Model building

Chain builder

Most large molecules explored by biochemists are chain structures composed of residues of one or several types. It is recommended to assemble such molecules using the chain builder. It is not just convenient; essentially, the residues manipulated by the builder include atoms with specified molecular mechanics types. Their correct specification is not a trivial task. This makes the chain builder a basic tool to construct molecules.

Drawing with the mouse

A molecule can be drawn with a mouse. By default in Abalone the ad hoc mode is enabled. In this mode default force constants are associated with atoms. Therefore, molecule drawn immediately ready for some manipulations. For example, the geometry optimizer works. This is a rough model. It can be incrementally improved by adding accurate partial charges and force constants.

Auxiliary tools

There are a number of tools to help create and edit models:





Software for