Abstract We present the first package of Java classes specifically aimed at the handling of structural and biophysical problems. To enable object-oriented programming a basis of fundamental Java classes is required which deals with basic operations of vectors, matrices, amino acid sequences, crystal symmetries and PDB files. Five classes, which carry out these basic operations, were constructed and bundled together with several utility functions in the PCSB package. Furthermore, to demonstrate their applicability and to obtain programs handling common tasks in structural laboratories, we present the first six applications of PCSB. All applications are portable to different platforms and require only the Java Runtime Environment to be installed on the system. Availability: http://www24.brinkster.com/hofmanna/pcsb/ Contact: [email protected] Supplementary information: A manual for PCSB describing the Java classes as well as the applications is available as PDF file. * To whom correspondence should be addressed.