relax 1.3.4

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relax version 1.3.4
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Keywords Bruker ncproc parameter, hybridisation, N-state model, MOLMOL, NOE distance restraints, pseudo-atoms, structure
Release type Major feature
Release date 12 August 2009
The PDF version of the relax 1.3.4 user manual The relax 1.3.4 user manual

Description

This is a major feature release featuring innumerous changes and bugfixes. New features include support for spin containers for psueedo atoms, NOE distance restraints, improved structure handling with multiple molecules and multiple models, the N-state model with equal and fixed probabilities, handling of the Bruker ncproc parameter, return of hybridisation, return of MOLMOL macros for illustrating model-free parameters, and initial support for the new Frame Order theories.


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 1.3.4
(12 August 2009, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.4


Features

  • The file format of peak intensity lists is now automatically detected (supporting Sparky, XEasy and NMRView).
  • Initial support for a generically formatted peak intensity file (note, this is not yet usable).
  • Error analysis for peak intensities is significantly improved with support for baseplane RMSD, a subset of spectra replicated, and all spectra replicated for both peak heights and peak volumes.
  • NOESY distance restraints (in Xplor or generic format) can now be used in the N-state model via the noe.read_restraints user function.
  • Psuedo atoms/spin containers are now supported via the spin.create_pseudo user function (used for the NOE distance restraints).
  • Support for multiple molecules and/or multiple models within relax.
  • Multiple molecules (as one or more PDB files) can now be read in as individual molecules of different models.
  • Multiple models (as one or more PDB files) can now be read in as multiple molecules of the same model.
  • The internal PDB writer can now generate a file with multiple molecules and multiple models.
  • The N-state model with fixed and equal probabilities is now supported.
  • The bond length values for RDCs are now hard-coded (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).
  • Added the Bruker ncproc parameter to handle Topspin's integer scaling of FID intensities (to the spectrum.read_intensities user function).
  • Hybridisation support, present in relax 1.2, has returned allowing data pipes to be merged (i.e. to hybridise two model-free data pipes with a different diffusion tensor for sets of spins).
  • The initial code for relaxation dispersion analyses has been added (note, this is not yet usable).
  • Initial support for the new Frame Order theories, using the isotropic cone model for RDC data of domain dynamics.
  • MOLMOL macro support for plotting model-free parameter values onto the structure has returned.


Changes

  • The XH bond vector distribution PDB and Pymol representation is now restored.
  • The new user function class 'spectrum' contains all functions associated with spectral data.
  • Spectral data is now identified by unique spectrum ID strings.
  • The noe.read and relax_fit.read user functions have been merged into spectrum.read_intensities.
  • The relax_fit.mean_and_error user function is now called spectrum.error_analysis.
  • The noe.error user function is now called spectrum.baseplane_rmsd.
  • The new spectrum.integration_points user function is used to specify the number of points used in a volume integration.
  • The R1 and R2 relaxation time period is now specified using relax_fit.relax_time.
  • grace.write will now show a warning when an empty file is being created.
  • Replicated spectra are now specified explicitly via spectrum.replicated.
  • Extensive code base clean up - including formatting, unused imports, comments, typos, etc.
  • Complete redesign of the structural information storage.
  • Massive speed up of the structure.vectors user function.
  • More element types of standard protein PDB atom names are identified (to support PDB files with a blank element column).
  • Information is now printed out when reading RDCs and PCSs to aid the user identify usage faults.
  • The RDC and PCS data is now checked before being loaded into relax.
  • The N-state model grid search now handles alignment tensor parameters.
  • For better optimisation, the grid search lower bound for alignment tensor elements has changed from 0 to -1e-3.
  • Improvement to the algorithm for determining attached atoms in the internal PDB reader - a 2 rather than 1 Angstrom radius sphere is now being searched.
  • The molecule.name user function can now name unnamed molecules.
  • The diagonalised alignment tensor is now created.
  • Spin numbers can now be set to None, adding support for polymers where the atom name rather than number is used.
  • The Q factor is now calculated as Clore's R-factor divided by N, matching the Pales default mode (both Q factors are now calculated and stored).
  • The force flag has been introduced to the mol/res/spin naming and numbering user functions, where the default is now not to overwrite.
  • Redesign of the spin.create and residue.create user functions - respectively residue and molecule names and numbers are used instead of the res_id and mol_id arguments, allowing residues and molecules to be created as needed.
  • Modified the full_analysis.py script to perform 500 Monte Carlo simulations and turned on automatic looping.
  • Support for non-identical sequences in different PDB files within the same data pipe (only as different molecules, not different models).
  • Modified the structure.vectors user function to fail if no vectors are found, saving the user a lot of sanity when fixing a non-functional script.
  • A quadratic, flat-bottomed well potential has been added for the NOE distance restraints.
  • For the N-state model, a default of inverse sixth power averaging of NOE distance restraints is being performed.
  • The pcs.centre user function can now accept pseudo-atoms.
  • The pcs.centre user function can now handle multiple paramagnetic centres.
  • The new maths_fns.rotation_matrix.R_axis_angle() function generates a rotation matrix from the axis-angle notation.
  • The new maths_fns.rotation_matrix.random_rot_axis() and maths_fns.rotation_matrix.R_random_axis() functions are used to generate random rotation matrices.
  • The new maths_fns.rotation_matrix.R_random_hypersphere() function generates a pure random rotation matrix.
  • The new maths_fns.rotation_matrix.quaternion_to_R() function generates a rotation matrix from a quaternion.
  • The new maths_fns.kronecker_product.kron_prod() function is used to calculate the Kronecker product.
  • Converted the user function n_state_model.set_type to align_tensor.reduction.
  • Renamed n_state_model.set_domain to align_tensor.set_domain.
  • The statistics ordering has been improved when profiling.
  • align_tensor.init can now accept any type of float or int (python or numpy).
  • Removed the checks to see if the RDC or PCS data is already loaded, allowing sequential loading by a few calls to rdc.read and pcs.read.
  • Large improvements to the information printed by the align_tensor.display user function.
  • Removed a check for the presence of the alignment tensor so that align_tensor.init can be used to reset the tensor values.
  • Created the six transpose functions for rank-4, 3D tensors in maths_fns.kronecker_product.transpose_ij().


Bugfixes

  • A bug in the Monte Carlo simulations for relaxation curve-fitting has been fixed (bug #12670).
  • Fixes for the Pymol PDB file opening and pymol.cartoon user function.
  • The molecular centre of mass is now correctly calculated.
  • Grace plots (http://plasma-gate.weizmann.ac.il/Grace/) were sometimes corrupted due to data being stored in numpy arrays and not Python lists (bug #12679).
  • Fix for the value.read user function, the directory and 'sep' arguments were being ignored.
  • Multiple failures of structure.load_spins for different PDB file layouts have been fixed (bug #12735).
  • Model-free optimisation failures on Mac OS X for PowerPC (bug #12573).
  • Many PDB file reading fixes for different multi-molecule/multi-model formats.
  • The '-' character is now allowed in molecule, residue, and spin names (was a bug if the file name contains a '-' character).
  • Bug fixes for handling molecules other than proteins and RNA via the Scientific python PDB reader.
  • The internal PDB reader no longer considers the END record to be a molecule.
  • Fix for a rare circular import failure of the RelaxError and RelaxWarning systems when running with the --debug command line flag.
  • Significant simplifications of the RelaxError system, fixing a state saving bug with --debug.
  • Fix for the retarded Scientific python PDB reader splitting a perfectly good molecule into 2 when it can't recognise a residue type.
  • Linear constraints and now supported for the N-state models without probabilities.
  • Modified the full_analysis.py script to name spins if the sequence data contains no spin name info.
  • All column arguments now default to None for the RDC and PCS reading so if residue numbers are non-existent, then they will not be read from the default column.
  • Bug fixes for the N-state model with N = 1 (allowing relax to mimic Pales http://www.mpibpc.mpg.de/groups/griesinger/zweckstetter/_links/software_pales.htm).
  • Bug fix for the PCS alignment tensor fitting, the paramagnetic-nuclear spin distance was being incorrectly determined.
  • The Q factors for the RDCs and PCSs were completely incorrect (found by comparing to Pales).
  • All the value.*() user functions have now been converted from the relax 1.2 to the relax 1.3 design.
  • Fixes for some circular import issues in generic_fns.minimise and generic_fns.value.
  • All the relax_data.*() user functions have now been converted to the relax 1.3 design.
  • Bug fix for the spin.copy user function, non-empty spin containers are no longer overwritten if the name and num are set to None.
  • Fix for the latex_mf_table.py sample script (bug #13163).
  • Rex values in XML results file not in s-1 (bug #13162).
  • Fix for the structure.create_diff_tensor_pdb user function which was creating weird shaped ellipsoid diffusion tensor representations when α and β were unequal (bug #13032).
  • Sparky assignments such as '004N-H' are now handled.
  • Fixed a bad apostrophe character causing the 'full_analysis.py' script to fail.
  • Removed a check disallowing multiple steady-state NOE data sets at the same spectrometer frequency.
  • Bug fix for the results reading from_xml() method, the molecule name was being evaluated causing results.read to fail.
  • Fixes for the model-free Monte Carlo simulation methods for deselected spins.
  • Models with high te values (>200 ns) were not being eliminated in the full_analysis.py sample script (bug #13259).
  • Monte Carlo simulations were failing in the model-free.py sample script (bug #13442).
  • The model-free minimisation statistics are no longer reset by the Monte Carlo simulation setup.
  • A number of bug fixes for Python 2.6 support.
  • Model selection between data pipes of different type is now allowed.
  • Bug fix for the maths_fns.rotation_matrix.R_2vect() function as the rotation axis is not always of unit length.
  • The diffusion tensor geometric object PDB representation is now correctly generated.
  • The isotropic cone geometric object PDB representation is now correctly generated.
  • The Hetrogen section was failing with MC simulations in the structure.write_pdb user function.
  • pymol.cartoon was failing when multiple proteins were loaded.
  • Bug fix for the maths_fns.rotation_matrix.R_to_axis_angle() function, the axis needs to be normalised.
  • Bug fixes for the grace.write user function.
  • Monte Carlo simulations failed when all parameters except for the diffusion tensor were fixed.
  • The diffusion and alignment tensor *_sim and *_err elements are now present and read from a results file.
  • The align_tensor.matrix_angles user function now avoids NaN problems through arccos of numbers > 1.
  • Bug fixes for the updating of the diffusion tensor MC simulation data structures.
  • Fix for the copying of diffusion tensors data structures.
  • relax and the sample scripts are more compatible with non-Unix operating systems by using the Python os.sep and os.pardir rather than '/' and '..' for directory separators and the parent directory.
  • Caught a NaN problem in the N-state model, RDC Q factor code causing failures in MS Windows.


Links

For reference, the following links are also part of the announcement for this release:


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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