X-PLOR is a sophisticated computer programme that provides an interface betweeen theoretical foundations and experimental results in structural biology, with specific emphasis on X-ray crystallography and nuclear magnetic resonance of large biological molecules. This manual to X-PLOR Version 3.1 presents the theoretical background, syntax and function of the programme and also provides a comprehensive list of references and sample input files with comments. It is intended primarily for researchers and students in the fields of protein chemistry, structural biology and computational moecular biology.