We have developed a software package that models the anisotropic temperature factors of protein structures derived from crystallographic data using normal mode vectors. We hypothesize that the intrinsic flexibility of a structure is largely responsible for the variability in atomic coordinates and can be modeled using normal modes. The package is written in C/C++ and utilizes the CLIPPER libraries from the Collaborative Computational Project Number 4 (CCP4) for handling most crystallographic functions. Furthermore, the file formats and input conventions from CCP4 are used so that our program can be easily integrated into a crystallographer's toolset. The software package was tested on two systems, formiminotransferase cyclodeaminase (FTCD) and the KcsA potassium ion channel. In both cases, the improved description of the thermal fluctuations by the anisotropic models allowed drops in the R values as well as provided better electron density maps for making adjustments to the atomic coordinates and inserting missing atoms. These two examples show that the new normal-mode-based refinement is an effective way for describing anisotropic thermal motions in X-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions.