relax SVN archive

Clean up of the frame order target function code.

This matches the previous changes (r23197), the deletion of the frame_order.average_position user
function. The changes include the removal of the translation optimisation flag as this is now
always performed, and the removal of the flag which causes the average domain rotation pivot point
to match the motional pivot point as these are now permanently decoupled.

Deletion of the frame_order.average_position user function and all of the associated backend code.

This user function allowed the user to specify five different types of displacement to the average
moving domain position:

- A pure rotation, with no translation, about the pivot of the motion in the system.
- A rotation about the pivot of the motion of the system together with a translation.
- A pure translation with no rotation.
- A rotation about the centre of mass of the moving domain with no translation.
- A rotation about the centre of mass of the moving domain together with a translation.

Now the last option will be the default and only option. This option is equivalent to the standard
superimposition algorithm (the Kabsch algorithm) to a hypothetical structure at the real average
position.

The other four are due to the history of the development of the theory. These limit the usefulness
of the theory and will only cause confusion.

Initialized merge tracking via "svnmerge" with revisions "1-23194" from
svn+ssh://bugman@.../svn/relax/trunk

Creation of a branch for cleaning up the frame order analysis.

As this analysis has been in development for many years, a lot of code that was developed for the
theory is no longer needed. Some of this is also a potential source of user confusion. It also
results in many unexpected bugs.

Modified the pivot point PDB representation script to include the shifted pivot.

This is for the 2nd rotor model of CaM frame order in the test suite.

Fix for commit r23154 - the frame_order.py log file is bzipped.

Added a relax script for creating a PDB representation of the original pivot point.

This is for the 2nd rotor model of CaM frame order in the test suite. The resultant PDB file has
been added to the repository.

Modified the 2nd rotor model of CaM frame order optimisation script.

The frame_order.pdb_model user function is now used to create a PDB representation of the rotor
motions for the real, expected parameters and for the optimisation results when the pivot point is
fixed.

In addition, the pymol.cone_pdb user function has been replaced by the pymol.frame_order user
function. All new files have been added to the repository.

Improvements for the rotor PDB representation shown by the pymol.frame_order user function.

The stick radius width change is now only for the rotor PDB object, and not everything in PyMOL.

Modified the frame_order.pdb_model user function so that the three PDB files are optional.

This allows only certain components of the frame order theory to be represented in PDB format.