relax SVN archive

Updated the CHANGES file for relax 3.3.5.

Introduced the nested_params_ave_dom_pos argument to the frame order auto-analysis.

This allows the average domain position to be set to no rotations and translations rather than
taking the average position from the rotor or free-rotor model. This can be useful when large
motions are present causing the rigid model to have unreasonable domain positions.

Added the relax 3.3.5 PDF manual to the repository.

Updated the version number to relax 3.3.5.

relax version 3.3.5.

This is a major feature and bugfix release. It fixes an important bug in the Monte Carlo simulation
error analysis in the relaxation dispersion analysis. Features include improvements to the NMR
spectral noise error analysis, expansion of the grace.write user function to handle both first and
last point normalisation for reasonable R1 curves in saturation recovery experiments, the
implementation of Needleman-Wunsch pairwise sequence alignment algorithm using the BLOSUM62, PAM250
and NUC 4.4 substitution matrices for more advanced 3D structural alignments via the structure.align
and structure.superimpose user functions as well as any of the other structure user functions
dealing with multiple molecules, expansion of the structure.rmsd user function to allow the RMSD to
be calculated between different molecules rather than just models, expansion of the
structure.find_pivot user function to allow it to operate on different molecules, conversion of the
structure.displacement, structure.rmsd, structure.superimpose and structure.web_of_motion user
functions to a new pipes/models/molecules/atom_id design to allow the user functions to operate on
different data pipes, different structural models and different molecules, addition of the
displace_id argument to the structure.align and structure.superimpose user functions to allow finer
control over which atoms are translated and rotated by the algorithm, large improvement for the PDB
molecule identification code affecting the structure.read_pdb user function, creation of the
lib.plotting package for assembling all of the data plotting capabilities of relax, implementation
of the new structure.atomic_fluctuations user function for creating text output or Gnuplot graphs of
the correlation matrix of interatomic distance, angle or parallax shift fluctuations, the
implementation of ordinary least squares fitting, and improvements for the pcs.corr_plot and
rdc.corr_plot user functions.

Disabled the General.test_bug_23187_residue_delete_gui GUI test.

This is essential as a wxPython bug in Mac OS X systems causes this test to trigger a 'Bus Error'
every time the GUI tests are run, killing relax.

Merged revisions 27321-27323 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27321 | bugman | 2015-01-27 09:48:41 +0100 (Tue, 27 Jan 2015) | 7 lines

Created the Structure.test_pdb_combined_secondary_structure system test.

This is used to demonstrate a problem in the handling of secondary structure metadata when combining
multiple PDB structures. It appears as if the chain ID is preserved as the original ID and is not
updated to match the new IDs in the output PDB.
........
r27322 | bugman | 2015-01-27 10:50:56 +0100 (Tue, 27 Jan 2015) | 9 lines

Bug fix for the PDB secondary sheet handling when combining multiple PDB structures.

The helix and sheet metadata now converts the original chain IDs into molecule indices, shifted to
new values based on the currently loaded data, when the structure.read_pdb user function is
executed. When the structure.write_pdb user function is executed, the molecule indices are
converted into new chain IDs. This allows the chain IDs in the HELIX and SHEET records to match
those of the ATOM and HETATOM records.
........
r27323 | bugman | 2015-01-27 10:51:34 +0100 (Tue, 27 Jan 2015) | 5 lines

Updated the Structure.test_metadata_xml system test for the changed PDB metadata handling.

The helix and sheets IDs are now molecule indices.
........

Updated the Structure.test_metadata_xml system test for the changed PDB metadata handling.

The helix and sheets IDs are now molecule indices.

Bug fix for the PDB secondary sheet handling when combining multiple PDB structures.

The helix and sheet metadata now converts the original chain IDs into molecule indices, shifted to
new values based on the currently loaded data, when the structure.read_pdb user function is
executed. When the structure.write_pdb user function is executed, the molecule indices are
converted into new chain IDs. This allows the chain IDs in the HELIX and SHEET records to match
those of the ATOM and HETATOM records.

Created the Structure.test_pdb_combined_secondary_structure system test.

This is used to demonstrate a problem in the handling of secondary structure metadata when combining
multiple PDB structures. It appears as if the chain ID is preserved as the original ID and is not
updated to match the new IDs in the output PDB.