relax SVN archive

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In addition, the pymol.cone_pdb user function has been replaced by the pymol.frame_order user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.

Fix for bug #22041, the PDB atom serial number error from the structure.write_pdb user function.

This was reported at https://gna.org/bugs/?22041.

The problem is that the structure.write_pdb user function preserves the atom numbering from the
original structure and uses that for the atom serial number. However the atom serial number must be
replaced with sequential values to produce a valid PDB file. This is fatal for any CONECT records.

Created the Structure.test_bug_22041_atom_numbering system test to catch bug #22041.

This was reported at https://gna.org/bugs/?22041.

The problem is that the structure.write_pdb user function does not create the correct atom serial
numbers.

Another fix for the dead link finding script.

And some more improvements for the dead link finding script.

More improvements for the dead link finding script.