Aids Understanding of Complex Systems 1. A ribbon representation of the backbone with prosthetic groups highlighted 4. A ribbon representaion with the separate peptide chains indictaed and prosthetic group highlighted 5. A single peptide chain and prosthetic group 6. Before any effective modelling can be achieved a 'good' model is required.
Most modelling packages allow the construction of molecules 'on screen'.
Usually a library of accurate molecular fragments are available and can be edited to build the desired structures. A model that is built from standard fragments will not accurately respresent a given structure. In order to obtain a good model the structure must be refined. This process is often called optimization or energy minimization. QM calculations solve approximations to Schroedinger's equation in order to determine electron density, energy, and other molecular properties.