Some of the steps in modeling transition states for enzyme-catalyzed reactions are often difficult for users to run, but by looking at various worked examples of transition state location, refinement, characterization, etc., the general principles and ideas used in each step can be better understood.
All examples start from a PDB file, in most cases this would be downloaded from the Protein Data Bank and would be referred to by its accession code. Each example gives a description of the sequence of steps used in obtaining one or more transition states in an enzyme-catalyzed reaction.