10 Swiss-PdbViewer

The aim of Swiss-PdbViewer is to help biologists compare proteins structures, by the mean of a free user-friendly integrated package. As molecular biologists tend to work more with Macintoshes and PCs than with UNIX systems, Swiss-PdbViewer has initially been developed on microcomputers, although a X-Window version is also planned.

A more complete description of the program features, as well as executables, user guide and tutorial can be found on the ExPASy server:

10.1 Using Swiss-PdbViewer as an interface to SWISS-MODEL

As explained in the chapter 6.6, the SWISS-MODEL server functions in two modes. In order to obtain a reliable model, one may need to use the server in "Optimise mode", which requests the user to edit the alignment so that insertions and deletions (indels) are located in reasonable locations (generally in loops, as secondary structure elements tend to be conserved among homologous proteins). Swiss-PdbViewer let the user interactively alter the indels placement, and a visual feedback is provided in real time. Once the best alignment has been decided, a direct submission to SWISS-MODEL can be performed, Swiss-PdbViewer taking care of providing alignments and command files formatted correctly.

PDB files do not necessarily contain all amino-acids, nor all atoms of an amino-acid. Missing atoms are generally part of amino-acids whose side chain points toward the solvent. Indeed, these side chains are more labile and might provide insufficient electronic density to be precisely located.

In some cases alternate atoms positions are given, when electronic density depicts two allowed atom positions for the same atom. SWISS-MODEL can be confused by such incomplete PDB files, therefore all PDB files have been passed through a filter that renumbers all chains from 1, store only one chain by file, and removes uncertain information, as well as the header, solvent molecules and HETATMs. These files are named EXPDB and are the starting point of all comparative modelling. It is therefore very important to prepare your best alignments using such files. Swiss-PdbViewer will not allow you to submit modelling requests if you are not using EXPDB files as templates.