Chimera

The UCSF Chimera program displaying the PDB code 1VRT as a ribbon diagram.

Chimera is a good program for visualization of proteins and small molecules and is freely available for downloading at the UCSF Chimera website.

It also includes plugins for interfacing with the DOCK program. The DOCK Prep module prepares a protein complex for redocking, while the DOCK View module allows the convenient browsing of docked results. To start learning how to use chimera, go to Help > Tutorials, or the Chimera Tutorial.

ViewDock Tool

Useful for reading mol2 files produced by dock. Access from Tools > Surface/Binding Analysis > ViewDock. Can read the energy, rmsd and cluster size of each pose reported by dock and sort by these columns.

Useful Command line

calculating distance between 2 atoms

  distance #1.1@N2 #0:71@HG2

picking a selection

  sel #0:47-50,67,71,80-82,92-110,146,149,159-162

Enabling the Toolbar

Favorites > Preferences > Tools and select the features you want. Viewdock can be placed here. Click Save to make these changes permanent.