Economou Lab-Teaching BIO501



SwissPDB Viewer-an introduction

Basic skills for the retrieval of protein 3D structure files (pdb) and analysis of protein structures

Molecular Biology and Biomedicine and Protein Biotechnology  


Swiss-PdbViewer (or DeepView) is a molecular structure viewer with a user-friendly interface.

Macromolecules can be: visualized in several formats, coloured , rotated, mutated, truncated, superimposed with homologues etc. It is available for Mac, PC and Linux (download).

Useful SwissPDB Viewer sites:

Basic Tutorial (strongly recommended)

Advanced Tutorial

Discussion List


Downloading pdb files:

Protein structures are determined either by X-ray crystallography or by NMR. The data describing the three dimensional co-ordinates for all the atoms of the protein is contained in a pdb (protein data bank) file that has a name like "1XMN.pdb". To download protein structure files that can be viewed and modified with SwissPDB Viewer on your computer:

If you only have the name of the protein>

PubMed (chose "Structure" from the drop down menu left of the query window and write protein name in the query window) or


If you know the file name of the structures>

RCSB-PDB (write the file name in the query window)

PDBsum (write the file name in the query window)

For more protein structure-related links

For more protein-related links