From MarcsHomepage


O is a general purpose macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules. Unlike other molecular modelling programs O is a graphical display program built on top of a versatile database system. All molecular data is kept in this database, in a predefined data structure.

The powerful macro facility of O enables the user to customize the use of the program to satisfy his or her specific needs. The current version of O is mainly aimed at the field of protein crystallography

The program is the work of Alwyn Jones and Morten Kjeldgaard.

The current version is available for SGI and some other Unix-graphics-workstations and for Windows

User Interface


The user-interface consists of a main OpenGL-window and the usual startup terminal from which you have typed the command "ono" (if you are on a UNIX-box) or "ont" if you use Windows.
Due to the fact, that O comes from the ancient past of UNIX-programs, it has a quite weird interface compared to nowadays standards. with strange menus and many commands which can´t be memorized easily or found in other programs (Unix or Windows-based). Would you -for example- guess that the command to read a PDB-file from disk (usually File/Open, File/Read or maybe Molecule/Read or so) is "sam_atom_in"????

O is a very powerful program and is routinely used by many users, mainly crystallographers, who take it for model-building, but to me it seems, that this program lacks a user interface which resembles 99% of all other programs sold or used today.
Therefore, especially if you come from the Windows-or Apple world, your learning-curve will be very steep. Maybe die-hard UNIX-users don´t have a problem here, but I doubt this.


Some of the features of O:

  • Display and manipulation of PDB-files
    • Drawing of molecules
    • Real time rotation, translation and scaling
    • Labeling, colouring and display according to different user-editable criteria
    • Translation, rotation and manipulation of residues and atoms
    • Hardware-3D-display of models
  • Display of electron density files from X-ray-crystallography experiments
    • Display of electron density from different programs (CCP4, X-PLOR, PROTEIN, etc.)
    • Display and manipulation of skeletonized density maps
    • Masking of electron density maps
  • Building of amino-acid chains into electron-density maps
    • Automated build of backbone chains
    • Regularization of a modelled structure
    • Fitting of atoms into a given electron density
  • Crystallographic tools
    • Display of unit cells
    • Calculation and manipulation of crystallographic symmetry operations
    • Interactive Patterson-map-viewing/manipulation
    • Molecular replacement