Author: bugman
Date: Fri Aug 14 11:44:34 2009
New Revision: 9314
URL: http://svn.gna.org/viewcvs/relax?rev=9314&view=rev
Log:
Merged the relax 1.3.4 CHANGES file into the 1.3 line.
The command used was:
svn merge -r9296:9297 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.4 .
Modified:
1.3/docs/CHANGES
Modified: 1.3/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/CHANGES?rev=9314&r1=9313&r2=9314&view=diff
==============================================================================
--- 1.3/docs/CHANGES (original)
+++ 1.3/docs/CHANGES Fri Aug 14 11:44:34 2009
@@ -1,3 +1,127 @@
+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
'alpha' and 'beta' 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.
+
+
+
Version 1.3.3
(29 November 2008, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.3
@@ -14,7 +138,7 @@
* The results.write() and results.display() now only support XML
output.
* More information is now extracted from the Modelfree mfout files.
* The version of the Modelfree program is checked and if it is an
old, buggy version, relax will refuse to execute it.
- * The system tests can now handle the sometimes large differences in
Modelfree results between the GNU gcc and Portland C compiler versions.
+ * The system tests can now handle the sometimes large differences in
Modelfree results between the GNU gcc and Portland C compiler versions.
* Fixes and improvements to much of the API documentation.
Bugfixes:
@@ -281,10 +405,10 @@
Changes:
* The relax core design diagram in the development chapter of the
manual has been updated.
- * Three flow diagrams have been added to the relax manual detailing
the steps of different model-free analysis protocols.
+ * Three flow diagrams have been added to the relax manual detailing
the steps of different model-free analysis protocols.
* Spin systems are now identified when deselected by the
'eliminate()' user function.
* The model-free Molmol cutoff for fast and slow motions has been
changed from 100 to 200 ps.
- * For the clarification of bug #8059 a RelaxNoTensorError is raised
instead of returning None when no diffusion tensor data is present.
+ * For the clarification of bug #8059 a RelaxNoTensorError is raised
instead of returning None when no diffusion tensor data is present.
* The Scons target 'source_dist' now creates and GPG signs both the
'tar.bz2' and 'zip' source distribution packages. (see task #4087)
Bugfixes:
r9314 - /1.3/docs/CHANGES