Molecular-geometry calculations in the superspace framework of incommensurate structure analysis are presented in detail. In particular, a method is described for attaching atoms to groups of others without the necessity of introducing further modulation functions. Modified structure-factor expressions are derived to simplify the application of constraints to modulation functions by introducing internal coordinate reference points in a more general way. The consequences of such changes are discussed. The results can be useful to improve the existing algorithms for incommensurate structure refinement and the analysis and presentation of results, especially for recently discovered incommensurate structures of large organic molecules. Some ambiguities still existing in the superspace approach related to molecular geometry are clarified. The results may also be useful for the compilation of a database describing incommensurate structures. [References: 22]