relax SVN archive

Added the geometric module to the specific_analyses.frame_order package __all__ list.

Fixes for the titles in the frame order geometric representation from frame_order.pdb_model.

There were a few bugs for a number of the frame order models preventing this code from working.

Reverted the lines under the table titles for http://www.nmr-relax.com/download.html.

Fixes for the MC simulation rotor objects in the frame order geometric representation.

The axes of the Monte Carlo simulation rotors objects were being set to the original values and not
to the simulation values.

Fix for the internal structural object MolContainer.last_residue() method.

This can now operate when no structural information is present, returning 0 instead of resulting in
an IndeError.

Removed an accidentally committed change to http://www.nmr-relax.com/download.html.

The relax software tables at http://www.nmr-relax.com/download.html are now fixed cell width.

Changes to the rotor object in the frame order geometric representations.

For the isotropic and pseudo-elliptic cone models, the rotor is now halved. Instead of having two
axes radiating from the central pivot and terminating in the propeller blades, now only the positive
axis is shown lying in the centre of the cone.

Changed the alternative representation names for the frame order geometric objects.

The aim is to put both representations on a more equal footing, as they are identical solutions.
Hence the inverted representation might be the correct representation of the domain motions. So
instead of calling these 'positive' and 'negative', the 'A' and 'B' notation will be used.

This affects the names of the files produced by the frame_order.pdb_model user function as well as
the internal titles. Instead of ending the files with "*_pos.*" and ""*_neg.*", these have been
changed to "*_A.*" and ""*_B.*". The atoms used for the titles have also been renamed, and the
pymol.frame_order user function now labels the titles using the 'A' and 'B' notation.

Added titles to the frame order geometric representation PDB files from frame_order.pdb_model.

These are in the form of special Ti atoms placed 40 Angstrom away from the pivot along the z-axis of
the system, or shifted 3 more Angstrom for the Monte Carlo simulations. These are used to label the
alternative representations or the Monte Carlo simulation representations. The residue type is set
to TLE and this has been registered in the internal structural object.

The pymol.frame_order user function now calls the represent_titles() function to select these atoms,
hide them, and then add a long descriptive title. The atom name is used to distinguish between
different titles.