relax SVN archive

Added systemtest Relax_fit.test_curve_fitting_height_estimate_error() for the manual and automated analysis of exponential fit.

This is to prepare for new methods in the auto analysis protocol.

Fix for the axis permutation protocol in the frame order auto-analysis.

This would fail if a results file for the permuted model already exists as the pipe.copy user
function call was being performed too early.

Simplified the optimisation in the axis permutation part of the frame order auto-analysis.

Only the last, highest quality setting is used for optimisation.

Modified the frame order auto-analysis.

The axis permutation algorithm is now performed on all isotopic cone and pseudo-ellipse models.
This is just in case the non-global minima was found in the original optimisation. The isotropic
cone models possess two local minima whereas the pseudo-ellipse models possess three local minima.

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/.

Added the missing PDB files which should have been committed previously.

This are in test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy.

Created the other isotropic cone condition z <= x = y.

As there are no constraints in this model, this condition should not result in any major
differences, just the size of the cone being different and the optimisation having to decrease the
cone angle significantly to mimic the rotor.

Added the Gimp XCF file for the logo of the relax wiki (http://wiki.nmr-relax.com).

Created set of files showing the axis permutation problem for the isotopic cone frame order model.

This shows that there are two minima. However one has a chi-squared value of ~1, and the other a
value of ~150. Nevertheless, the optimisation could be trapped in the non-global minimum so the
frame_order.permute_axes user function should be used for the isotopic cones as well, just in case.

Added support for the isotopic cone models to the frame_order.permute_axes user function.

This is a simpler setup, but it uses the same permutation algorithm as derived for the
pseudo-ellipse models. Instead of setting the x and y cone angles separately, they are instead
averaged. And as the cone axis is undefined in the xy plane, the axis has been randomly selected as
being the axis perpendicular to both the z-axis and the reference frame x-axis.