relax SVN archive

Removal of some accidentally committed debugging code.

Added the full optimisation results for the large angle double rotor frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.

Simplified the PyMOL visualisation relax script created by the frame order auto-analysis.

This now consists of a single pymol.frame_order user function call. The other pymol user function
calls were unnecessary.

Changed some of the default values for the frame order auto-analysis.

The number of Sobol' quasi-random integration points were far too low to obtain any reasonable
results.

Added support for the 'pivot_disp' frame order parameter to the grid search.

This is required for the double rotor model.

Updated all of the CaM frame order system test chi-squared values.

These have changed slightly due to the rotation and translation changes (r24471).

Changed the CaM frame order test data superimposition values.

Because the domains are now defined via the molecule name rather than the residue numbers, the
centroid of rotation set to the CoM has been shifted as now the Ca2+ ions are included in the CoM
calculation. Therefore the superimpose.py script has been updated to not delete the Ca atoms (this
reverts r23354).

All of the frame order optimisation scripts have been updated with the new rotation Euler angles and
translation vector. To match this, the system test base script for the CaM frame order test data
has also had its rotations and translations updates, and the domain user function call changed to
use molecule names.

The script for representing the frame order dynamics for the CaM test data has been updated.

The domains of the system are now defined.

The CaM frame order test data optimisation scripts now save more state files.

The state of the true dynamics and the fixed pivot optimisation results are now stored as well.
This might be useful for extracting these results without redoing the calculations.

Updates for the frame order system tests for the float32 to float64 change (r24463).

Some chi-squared values have slightly changed.