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{{infobox relax release| version = 1.3.4| prev = 1.3.3| next = 1.3.5| keywords = Bruker ncproc parameter, hybridisation, N-state model, MOLMOL, NOE distance restraints, pseudo-atoms, structure| type = Major feature| date = 12 August 2009| manual = yes}} == Description ==
<section begin=description/>
This is a major feature release featuring innumerous changes and bugfixes. New features include support for spin containers for psueedo 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.
<section end=description/>
== Download ==
<section begin=download/>
<section end=download/>
== CHANGES file ==
<section begin=metadata/>
<section end=metadata/>
=== Features ===
<section begin=features/>
<section end=features/>
=== Changes ===
<section begin=changes/>
* The new user function class 'spectrum' contains all functions associated with spectral data.
* Spectral data is now identified by unique spectrum ID strings.
* The [http://www.nmr-relax.com/manual/noe_read.html noe.read() ] and [http://www.nmr-relax.com/manual/relax_fit_read.html relax_fit.read() ] user functions have been merged into [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities()].* The [http://www.nmr-relax.com/manual/relax_fit_mean_and_error.html relax_fit.mean_and_error() user function ] is now called [http://www.nmr-relax.com/manual/spectrum_error_analysis.html spectrum.error_analysis()].* The [http://www.nmr-relax.com/manual/noe_error.html noe.error() user function ] is now called [http://www.nmr-relax.com/manual/spectrum_baseplane_rmsd.html spectrum.baseplane_rmsd()].* The new [http://www.nmr-relax.com/manual/spectrum_integration_points.html spectrum.integration_points() user function ] is used to specify the number of points used in a volume integration.* The R1 R<sub>1</sub> and R2 R<sub>2</sub> relaxation time period is now specified using [http://www.nmr-relax.com/manual/relax_fit_relax_time.html relax_fit.relax_time()].* [http://www.nmr-relax.com/manual/grace_write.html grace.write() ] will now show a warning when an empty file is being created.* Replicated spectra are now specified explicitly via [http://www.nmr-relax.com/manual/spectrum_replicated.html 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 [http://www.nmr-relax.com/manual/structure_vectors.html 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<sup>-3</sup>.
* 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 [http://www.nmr-relax.com/manual/molecule_name.html 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 [http://www.nmr-relax.com/manual/spin_create.html spin.create() ] and [http://www.nmr-relax.com/manual/residue_create.html 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 [http://www.nmr-relax.com/manual/structure_vectors.html 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 [http://www.nmr-relax.com/manual/pcs_centre.html pcs.centre() user function ] can now accept pseudo-atoms.* The [http://www.nmr-relax.com/manual/pcs_centre.html 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.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 [http://www.nmr-relax.com/manual/n_state_model_set_type.html n_state_model.set_type() ] to [http://www.nmr-relax.com/manual/align_tensor_reduction.html align_tensor.reduction()].* Renamed [http://www.nmr-relax.com/manual/n_state_model_set_domain.html n_state_model.set_domain() ] to [http://www.nmr-relax.com/manual/align_tensor_set_domain.html align_tensor.set_domain()].
* The statistics ordering has been improved when profiling.
* [http://www.nmr-relax.com/manual/align_tensor_init.html 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 [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() ] and [http://www.nmr-relax.com/manual/pcs_read.html pcs.read()].* Large improvements to the information printed by the [http://www.nmr-relax.com/manual/align_tensor_display.html align_tensor.display() user function].* Removed a check for the presence of the alignment tensor so that [http://www.nmr-relax.com/manual/align_tensor_init.html 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().
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* A bug in the Monte Carlo simulations for relaxation curve-fitting has been fixed ([https://gna.org/bugs/?12670 bug #12670]).
* Fixes for the Pymol PDB file opening and [http://www.nmr-relax.com/manual/pymol_cartoon.html 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 ([https://gna.org/bugs/?12679 bug #12679]).
* Fix for the [http://www.nmr-relax.com/manual/value_read.html value.read() user function], the directory and 'sep' arguments were being ignored.* Multiple failures of [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins() ] for different PDB file layouts have been fixed ([https://gna.org/bugs/?12735 bug #12735]).
* Model-free optimisation failures on Mac OS X for PowerPC ([https://gna.org/bugs/?12573 bug #12573]).
* Many PDB file reading fixes for different multi-molecule/multi-model formats.
* 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 [http://www.nmr-relax.com/manual/spin_copy.html 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 ([https://gna.org/bugs/?13163 bug #13163]).
* Rex values in XML results file not in s<sup>-1 </sup> ([https://gna.org/bugs/?13162 bug #13162]).* Fix for the [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb() user function ] which was creating weird shaped ellipsoid diffusion tensor representations when '&alpha' ; and '&beta' ; were unequal ([https://gna.org/bugs/?13032 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 [http://www.nmr-relax.com/manual/results_read.html 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 ([https://gna.org/bugs/?13259 bug #13259]).
* 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 [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb() user function].* [http://www.nmr-relax.com/manual/pymol_cartoon.html 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 [http://www.nmr-relax.com/manual/grace_write.html 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 [http://www.nmr-relax.com/manual/align_tensor_matrix_angles.html 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.
<section end=bugfixes/>
== Links == <section begin=links/>For reference, the following links are also part of the announcement for this release:* [http://wiki.nmr-relax.com/Relax_1.3.4 Official release notes]* {{gna link|url=gna.org/forum/forum.php?forum_id=2108|text=Gna! news item}}* [http://article.gmane.org/gmane.science.nmr.relax.announce/24 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00016.html Mail archive]* [https://mail.gna.org/public/relax-announce/2009-08/msg00000.html Local archives]* [http://marc.info/?l=relax-announce&m=135070664625007&w=2 MARC]<section end=links/> == Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
{{:relax release see also}}
[[Category:Frame order analysis]]
[[Category:Model-free analysis]]
[[Category:N-state model analysis]]
