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Changes
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Symbol formatting for Ca2+.
* Parameter update for the 2<sup>nd</sup> rotor CaM frame order test model optimisation script. The Euler angles for the rotation about the motional pivot have been replaced by the translation vector and Euler angle CoM rotation parameters.
* Large increase in precision for the 2<sup>nd</sup> CaM frame order free rotor model test data set. The higher precision is because the number structures in the distribution is now 20 million rather than 999,999 and the numpy.float128 data averaging has been used.
* Updated the CaM frame order test model superimposition script. The Ca2Ca<sup>2+ </sup> atoms are now deleted from the structures before superimposition so that the centroid matches that used in the frame order analysis.
* The average domain rotation centroid is printed out when setting up the frame order target functions. This is to help the user understand what is happening in the analysis.
* Faster clearing of numpy arrays in the lib.frame_order modules. The x[:] = 0.0 notation is now used to set all elements to zero, rather than nested looping over all dimensions. This however has a negligible effect on the test suite timings.
* Updated all of the frame order scripts for the frame_order.pdb_model and pymol.frame_order changes. These are the scripts for the CaM frame order test data.
* Redesign of the average domain position part of the [http://www.nmr-relax.com/manual/frame_order_pdb_model.html frame_order.pdb_model user function]. The Monte Carlo simulations are now represented. If the file root is set to the default of 'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a compressed version. Each simulation is in a different model, matching the geometric representation '*_sim.pdb' files. The original structure is copied for each model, and then rotated to the MC simulation average position.
* Change all of the [http://www.nmr-relax.com/manual/domain.html domain user function] calls in the frame order CaM test data scripts. The domains are now identified by the molecule name rather than the range of residues. This allows non-protein atoms, for example the Ca2Ca<sup>2+ </sup> atoms, to be rotated to the average domain position as well.
* The PyMOL disable command is now used by the [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function]. This is to first disable all PyMOL objects prior to loading anything, to hide the original structures and any previous frame order representations, and then to hide all of the Monte Carlo simulation representations. This is to simplify the picture initially presented to the user while still allowing all elements to be easily found.
* The [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function] now centers and zooms on all objects.
* The CaM frame order test data optimisation scripts now save more state files. The state of the true dynamics and the fixed pivot optimisation results are now stored as well. This might be useful for extracting these results without redoing the calculations.
* The script for representing the frame order dynamics for the CaM test data has been updated. The domains of the system are now defined.
* Changed the CaM frame order test data superimposition values. Because the domains are now defined via the molecule name rather than the residue numbers, the centroid of rotation set to the CoM has been shifted as now the Ca2Ca<sup>2+ </sup> ions are included in the CoM calculation. Therefore the superimpose.py script has been updated to not delete the Ca atoms. All of the frame order optimisation scripts have been updated with the new rotation Euler angles and translation vector. To match this, the system test base script for the CaM frame order test data has also had its rotations and translations updates, and the [http://www.nmr-relax.com/manual/domain.html domain user function] call changed to use molecule names.
* Updated all of the CaM frame order system test chi-squared values. These have changed slightly due to the rotation and translation changes.
* Added support for the 'pivot_disp' frame order parameter to the grid search. This is required for the double rotor model.