Much information about the slow motions of a protein can be obtained by looking at the deformation energies for each atom. The entry ``Show deformation'' in the Deformation menu shows the reference conformation with a color code representing the deformation energies. Blue atoms correspond to small deformation energies, green atoms are close to the deformation threshold, and red atoms are in particularly flexible regions of the protein. Blue and green atoms are thus below the deformation threshold and candidates for domains in a subsequent domain analysis; if you find that most of your atoms are yellow or red, you should increase the deformation threshold before starting the domain analysis. However, you should also consider the possibility that your protein has no domains, either because it is too flexible to allow a description of its slow motions by quasi-rigid substructures, or because the deformation associated with these motions is uniformly distributed over the whole protein.
Although the energy scale for the deformation energies is arbitrary (see Ref. 1 for a detailed discussion), it is nevertheless an absolute scale independent of the specific protein. This means that deformation energy values can be compared between proteins and, in the case of a normal mode based analysis, between modes. If a certain protein requires a higher deformation threshold than another protein for a useful domain decomposition, this indicates that the first protein has a higher overall flexibility and less rigid domains. A domain decomposition should therefore never be published without quoting the deformation threshold used for it.
For a more detailed visualization, the deformation energy information can be exported in two formats. Using the Deformation menu entry ``Write VRML file...'', you can write a VRML version of DomainFinder's deformation visualization. With the menu entry ``Write PDB file...'' you can produce a PDB file which contains the deformation energy values coded in the temperature factor field for each atom. A temperature factor of 99 indicates atoms whose deformation energy exceeds twice the deformation threshold; values between zero and 79.2 correspond linearly to deformation energies between zero and twice the deformation threshold.