relax SVN archive

Added some transparency to the cone in pymol.cone_pdb().

Fix for the frame_order.cone_pdb() user function - the cone is already in the PDB frame, no rotation required.

Fix for the average domain rotation in pymol.cone_pdb().

The pymol angle should be degrees, and the rotation is passive not active.

pymol.cone_pdb() is now rotating the moving domain to the average position for the frame order theory.

Modified frame_order.domain_to_pdb() to remove the file ending if given.

This allows the structure to be rotated in pymol.

Created the frame_order.domain_to_pdb() user function to associated PDB files with domains.

This will be used to rotated the moving domain to the average position within pymol.

Rewrote frame_order.cone_pdb() to handle all of the frame order models.

The start_res arg to create_cone_pdb() is now actually the number of the starting residue of the cone.

Modified the pymol.cone_pdb() user function to handle x, y, and z-axes.

Modified create_cone_pdb() to accept a pre-made structural object and to create a file only when asked.