After starting DomainFinder, click on the button labeled ``Conformation comparison'' to switch to conformation mode. You can switch between modes at any time if you wish to use both modes on the same protein. Load the reference structure via the File menu entry ``Load reference conformation'', then the second structure via ``Load comparison conformation''. Note that it does make a difference which of the two conformations is used as a reference; better results are obtained if the reference conformation is the one with a larger exposed surface, i.e. an ``open'' conformation. Once the two conformations have been loaded, DomainFinder eliminates global translational and rotational motion between them, and displays the remaining RMS difference.
If you wish to verify that your two conformations are indeed compatible, you can select ``Show both conformation'' from the File menu. This will show both conformations together, one in black and one in red, with the two positions of each atom linked by a blue line. Erratic blue lines indicate a mismatch between the two configurations. This display can also serve as a first impression of the difference between the two conformations.
Protein structures obtained from experiment are always subject to experimental inaccuracies. These inaccuracies can distort the deformation energy calculation, since a random error on each atom position is indistinguishable from a high overall deformation. DomainFinder can eliminate such experimental noise while keeping the important large-scale differences between the conformations; the details of this procedure have been described in Ref. 1. The amount of noise filtering can be adjusted using the slider labeled ``Noise filter''. Its value is the amount by which the RMS distance between the conformations will be reduced by filtering, given in nm (nanometers). The default value of 0.01 nm is good for most cases; you should choose a larger value if one or both conformations have high experimental inaccuracies, as indicated e.g. by a high crystallographic resolution. A smaller value must be chosen if the total RMS distance between the conformations is very small, i.e. smaller than about 0.1 nm. You can verify the effect of the filter visually using the File menu entry ``Show filter effect''. It produces a display showing the original comparison conformation and its filtered equivalent. The reference conformation is not changed by filtering. The File menu entry ``RMS distances'' shows the three RMS distances between reference, comparison, and filtered comparison conformations.
Next you must choose the deformation threshold, i.e. the deformation energy value that you consider the highest acceptable one for regions classified as rigid. The default value is a good starting point; you may have to increase it significantly for small proteins. Note that the deformation energy definition used by DomainFinder is larger than the one described in Ref. 1 by a factor of five; this factor was introduced to make typical deformation energies for conformation-based analysis similar to those for normal mode-based analysis.
The following steps are the same as for an analysis based on normal modes, and are described in sections 6 and 7.