relax SVN archive

Change for how the CaM frame order free-rotor pseudo-ellipse test script handle the average position.

This should have been updated earlier (r23397).

Updated a number of the CaM frame order system tests for the higher precision data.

The new data results in chi-squared values at the real solution to be much closer to zero.

Change for how the CaM frame order system test scripts handle the average domain position rotation.

The trick of pre-rotating the 3D coordinates was used to solve the {a, b, g} -> {0, b', g'} angle
conversion problem in the rotor models no longer works now that the average domain position
mechanics has been simplified. Instead, high precision optimised b' and g' values are now set, and
the ave_pos_alpha value set to None.

The high precision parameters were obtained with the frame_order.py script located in the directory
test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target function was modified so
that the translation vector is hard-coded to [-20.859750185691549, -2.450606987447843,
-2.191854570352916] and the axis theta and phi angles to 0.96007997859534299767 and
4.0322755062196229403. These parameters were then commented out for the model in the module
specific_analyses.frame_order.parameters so only b' and g' were optimised. Iterative optimisation
was used with increasing precision, ending up with high precision using 10,000 Sobol' points.

The CaM frame order system test mesg_opt_debug() method not prints out the translation vector.

This is printed out at the end of all CaM frame order system tests to help with debugging when the
test fails.

Changed the average domain position parameter values in the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
The translation vector coordinates are now set, as well as the CoM Euler angle rotations. These
come from the log file of the test_suite/shared_data/frame_order/cam/superimpose.py script, and are
needed due to the simplification of the average domain position mechanics now mimicking the Kabsch
superimposition algorithm.

Improved the value setting in the optimisation() method of the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.

Merged revisions 23392 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23392 | bugman | 2014-05-24 08:53:35 +0200 (Sat, 24 May 2014) | 3 lines

All three file arguments for the pymol.frame_order user function are now optional.
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All three file arguments for the pymol.frame_order user function are now optional.

Missing import from the trunk merge.

Merged revisions 23389 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23389 | bugman | 2014-05-23 19:39:53 +0200 (Fri, 23 May 2014) | 6 lines

Small speed up for all the isotropic cone and pseudo-elliptic cone frame order models.

The vector length calculation for the numeric PCS integration has been simplified and shifted
outside of a loop to take advantage of the speed of numpy.
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