The following tools allow visualization of macromolecular structures in PDB format (i.e. experimental structures and models). SWISS-MODEL results are best viewed and manipulated with the program DeepView (Swiss-PdbViewer), which also allows to modify the target template alignment for the SWISS-MODEL "project mode".
- DeepView The Swiss-PdbViewer
- DINO Protein Structure Visualization for Linux
- Molscript a program for displaying molecular 3D structures such as proteins.
- POV-RAY Open Source Raytracing software
- JMOL an open-source Java viewer for chemical structures in 3D
- PyMOL is a Python based open-source viewer for visualization of macromolecular structures
- Chimera extensible program for interactive visualization and analysis of molecular structures