This is a major feature release featuring innumerous changes and
bugfixes. New features include support for spin containers for psuedo
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.
The new relax versions can be downloaded from either
http://nmr-relax.com/download.html or http://download.gna.org/relax/.
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 (see section 3.6 of the relax manual for
details).
The full list of changes is:
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,
https://gna.org/bugs/?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, https://gna.org/bugs/?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,
https://gna.org/bugs/?12735).
* Model-free optimisation failures on Mac OS X for PowerPC
(bug #12573, https://gna.org/bugs/?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,
https://gna.org/bugs/?13163).
* Rex values in XML results file not in s-1 (bug #13162,
https://gna.org/bugs/?13162).
* Fix for the structure.create_diff_tensor_pdb() user function
which was creating weird shaped ellipsoid diffusion tensor
representations when 'alpha' and 'beta' were unequal (bug #13032,
https://gna.org/bugs/?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,
https://gna.org/bugs/?13259).
* Monte Carlo simulations were failing in the model-free.py
sample script (bug #13442, https://gna.org/bugs/?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.
relax version 1.3.4.