also provide direct links to EDS data, e.g., PyMol, Chimera and Coot.) If you have Java installed you will also be able to use the density viewers provided by EDS. To test if this works properly, click this link; after a little while you should see something like this.

A set of links that is particularly relevant to this practical can be found here. Check this page out before you continue with the practical!

Throughout the practical you will encounter questions (in red font on a yellow background, just like this text). Discuss these with your co-worker(s) and write down your answers (so your tutor can ask you to explain or defend them)!


If you have previously started with this tutorial and wish to continue, select the section with which you want to continue from the pop-up menu below and then hit the "Go!" button. Otherwise just click the "Next" button below.

Good luck and have fun!



History ...

Gerard teaching this practical... (2004 EMBO course in Cambridge, UK).

  1. Practical by Gerard Kleywegt, Uppsala University.
    Developed for the 2001 EMBO Bioinformatics course in Uppsala.
  2. Updated for the 2002 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  3. Updated for the 2002 course in X-ray Crystallography in Uppsala.
  4. Updated for the 2002 BioCrys course on Basic Crystallography in Oeiras, Portugal.
  5. Updated for the 2002 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  6. Updated for the 2003 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  7. Updated for the 2003 course in X-ray Crystallography in Uppsala.
  8. Updated for the 2003 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  9. Updated for the 2004 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  10. Updated for the 2004 course (March) in X-ray Crystallography in Uppsala.
  11. Updated for the 2004 EMBO lecture course on "3D Structure Databases - Uses for Biological Problem solving" in Cambridge, UK.
  12. Updated for the 2004 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  13. Updated for the 2004 course (December, this time) in X-ray Crystallography in Uppsala.
  14. Updated for the 2005 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  15. Updated for the one-day workshop on Validation in Sao Paulo, Brazil, 1 July, 2005.
  16. Updated for the 2005 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  17. Updated for the 2005 course in X-ray Crystallography in Uppsala.
  18. Updated for the 2006 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  19. Updated for the 2006 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  20. Updated for the 2006 course in X-ray Crystallography in Uppsala.
  21. Updated for the 2007 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  22. Updated for the 2007 course in X-ray Crystallography in Uppsala.
  23. Updated for the 2008 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  24. Updated for the 2008 Cold Spring Harbor Macromolecular Crystallography Course in Beijing (China).
  25. Updated for the 2008 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  26. Updated for the 2008 course in X-ray Crystallography in Uppsala.
  27. Updated for the 2009 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
  28. Updated for the 2009 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  29. Updated for the 2010 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  30. Updated for the 2011 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  31. Updated for the 2012 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
  32. Updated for the 2013 Macromolecular Crystallography Course in Cold Spring Harbor (NY).


Practical "Model Validation" - EMBO Bioinformatics Course - Uppsala 2001 - © 2001-2013 Gerard Kleywegt (Check links)

Latest update on 10 October, 2013.