Geometry is the TNT program which performs all tasks related to standard stereochemistry. Its basic function in refinement is to read a coordinate file, along with its corresponding sequence file and standard geometry library, to calculate the function value, gradient, and curvature of the stereochemical residual function. Its other great task is to produce the list of worst violations of each kind of stereochemistry. Both of these tasks are accessed via the shell scripts tnt and geometry.
Geometry also has a very useful tool for the evaluation of the quality of a standard library. One can read a coordinate file and a library and, instead of looking for outliers, look at the standard values the library would have to have to match the coordinates. If one has a number of high resolution models they can all be read into Geometry and its list can be checked for systematic differences between the coordinates and the library. This list is generated with the $tntbin/report_geo script.