This is a major feature release which includes many bug fixes and a
security fix. Major additions include the addition of 9 new frame
order models, execution locking, support for CCPN Analysis 2.1 peak
lists, Monte Carlo simulations for the N-state model, optimisation of
the Ln3+ position in the N-state model, weighting of RDCs and PCSs
during optimisation, and no longer using execfile() closing a security
hole.
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 (described in section 3.6 of the relax
manual).
The full list of changes is:
Features:
* Addition of Michael Bieri's model-free data extraction script.
* Added support for CCPN Analysis 2.1 peak lists (exported in
Sparky format).
* Execution locking has been implemented to prevent threaded
execution from killing relax. This will be useful for the relax GUI.
* Scripts are now run as modules rather than using execfile(),
closing a security hole.
* Created the frame_order.domain_to_pdb() user function to
associate PDB files with domains in the current data pipe.
* Rewrote frame_order.cone_pdb() to handle all of the frame
order models.
* The sign of the RDC can be inverted to correct for the
negative 15N gyromagnetic ratio.
* Better identification of the molecule end in the internal PDB
reader.
* Implemented Monte Carlo simulations for the N-state model.
* The grid_search() user function argument incs can now be a
list with None elements to fix parameters.
* Expanded the number of frame order models to include the
'free rotor', 'rigid', 'rotor', 'iso cone, free rotor', 'iso cone,
torsionless', 'iso cone', 'pseudo-ellipse, free rotor',
'pseudo-ellipse, torsionless', and 'pseudo-ellipse'.
* Pre-defined probabilities can now be used in the 'fixed'
N-state model optimisation.
* The Ln3+ position can be directly optimised in the N-state models.
* The pcs.back_calc() user function now does something.
* Created the n_state_model.elim_no_prob() to remove
structures with zero probability.
* Created the align_tensor.fix() user function for fixing the
alignment tensor during optimisation.
* The alignment tensor optimisation is now optional within the
population N-state model target fn.
* The RDCs and PCSs can now be given optimisation weights.
* Per point comments are now included in the Grace files.
* The RDC and PCS correlation plots now also show the
experimental errors.
* The RDC and PCS back-calculation user functions now add the
alignment ID to the RDC and PCS if absent to allow both data types to
be back-calculated in the absence of measured data.
* The N-state model calculate() method now stores the
back-calculated RDCs and PCSs and Q factors.
* The PyMOL module pymol.cmd is now available within the pymol
user function class, accessible as pymol.cmd from the prompt/script
interface.
Changes:
* API documentation improvements with epydoc docstring fixes.
* Numerous new system tests to catch bugs and prevent bugs
appearing in the future.
* Peak intensity data is now internally handled differently to
improve its flexibility. This will be beneficial for handling Bruker
PDC (Protein Dynamic Center) files, relaxation dispersion data, and
adding new types of relaxation data.
* The 'scons clean' target now removes temporary relax save files.
* The molecule type can now be specified.
* Improved the diffusion tensor print out.
* pipe.delete() without args will now delete all data pipes.
* Added some checks to the dauvergne_protocol model-free
analysis for the required previously optimised results.
* Shifted the steady-state NOE specific analysis code into its
own package.
* Shifted the debug and pedantic flags into the __main__
namespace for better access from other modules.
* Modified the specific code API to remove a number of
references to spin_id, as not all analyses use spins.
* Renamed the results_folder arg to results_dir in the NOE
auto-analysis, and rearranged the args.
* Citations now include the status if not 'published'.
* Created a new directory 'graphics' for all relax artwork.
* The structure.load_spins() user function now gives a
RelaxWarning if no data could be found.
* The negative cones and z-axes are now not created for the
pseudo-ellipses in frame_order.cone_pdb().
* Added some transparency to the cone in pymol.cone_pdb().
* Modified the pymol.cone_pdb() user function to handle x, y,
and z-axes.
* Modified create_cone_pdb() to accept a pre-made structural
object and to create a file only when asked.
* Switched the names of the Pseudo_elliptic and
Pseudo_elliptic2 classes.
* Created a API common specific code set_selected_sim() method
for a single global model.
* Created a API common specific code model_loop() method for a
single global model.
* All objects placed into the relax data store structure are
now stored in the XML save file.
* Parameters can be fixed to the original values during the
frame order grid search.
* The user function argument checker
arg_check.is_int_or_int_list() can now allow for None list elements.
* The frame order model can be overwritten by
frame_order.select_model().
* Shifted to using numpy.sinc() for the frame order equations.
* Switched the theta and phi angles in
cartesian_to_spherical() to match the rest of relax.
* Created a new module for performing coordinate
transformations (maths_fns.coord_transform).
* The pipe.display() user function now places quotation marks
around the pipe names and shows which is the current data pipe.
* The align_tensor.display() user function now prints out the
generalized degree of order (GDO) value.
* The back-calculated alignments tensors are now being stored
in the current data pipe.
* Removed the docstring length check from the code validator script.
* The loading of RDCs and PCSs for non-existent spins now only
throws a RelaxWarning.
* The select.read() and deselect.read() user functions can now
accept file handles or dummy file objects.
* Limit arrays are now sent into the minfx generic interface
for limiting simulated annealing.
* The align_tensor.delete() user function can now be used to
remove all tensors simultaneously.
* Made a RelaxError less stringent so that the paramagnetic
centre can be unfixed.
* Initialising an alignment tensor now adds the ID to the
alignment ID list.
* Changes to the NOE auto-analysis for the GUI: The output
filename can be specified; The folder, where results files will be
placed, can be specified; The label of heteronucleus and proton of
peak lists and PDB file can be selected; The sequence is read either
by sequence file or PDB file; Removed white spaces and progress
output.
* Changed the alignment tensor parameter scaling back to 1 as
this was slowing down the optimisation.
* The rdc.back_calc() user function without an ID arg will
back-calculate RDCs for all alignments.
* Renamed the pcs.centre() user function to paramag.centre()
to abstract for the PRE.
* Better support for RDC and PCS correlation plots with and
without errors.
* Inverted the x and y axes in the RDC and PCS correlation plots.
* Better support for tensor-less N-state model optimisation.
* The align_tensor.copy() tensor_to arg can now be None, this
is useful for copying between data pipes.
* Added a function for the pseudo-elliptical cosine function,
this is a numerical approximation generated by series expansion.
* Added a method for translating pymol.cmd.do() commands into
specific pymol.cmd functions. This prevents problems with commands
being executed asynchronously. For example images were being saved
before ray-tracing was complete.
* The RDC and PCS correlation plots now only show selected spins.
Bugfixes:
* The loading of Monte Carlo simulation data from relax 1.2
version results files has been fixed (bug #17361,
https://gna.org/bugs/?17361).
* Bug fix for the relaxation data add_data_to_spin() function
- missing data for individual spins was not properly eliminated.
* For the 1.2 results files, the data is being extracted even
if the spin is not selected.
* Sparky peak lists from CCPN Analysis 2.1 can now be read
(bug #17341, https://gna.org/bugs/?17341).
* Fix for the broken grace.view() user function (bug #17344,
https://gna.org/bugs/?17344).
* Added 'CH' and 'OT' as carbon and oxygen atoms to the
internal PDB reader (bug #17343, https://gna.org/bugs/?17343).
* The script path is now being removed from sys.path as this
was causing incorrect scripts to be loaded if multiple scripts are
executed sequentially or nested.
* Fix for the 'list index is out of range' error when
differently sorted peak lists, or lists with missing data are loaded
(bug #17276, https://gna.org/bugs/?17276).
* Fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz)
ellipsoidal diffusion parameters.
* Fixes for some currently unused, but useful, diffusion
tensor internal API functions.
* Fix for the NOE auto-analysis - the spins are now named to
the value of the 'heteronuc' arg.
* Fix for the frame_order.cone_pdb() user function - the cone
is already in the PDB frame, no rotation required.
* Fix for the average domain rotation in pymol.cone_pdb().
* Bug fix for the frame_order.pivot() user function - it is
now functional.
* The base contents of the relax data store are no longer
saved with a call to results.write().
* Fix for the pcs.back_calc() user function for when multiple
structures are loaded.
* Fix for rdc.read() when neg_g_corr is set to True and the
RDC list contains entries with None.
* Fix for the failure of model elimination in the full
analysis script (bug #13259, https://gna.org/bugs/?13259).
* Added a catch in iso_cone_S_to_theta() for bad order parameters > 1.
* The attached proton PDB name is no longer hardcoded to 'H'
in the dauvergne_protocol auto analysis.
* When loading save states, data pipe names are always
converted to a string to avoid unicode problems.
* Hardcoded the factorial() function to return support for
Python 2.4 and 2.5.
* Small fixes and improvements to the rdc.back_calc() user
function - align IDs are being used instead of RDC IDs so RDCs can be
back-calculated even if measured RDCs are not present. And spin info
is also being checked for better error reporting to the user.
* Fix for the alignment tensor rotation matrix - it is now
always in the right handed universe.
* Bug fix for the RDC back_calc() function - the align_id arg
was being ignored.
* Fix for the RDC back_calc() function for when N=1 in the
N-state model, the bond vector structure was not correct.
* Fixes for the N-state model target function setup for when
no parameters are optimised.
* Fix for the Grace write_xy_data() function for when data
values of None are passed in.
* Bug fix for the RDC back-calculation function.
* Bug fix for the control of PyMOL (as a module).
* Small fix for the grace.write_xy_header() function, the
symbol numbers now range only between the legal values of 1 to 10.
relax version 1.3.6.