User Guide


Tips & Tricks








Art Gallery






back to Expasy

Last modified
31 March 98
by N.Guex

Glaxo Wellcome
Experimental Research

presents the


v 3.0


Nicolas Guex & Manuel C. Peitsch

Key Words:

PDB; protein; modelling; visualisation; comparison; electron density map; ray-tracing.

This site can be accessed from the following servers




Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server running in the Geneva Biomedical Research Center. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density.

In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images.