The US-SOMO approach, fully described in another article in this issue (Brookes et al. 2009), is based on building a direct correspondence between groups of atoms within each residue in a biomacromolecule and the beads used to represent them. The bead models can be used to estimate the translational diffusion coefficient, the sedimentation coefficient, Stokes radius, rotational correlation time, intrinsic viscosity, and radius of gyration for comparison with results from hydrodynamic experiments and other related techniques. The bead models can also be used where the beads serve as scattering centers for the simulation of small-angle X-ray and neutron scattering data. US-SOMO generates a model of a macromolecule as an ensemble of rigid, non-overlapping spheres (beads) of different radii, utilizing a very well developed computational approach to calculate the hydrodynamic parameters (reviewed in García de la Torre and Bloomfield 1981; Spotorno et al. 1997; Carrasco and García de la Torre 1999). For instance, amino acids in proteins are usually represented with two beads, one for the atoms of the main chain and one for those of the side chain. The beads initial volumes are determined by the volumes of the atoms assigned to each bead and the volume of the theoretically bound water of hydration (Kuntz and Kauzmann 1974). Their position is determined by rules outlined in Rai et al. (2005), and several options are available to remove the bead overlaps while maintaining as much as possible the original surface envelope (Rai et al. 2005; Brookes et al. 2009). To improve the accuracy of the computations and reduce the computational load, an accessible surface area scan is performed on the original structure, identifying buried and exposed residues. Only the beads representing the exposed residues are used in the hydrodynamic computations. The residue definitions and their associate parameters reside in user-modifiable tables, affording a great flexibility in modeling. The program loads structures from protein data bank (PDB; Berman et al. 2000) formatted files, recognizing properly coded residues, and prompting the user when new residues are encountered. Currently, 64 residues containing ~300 different atom types are defined in the US-SOMO tables, including all standard amino acids, ribo- and deoxyribonucleosides and nucleotides, carbohydrates, and several co-factors. The program uses dynamic memory allocation and the size of the structure is theoretically limited only by the available memory in the computer. The original structures and the generated bead models can be visualized using the integrated molecular visualization program RasMol (Sayle and Milner-White 1995; http://openrasmol.org/#Software). Several extensions are planned within the Open AUC Project, including a mechanism to describe flexible structures and the application of grid procedures to treat very large structures and complexes.