SwissPDBViewer

From MarcsHomepage

Introduction

SwissPDBViewer has originaly been developed by Nicholas Guex with help from Glaxo Wellcome, and is originally based on Macintosh-computers (OS 9). Version 3.5b1, has been ported to Windows, SGI, and Linux. I have reviewed the Windows and SGI-version. All platform-versions should be quite similar -the overall look and feel of the Windows version is the same as with other applications ported from the Mac (Photoshop, Endnote, to name a few), and the SGI-version is comparable.

For porting the application from Mac OS 9, an experimental toolkit from Metrowerks was used, which apparently did not made it to the market or is not widely used.

Whatever the reason, the result of this is an interface, which feels and behaves a bit clumsy under operating-systems other than Mac and Windows (although both the SGI and Linux-version are usable, they feel alien and behave weird and somewhat buggy quite frequently).

Since there was no update of the software after version 3.7 which is several years old now, the project can be considered dead. The software is still useable though, especially on it's original platform and Windows.

User Interface

Spdbv1.jpg

The user-interface of SwissPDBViewer is based on the Macintosh-version, which means, you get an easy-to-use point and click GUI, which can be used productively from day one on, even from people with little computer-knowledge. Everything can be selected from lists and menus, you don´t have to learn a more or less cryptic command-language.

SwissPDBViewer normaly provides you only with a wireframe-display of the molecule, which is quite fast, even on very slow PC´s, but which is a bit confusing from time to time especially when dealing with large structures (there´s even no backface-elimination). The more recent versions of SwissPDBViewer got OpenGL image-rendering supporting more recent hardware. The software-only wireframe mode is still available and usefull if you have a slow computer or need to display large molecules.

Version 3.7 also has a rudimentary scripting language, which can be used to automate tasks.

Features

The list of features for SwissPDBViewer is a bit too long for complete display, see the reference on the SwissPDBViewer/DeepView-homepage mentioned above. I will give only a short overview of some of the main capabilities of the program and review the goodies I like most.

  • Viewing, manipulating and modelling of multiple molecules in layers (separating them cleanly from one another)
  • Interactive Ramachandran-Plot-manipulation for protein modelling -i.e. you can change the phi/psi-value of a selected amino-acid in the diagram and it will move on screen.
  • Capping (addition of C-terminal OXT-entries in the PDB-record) for multi-chain-molecule-fragments.
  • Writes correct PDB (with some extensions properly separated from the coordinate-section). A thing Molmol for example still does not do.
  • Interface to the SwissModel database for homology-modelling from known sequences
  • Output to Quickdraw3D and POVRay for publication-grade imaging
  • Interface to Molecular Dynamics (MD) software-packages (AMBER, CHARMM, GROMOS (not yet implemented)) for energy minimization

Some (imho :) nice images prepared with SwissPDBViewer and Povray can be found on my Diploma -page.