Difference between revisions of "Relax 3.3.5"

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(→‎CHANGES file: Updated the metadata from the CHANGES file.)
(→‎Features: Updated the feature list to match the CHANGES file.)
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<section begin=features/>
 +
* Improvements to the NMR spectral noise error analysis.
 +
* Addition of the new spectrum.error_analysis_per_field user function to quickly perform a per-NMR field spectrum error analysis.
 +
* Added spectrum.sn_ratio user function to calculate the signal to noise ration for all spins, and introduced the per-spin sn_ratio parameter for the NOE, relaxation curve-fitting and relaxation dispersion analyses.
 +
* Added the new select.sn_ratio and deselect.sn_ratio user functions to change the selection status of spins according to their signal to noise ratio.
 +
* Expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments.
 +
* Conversion of the structure.align, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a standardised pipes/models/molecules/atom_id argument design to allow the user functions to operate on different data pipes, different structural models and different molecules simultaneously and to restrict operation to a subset of all spins.  This is also used by the new structure.atomic_fluctuations user function.
 +
* 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 independently of the align_id atom ID for selecting atoms used in the superimposition.
 +
* Large improvement for the PDB molecule identification code affecting the structure.read_pdb user function allowing discontinuous ATOM and HETATM records with the same chain ID to be loaded as the same molecule.
 +
* Creation of the lib.plotting package for assembling all of the data plotting capabilities of relax into a unified software independent API.
 +
* 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, measured as sample standard deviations, between different molecules.
 +
* The implementation of ordinary least squares fitting.
 +
* And improvements for the pcs.corr_plot and rdc.corr_plot user functions.
 +
* 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 user function.  The Needleman-Wunsch algorithm is implemented as in the EMBOSS software to allow for gap opening and extension penalties as well as end penalties.  This is also used in all the other structure user functions dealing with multiple molecules - structure.atomic_fluctuations, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose, structure.web_of_motion.
 +
* Improved support for PDB secondary structure metadata for the structure.read_pdb and structure.write_pdb user functions.
 
<section end=features/>
 
<section end=features/>
  

Revision as of 16:55, 27 January 2015


Description

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.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.3.5
(27 January 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.5


Features

  • Improvements to the NMR spectral noise error analysis.
  • Addition of the new spectrum.error_analysis_per_field user function to quickly perform a per-NMR field spectrum error analysis.
  • Added spectrum.sn_ratio user function to calculate the signal to noise ration for all spins, and introduced the per-spin sn_ratio parameter for the NOE, relaxation curve-fitting and relaxation dispersion analyses.
  • Added the new select.sn_ratio and deselect.sn_ratio user functions to change the selection status of spins according to their signal to noise ratio.
  • Expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments.
  • Conversion of the structure.align, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a standardised pipes/models/molecules/atom_id argument design to allow the user functions to operate on different data pipes, different structural models and different molecules simultaneously and to restrict operation to a subset of all spins. This is also used by the new structure.atomic_fluctuations user function.
  • 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 independently of the align_id atom ID for selecting atoms used in the superimposition.
  • Large improvement for the PDB molecule identification code affecting the structure.read_pdb user function allowing discontinuous ATOM and HETATM records with the same chain ID to be loaded as the same molecule.
  • Creation of the lib.plotting package for assembling all of the data plotting capabilities of relax into a unified software independent API.
  • 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, measured as sample standard deviations, between different molecules.
  • The implementation of ordinary least squares fitting.
  • And improvements for the pcs.corr_plot and rdc.corr_plot user functions.
  • 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 user function. The Needleman-Wunsch algorithm is implemented as in the EMBOSS software to allow for gap opening and extension penalties as well as end penalties. This is also used in all the other structure user functions dealing with multiple molecules - structure.atomic_fluctuations, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose, structure.web_of_motion.
  • Improved support for PDB secondary structure metadata for the structure.read_pdb and structure.write_pdb user functions.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.


See also


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