relax version 1.2.4.
This is a long overdue release which includes many new features,
changes, and bugfixes. Molmol macros which plot parameter values onto
the structure using arbitrary colour gradients through the X11
colours, Molmol colours, or RGB vectors can now be created by the
program. A test suite has been added to aid in debugging and checking
that new code does not break the functionality of the program. The
relax manual has been significantly updated. Hyperlinks are now
present. The chapter 'Open source infrastructure' has been added and
the development chapter has been rewritten. Hybrid runs are now
supported. Half the protein can be analysed in one run, the other
half in another, and then the two combined into one hybrid run.
The full list of changes is:
Features:
* Added elimination of Monte Carlo simulations to the sample scripts.
* Creation of the relax test suite 'relax --test-suite'.
* Creation of the committers file.
* The hyperref LaTeX package is now used in the relax manual.
* Addition of a chapter called 'Open source infrastructure'.
* Rewrite of the 'Development of relax' chapter.
* Addition of the user function 'run.hybridise()'. (task #3122)
* The user function 'relax_data.read()' no longer deselects
residues when no data is
encountered. (bug #5501)
* Residues are deselected by the user functions
'grid_search()', 'calc()', and 'minimise()'
if k > n or if there is less than 3 data sets. (bug #5501)
* Mapping parameter values onto the structure through Molmol
macros. (task #3146)
* Added support for arbitrary colour gradients in the Molmol
macros. (task #3146)
* Addition of a file for colour operations. All X11 colours
and all Molmol colours can be
selected by name. (task #3146)
Changes:
* The 'full_analysis.py' sample script now only searches over
6^6 rather than 11^6 grid
points for the ellipsoid diffusion tensor to speed up the analysis.
* Updated the manual to replace the references to 'make' with
'sconstruct'.
* Extension of the installation chapter.
* Changed the square and round brackets to curly brackets and
replaced ':' with '=' in the
user function docstrings.
* All the model-free Molmol functions have been moved into
their own class Molmol.
* The null device can now be opened instead of a file for
writing by passing 'devnull' as
the name.
* Updated the release checklist so that the directory
'relax-x.x.x' is included in the
distributions rather than just 'relax'.
* Removed the bugs file 'docs/BUGS'.
Bugfixes:
* Small bugs in the sconstruct script have been removed.
* The value reading function can now handle rows which contain no data.
* The ellipsoid diffusion tensor was being incorrectly
initialised in the 'full_analysis.py'
script.
* Another Numeric version issue. The model m0 with no
parameters which used to be handled
okay by the grid search and minimisation code was failing due
to changes in Numeric.
* In certain situations, the angle folding function which is
called after model-free
minimisation used the wrong run name.
* Fixed the -fPIC option segfault problem on some Linux
systems. (bug #5473)
* Changed the tm grid search which was between 6-12 ns to be
between 1-12ns.
* Fixed some grammar in the intro chapter of the manual.
* Fixed a bug in the model-free sample script in the spheroid
diffusion tensor function.
* Removed the spaces in front of the \index{} commands from
the manual LaTeX source files.
* The diffusion parameters 'Diso', 'Dper', 'Dpar', 'Dratio',
'Dx', 'Dy', and 'Dz' are
generated on the fly. (bug #5559)
* Fixed the spacing after 'Gna!' in the manual.
* The 'grace.write()' user function now plots the associated
errors. (bug #5659)
* Fix to the parameter errors not being scaled in the
value.read() user function.
(bug #5670)
* Parameter errors were not always included in the results
file. (bug #5660)
* Removed the memory leak in the relaxation curve-fitting C
modules. (bug #5602)
* The user function 'value.set()' no longer raises RelaxError
in spectral density mapping
runs. (bug #5698)
* Fix to the broken Molmol pipe. (bug #5752)
* Fix of the failure of molmol.view() when the PDB is missing.
(bug #5753)
* Fix to the failure of relax_data.read() when relaxation data
is missing. (bug #5805)
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The 1.3 developmental branch.
A new unstable development branch has been created within the relax subversion repository. This branch is called the 1.3 series and is a copy of the last revision of the 1.2 stable branch. Any new features should be added to the 1.3 branch rather than 1.2. Bugs, however, can be fixed in the 1.2 line. As I'll merge all fixes in the 1.2 line back into the development line these changes should only be made in the 1.2 branch. The main cause for the fork is the planned implementation of MPI functionality for running relax on clusters. However any new functionality or extensions to the program are more than welcome. Bye, Edward ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.5.
This is mainly a bugfix release. A large number of bugs have been eliminated including bug #5977, bug #6288, bug #6383, bug #5806, bug #6384, bug #6388, bug #6389, and bug #5746. These are described in more detail below. To fix a few of these bugs large disruptive changes were required. This included the change of the local tm parameter name from 'tm' to 'local_tm' and the simplification of the model-free model_statistics() function and modification of the model-free calculate() function. Therefore regressions and new bugs may appear in this release, most likely when the local tm parameter is encountered or during model selection. The full list of changes is: Features: * The data analysis chapter has been split into four: The NOE, relaxation curve-fitting, model-free, and reduced spectral density mapping chapters. * A section called the 'The core design of relax' has been added to the the development chapter of the manual. * The 'Values, gradients, and Hessians' chapter of the manual is now complete. These are all the equations used during optimisation. * The Hessian kite diagram and the gradient construction diagram have been added to the 'Values, gradients, and Hessians' chapter of the manual. Changes: * The distribution archives now unpack to the directory 'relax-x.x.x' rather than just 'relax', where x.x.x is the version number. * All chapters of the manual have been edited and proofed. * The Sparky and XEasy peak intensity reading functions have been split to allow the easy addition of new peak intensity file types. * Test of AIC model selection between diffusion tensors added to the test suite. (To catch bug #5746) * Changing of the local tm parameter name of 'tm' to 'local_tm' to distinguish it from the global tumbling time 'tm'. (Preparation for fixing bug #6384) Bugfixes: * Fix of bug where self.relax.data.select_sim was treated as a list. (bug #5977) * The value.copy() function now handles the value of None. (bug #6288) * The global flag is now set by the relax_data.delete() function. (bug #6383) * The model-free model_statistics() function now tests for the presence of relaxation data. (bug #5806) * Sorting of global from local parameters in 'generic_fns/value.py' simplified and fixed by changing the parameter name 'tm' to 'local_tm'. (bug #6384) * Model-free parameters now set in the OpenDX mapping test of the test-suite. (bug #6388) * Failure of model elimination because of a 'local_tm' and 'tm' mix up. (bug #6389) * Modification of the model-free calculate() function and elimination of the 'combined' flag from the self.model_statistics() function. (bug #5746) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.6.
A quick release to fix the fatal 'devnull' ImportError (bug #6403). This bug effects those using Python versions < 2.4 and prevents relax from starting up. The solution was to import the object using a try statement to allow execution of the program. However if relax ever attempts to use 'devnull' a RelaxError is thrown, a message saying to upgrade to Python >= 2.4 is printed, and the program terminates. This is currently only a problem in the test-suite. The full list of changes is: Features: N/A Changes: N/A Bugfixes: * Added the missing PDB file used by one of the OpenDX tests of the relax test-suite. (bug #6404) * Fixed the fatal devnull import failure for Python versions < 2.4. (bug #6403) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.7.
This release adds full compatibility for MS Windows. Unless you would like to use relax on Windows or are a developer (a few debugging features have been added), this release can be safely ignored. To allow relax to properly function on MS Windows a number of changes were necessary. This includes a number of bug fixes, the creation of the 'relax.bat' batch file, and modifications to allow the C modules to be compiled. Pre-compiled Windows zip files will now be available for download from the relax download page (http://www.nmr-relax.com/download.html). The full list of changes is: Features: * The C modules now compile without problem on MS Windows. * The MS Windows binary distribution packages are now successfully built using the SCons build system. * The batch file 'relax.bat' has been created for running relax from the MS Windows command prompt. * The program introduction width is now 80 characters in MS Windows for proper display from the command prompt. Changes: * The program state is saved when a RelaxError occurs in debugging mode. * KeyboardInterupt during script execution in debugging mode will print the Python traceback. Bugfixes: * The sconstruct script no longer fails in MS Windows. (bug #6980) * Model selection is now functional on all operating systems. (bug #6873) * The use of the Unix only class 'Popen3' has been removed to allow relax to function on all non-Unix operating systems. (bug #6841) * If the XH bond vector length is 0, the vector is set to None rather than raising a RelaxError. (partial fix to bug #6503) * Fix for the sconstruct script failure on MS Windows due to ImportErrors caused by importing Unix specific code. (bug #6841) * Fix for ImportErrors in MS Windows preventing relax from running. (bug #6841) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.8.
This is a major bug fix release. A number of important bugs have been fixed including the failure of model selection between global diffusion models when using the local tm models (bug #7616), the failure of model elimination when the model 'm0' is used (bug #7226), and the failure in the reading of old model-free results files from relax versions prior to 1.2.5 (bug #7587). Additional bug fixes are detailed below. New features include preliminary support for RNA/DNA data and support for the 'grace.write()' user function for reduced spectral density mapping. The new relax versions can be downloaded from either http://www.nmr-relax.com/download.html or http://download.gna.org/relax/. The full list of changes is: Features: * Preliminary support for RNA/DNA. (bug #7241) * Significant improvements to the SCons build system (see 'scons --help'). * Expansion and improvement of the relax development chapter. * The grace.write() user function works with reduced spectral density mapping. (task #4002) Changes: * MS Windows installation instructions have been added to the manual. * The RelaxWarning system has been added to standardise warning messages. * The relax manual now describes the test suite. (task #3781) * The 15N CSA values in the sample scripts are now all -172 ppm. * The ambiguity cased by supplying the option 'None' together with Newton optimisation has been resolved in the documentation. (task #3630) * Optimisation tests have been added to the test suite. Bugfixes: * Model selection between the global diffusion models no longer fails if all residues of the local tm models have been deselected by model elimination. (bug #7192) * The 'angles.py' sample script no longer fails when residue specific relaxation data is missing (corrupt input data). (bug #7224) * Prior to executing Modelfree4, Dasha, Molmol, Grace, or OpenDX, tests are run to determine if the binary exists, is executable, and is in the system path. (bug #7225) * Model elimination when using the model-free model 'm0' no longer fails. (bug #7226) * The strict checking of the Da and Dr diffusion tensor parameters has been relaxed to allow for optimisation imprecision. (bug #7297) * The reading of Modelfree4 mfout results files no longer fails when residue specific relaxation data is missing (corrupt input data). (bug #7277) * If optimisation returns an infinite value or a NaN value, these are now caught and a RelaxError thrown. (bug #6503, task #3621) * The sigma(NOE) equations of Chapter 8 of the manual have been fixed. (bug #7402) * Files containing relaxation data not consisting of exactly 4 columns will now be read. (bug #7583) * Model-free results files from relax versions prior to 1.2.5 are now properly read. (bug #7587) * Model selection between the global diffusion models does not fail when the local tm models are included. (bug #7616) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.9.
This release fixes a important bug introduced into relax version 1.2.8. If you have installed 1.2.8, please upgrade to this new version. The problem was that relax was throwing a RelaxError saying that an infinite chi-squared value had been encountered when the chi-squared value was actually zero (see bug #7641). A few other small changes are detailed below. The new relax versions can be downloaded from http://www.nmr-relax.com/download.html or http://download.gna.org/relax/. The full list of changes is: Features: N/A Changes: * For Mac OS X compatibility, the interpreter has been changed from '/usr/bin/python' to '/usr/bin/env python'. Bugfixes: * The infinite chi-squared RelaxError when the chi-squared value is zero has been fixed. (see bug #7641, https://gna.org/bugs/?7641) * Profiling is now functional again. (see bug #7677, https://gna.org/bugs/?7677) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.10.
This is a major bug fix release which includes a number of feature enhancements. Significant changes include the addition of convergence tests to the 'full_analysis.py' script, the ability to compile the C modules on Mac OS X, more advanced spin system selection, the model-free and reduced spectral density mapping results files no longer being truncated, and improvements to the model-free section of the user manual by the addition of flow diagrams detailing the steps of different model-free analysis protocols. Significant bugfixes include more flexibility in the reading of XEasy text files, a number of fixes in the 'full_analysis.py' sample script, the proper setup of Monte Carlo simulation when reading results files, and a couple of MS Windows fixes. More details and additional features, changes, and bugfixes are detailed below. The new relax versions can be downloaded from either http://nmr-relax.com/download.html or http://download.gna.org/relax/. The full list of changes is: Features: * Addition of tests to the 'full_analysis.py' script for the identification of convergence. * Different columns can be specified for the residue number in the 'select.read()' and 'unselect.read()' user functions. * More advanced selection of spin systems or residues is possible through the use of the Boolean operators 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. * Addition of a sample script for the creation a LaTeX longtable of the model-free results. * The rows of the model-free and reduced spectral density results files are no longer truncated for deselected spin systems, hence all data is now stored in the results file. (see bug #8059, https://gna.org/bugs/?8059) 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. * 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 (https://gna.org/bugs/?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, https://gna.org/task/?4087) Bugfixes: * The C modules can now be compiled on Mac OS X. (see bug #7670, https://gna.org/bugs/?7670) * The order of the proton and heteronucleus dimensions and number of header lines in the XEasy text file is now automatically detected. (see bug #7676, https://gna.org/bugs/?7676) * The 'full_analysis.py' script now throws a RelaxError if only one round of optimisation of the global model has been executed. (see bug #7787, https://gna.org/bugs/?7787) * The model selection of the global model in the 'full_analysis.py' script has been fixed. (see bug #7863, https://gna.org/bugs/?7863) * Monte Carlo simulations no longer fail if the local tm global model has been selected in the 'full_analysis.py' script. (see bug #7875, https://gna.org/bugs/?7875) * The Monte Carlo simulation data in the model-free results file is now correctly read back into the program. (see bug #7755, https://gna.org/bugs/?7755) * The Monte Carlo simulation state used to be turned on after reading a results file containing simulations. (see bug #7890, https://gna.org/bugs/?7890) * After reading model-free results files, model selection would fail as the heteronucleus and proton data structures did not exist. (see bug #7891, https://gna.org/bugs/?7891) * The model-free Molmol fast correlation time macro (te < 100 ps and tf) no longer sets the bond length to zero when no parameter is present. * The docstring fetching Scons target no longer fails. (see bug #8182, https://gna.org/bugs/?8182) * The model-free 'S2 difference stored in a new run' test of the test suite now passes. (see bug #8183, https://gna.org/bugs/?8183) * The 'source_dist' Scons target now works on MS Windows. (see bug #7678, https://gna.org/bugs/?7678) * The MS Windows BAT file execution failure "python: can't open file 'C:\Program': [Errno 2] No such file or directory" has been fixed. (see bug #8201, https://gna.org/bugs/?8201) * The reading in of the results files from relax versions 1.2.0 to 1.2.9 in which deselected spin system lines are truncated now works. (see bug #8248, https://gna.org/bugs/?8248) ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.0.
This is the first release of the unstable 1.3 development line. In addition to all the capabilities of relax 1.2.10 the new features of this release include the addition of a unit test framework, preliminary support for PyMOL, the creation of PDB files, the ability to display the diffusion tensor encoded as a PDB file using PyMOL, the ability to display the distribution of XH bond vectors used in the analysis via a PDB file, the new user function class 'structure' containing the old user function 'pdb()' which has been split and redesigned, removal of apply(func, args) calls from the minimisation code, improved spin system selection using Boolean operators, and a few other small features, bugfixes, and program changes. As the user function names have been and will continue to be modified please do not expect either the backwards or forwards compatibility of relax scripts written for the 1.3 relax versions. The new relax versions can be downloaded from either http://nmr-relax.com/download.html or http://download.gna.org/relax/. The full list of changes is: Features: * Implementation of the PDB geometric representation of the Brownian rotational diffusion tensor using 'structure.create_diff_tensor_pdb()'. * Added a sample script for the creation of the PDB representation of the diffusion tensor. * Addition of the ability to calculate the centre of mass of the selected residues (not available as a user function). * The addition of PDB writing capabilities (not available as a user function). * Creation of the 'molmol.command()' user function to send Molmol commands to a running instance of Molmol. * Creation of the 'molmol.ribbon()' user function to apply the Molmol ribbon style (which is equivalent to clicking on 'ribbon' in the Molmol side menu). * Creation of the 'molmol.tensor_pdb()' user function for displaying the PDB geometric object of the diffusion tensor in Molmol over a loaded structure. * Preliminary support for PyMOL. * Creation of the 'pymol.view()' user function for launching PyMOL. * Creation of the 'pymol.cartoon()' user function for hiding everything, showing the cartoon representation, and colouring the cartoon by secondary structure. * Creation of the 'pymol.tensor_pdb()' user function, the equivalent of 'molmol.tensor_pdb()'. * A unit test framework for the test suite has been created and a few tests have been written (accessible through the --test-suite or --unit-test command line arguments). * Addition of the 'structure.create_vector_dist()' user function for creating a PDB representation of the XH bond vectors of selected residues from the structure. * Addition of the 'pymol.vector_dist()' user function for displaying the PDB representation of the XH vector distribution overlain over the structure within PyMOL. Changes: * The unmodified Hessian and turning the line search off are now specified by different regular expressions. (see task #3630, https://gna.org/task/?3630) * Splitting of the 'pdb()' user function into 'pdb.read()' and 'pdb.vectors()' (these have been subsequently renamed). (see task #3838, https://gna.org/task/?3838) * Created the JOBS file to describe the roles of the relax manager positions. * Removal of apply(func, args) calls from the minimisation code. * Addition of the io.file_root() function. * Addition of the RelaxImplementError for internal use. * Added the text "re-run relax with the '--debug' flag" to the RelaxFault error class. * Redesign of the diffusion tensor data structure 'self.relax.data.diff' for the automatic calculation of diffusion tensor parameters, vectors, and matrices when parameters are set or changed. * The 'pdb' user function class has been renamed to 'structure'. * The 'init_data()' user function has been renamed to 'reset()'. Bugfixes: * Fixed the selection of nucleic acids by name as Scientific python was prefixing 'R' to the single letter codes. ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.11.
This is another major bug fix release. Please upgrade to this version
if you wish to use relax for reduced spectral density mapping as
significant bugs in that part of relax have been identified and fixed.
Other significant changes include this being the only version of
relax which will run with Python 2.5, the addition of Grace plotting
abilities improving the analysis of relaxation exponential
curve-fitting, large simplifications for the user and automatic
looping over iterations in the 'full_analysis.py' script, and
improvements to the reading and writing of model-free results files.
See below for additional improvements.
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 Grace plotting abilities have been extended, especially
concerning relaxation exponential curve-fitting.
* A sample script has been added to plot the difference
between the measured and back calculated peak intensities.
* Automatic looping over iterations in the 'full_analysis.py'
sample script is now possible.
Changes:
* The 'full_analysis.py' sample script has been significantly
improved with all user modifiable options shifted to the top of the
script.
* The default CSA value is now -172 ppm.
Bugfixes:
* The previous release had problems reading results files from
relax versions 1.2.0 to 1.2.9, but now results files from all versions
can be read (see bug #8248, https://gna.org/bugs/?8248).
* The synopsis of the system/functional tests now says '[
Failed ]' if one the tests fails (see bug #8682,
https://gna.org/bugs/?8682).
* relax now works with Python 2.5 (see bug #9093,
https://gna.org/bugs/?9093).
* The writing of the model-free results file, which failed
under certain circumstances because of the 'heteronuc' and 'proton'
attributes, has been fixed (see bug #8996,
https://gna.org/bugs/?8996).
* The problem whereby there is data loss for deselected
residues when using 'results.write()' followed by 'results.read()' has
been resolved (see bug #8953, https://gna.org/bugs/?8953).
* Relaxation data can now be read if deselected spin systems
have a relaxation data value or error value set to 'None' (see bug
#9101, https://gna.org/bugs/?9101).
* The fatal bug of the reduced spectral density mapping values
being incorrectly calculated has been fixed (see bug #9238,
https://gna.org/bugs/?9238).
* When using the alternate model-free parameter set {S2f, tf,
S2s, ts}, the incorrect functions were being called (see bug #9189,
https://gna.org/bugs/?9189).
* A second fatal problem in the reduced spectral density
mapping code, the heteronuclear frequency being overwritten by that of
the proton, has been fixed (see bug #9259,
https://gna.org/bugs/?9259).
* Another problem with relax and Python 2.5, because of the
Scientific package, has been resolved (see bug #9390,
https://gna.org/bugs/?9390).
* The XH bond length is now correctly set in the reduced
spectral density mapping analysis (see bug #9562,
https://gna.org/bugs/?9562).
* The convergence test in the 'full_analysis.py' sample script
was failing if spin systems were deselected (see bug #9892,
https://gna.org/bugs/?9892 and bug #10022,
https://gna.org/bugs/?10022).
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relax version 1.2.12.
This is an important bug fix release. It fixes major issues with the writing of results files and with the failure of model elimination. The 'latex_mf_table.py' sample script has also been fixed. More details are given below. If you have encountered these problems, please consider upgrading to this version to solve the issues. 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: N/A Changes: N/A Bugfixes: * The 'latex_mf_table.py' sample script now works (see bug #10189, https://gna.org/bugs/?10189). * The missing 'num_ri' failure when writing the model-free and J(w) mapping results files has been solved (see bug #10323, https://gna.org/bugs/?10323). * Model elimination was failing in certain situations when applied to the global models (see bug #10320, https://gna.org/bugs/?10320). ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.13.
This release introduces new features and fixes a number of important bugs. The most significant feature is the consistency testing of relaxation data from different field strengths using the J(0), F_eta and F_R2 values as calculated in Fushman et al., (1998) JACS, 120, 10947-10952. Important bugs which have been fixed include the failure of Monte Carlo simulations when model-free model 'm0' is encountered causing the parameter errors for all subsequent residues to be zero, the failure of reading of Art Palmer's Modelfree 4 'mfout' file, and the handling of missing structural data. For a full description of the additions and fixes, please see below. 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: * Consistency testing has been added allowing datasets recorded at different magnetic fields to be checked using the consistency function values J(0), Feta, and FR2. * The 'full_analysis.py' script can now perform a model-free analysis in the absence of structural data. Changes: * Better support for MS Windows Vista in the scons build system and the relax introduction. * A file listing the unresolved residues is no longer necessary for running the 'full_analysis.py' script. * A few small documentation additions and fixes. Bugfixes: * The parameters Dpar and Dper are now properly checked upon initialisation of this spheroidal diffusion tensor. * Initialisation of an empty diffusion tensor to the default values of zero now works. * The default value of the Iinf relaxation curve fitting parameter can now be set. * Fix for the complete failure of the reading in of Art Palmer's Modelfree 4 'mfout' results file (see bug #8997, https://gna.org/bugs/?8997). * Fix for a rare ZeroDivisionError during Monte Carlo simulations (see bug #11004, https://gna.org/bugs/?11004). * relax no longer fails if XH bond vectors cannot be extracted from a PDB file (see bug #11378, https://gna.org/bugs/?11378). * The relax_data.display() user function no longer fails (see bug #11383, https://gna.org/bugs/?11383). * The selection of model-free model 'm0' causes Monte Carlo simulations to fail resulting in zero errors from that residue onwards (see bug #11476, https://gna.org/bugs/?11476). * Another column fusion bug in Modelfree 4's 'mfout' results file can be handled (see bug #11483, https://gna.org/bugs/?11483). * Optimisation fix - the steady-state NOE value, gradient, and Hessian is now properly calculated when an order parameter of exactly 0.0 is encountered. ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.2.14.
This is a minor bug fix release which fixes a minor bug in the consistency testing analysis and the compilation of the C modules in Windows when using Python 2.5. The relax manual has also had a minor facelift. 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: N/A Changes: * Improvements to the relax manual. * Copyright statements added to the sample scripts for identifying the author and date of the script. Bugfixes: * The C modules can now be compiled on Windows with Python 2.5. * Fixes for the calculation of the F_eta value in the consistency testing analysis. ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
Believe it or not, but we now have relax version 1.3.1!
Finally, it's arrived! The new and improved relax is finally ready
for release. It's taken 2 years to get here, 4400 individual changes,
and a complete rewrite of almost every last line of code - all in all
an impressive team effort. Although the jump from 1.3.0 to 1.3.1
appears small, the changes are so expansive that hardly any code is
preserved between these versions. In addition, the release includes
all changes which occurred between relax versions 1.2.10 and 1.2.14.
For this shiny new version, we have had complete redesign of relax.
This started all the way back in October of 2006 with the post
https://mail.gna.org/public/relax-devel/2006-10/msg00053.html. This
overhaul involves the new molecule-residue-spin data structure and the
elimination of the 'run' concept replacing it with the data pipe
paradigm.
No longer is relax constrained to handling a single spin type for the
entire system, or a single spin per residue. Multiple structures,
multiple residues per structure, and multiple spins per residue can be
handled, paving the way for using relax with small organic molecules,
with RNA and DNA, and for protein systems using not only 15N data but
also any data from carbons or other spin types. As for the data pipe
concept, this is the next logical step in the evolution of relax. The
'run' had significantly diverged from its original meaning, so now it
has been renamed to the pipe. Everything in relax is now associated
with a data pipe. These pipes can be created, merged with user
functions such as model_selection(), branched by copying, and the
entire contents preserved at any time into an XML formatted results
file - imagination is the only limitation as to what can be done with
these pipes. The progress of relax can be considered as the flow of
data through these pipes, with each user function modifying or using
the contents.
For for identifying and selecting spins, the spin identification
string concept has been introduced. The string is composed of three
components: the molecule id token beginning with the '#' character,
the residue id token beginning with the ':' character, and the atom or
spin system id token beginning with the '@' character. Each token can
be composed of multiple elements separated by the ',' character and
each individual element can either be a number, name, or range of
numbers separated by the '-' character. Hence the full id string
specification is "# :[, [, , ...]]
@[, [, , ...]],". Basic usage of the
Boolean operators and ('&') and or ('|') is also supported.
Note that in this version, not all parts of relax are currently
functional. Many, such as relaxation curve fitting, model-free
analysis, reduced spectral density mapping, consistency testing, etc.
are fully functional but if you do uncover a non-operational user
function, please submit a bug report or use the stable 1.2.14 version.
Conversion of the last parts of relax to the new design will not be
too hard, especially if all issues are reported. Note that this is a
development line and that scripts written for version 1.3.1 may not
work automatically in future 1.3 versions.
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:
* Complete redesign of relax
(https://mail.gna.org/public/relax-devel/2006-10/msg00053.html).
* Extension of the Grace plotting abilities to include series
data such as relaxation exponential curves.
* For easy reference, all physical constants have been shifted
to the 'physical_constants.py' module.
* Complete overhaul of the handling of structures with the
introduction of a structural object API.
* An internal structural object has been created, complete
with PDB reading and writing methods, to optionally replace the
Scientific python PDB object.
* Large improvements to the API documentation by the use of
epydoc formatted docstrings.
* All spins can be looped over simply by using the spin_loop()
generator function.
* Molecules, residues, and spins are now selected by the new
syntax of the spin identification string.
* Improvements and simplifications to the 'full_analysis.py'
script with all user modifiable variables shifted to the top of the
script as global variables.
* Automatic looping until convergence has been added to the
'full_analysis.py' script to further simplify usage.
* Setting the type of nucleus is now done with the value.set()
user function on a spin-by-spin basis. This is important for RNA,
small molecules and protein analyses with Ca and N data.
* A new analysis type, the N-state model for interpreting
domain motions using RDC and PCS
relax version 1.3.2.
This release solves many major bugs in the final stages of model-free analysis, especially when using the 'full_analysis.py' script. This version also marks the return of the NOE analysis. If you are using relax version 1.3.1, it is recommended that you upgrade to 1.3.2. Bugs which have been resolved include: problems reading PDB files; failure of the value.set(), fix() and value.write() user functions; non-functional model elimination; model selection issues in certain situations; and various Monte Carlo simulation issues. 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 NOE analysis has been converted to the new design and is fully functional again. Changes: * Internal abstractions to the relax data store by using the generic_fns.pipes API. * Added more literature references to the 'full_analysis.py' script. * Eliminated Monte Carlo simulations are better identified during user function execution. Bugfixes: * The generation of the cone geometric object for the N-state model is fixed. * Fixes for the relax_curve_diff.py and latex_mf_table.py sample scripts (identified by the relax data store abstraction). * Fixed the reading of relax 1.2 model-free results files (identified by the relax data store abstraction). * Various PDB file loading issues fixed. * value.set() no longer fails when the parameter being set already exists (bug #12406, https://gna.org/bugs/?12406). * Fix for the bug whereby model elimination does nothing for model-free models. This fix may solve other model-free related issues (bug #12407, https://gna.org/bugs/?12407). * Model elimination no longer fails when no diffusion tensor is loaded (bug #12408, https://gna.org/bugs/?12408). * The error when loading the PDB file through the reading of the results file in the 'final' stage of the 'full_analysis.py' sample script is fixed (bug # 12409, https://gna.org/bugs/?12409). * Model elimination is fixed in the 'full_analysis.py' script. * The fix() user function works again when the element argument is set to 'all'. * Fix for the duplication of sequence data during model selection. * Monte Carlo simulations were failing due to a missing sequence error (bug #12410, https://gna.org/bugs/?12410). * The model elimination error "AttributeError: 'SpinContainer' object has no attribute 'params'." has been fixed (bug #12411, https://gna.org/bugs/?12411). * A missing global chi-squared value was causing failure of global model selection (bug #12412, https://gna.org/bugs/?12412). * Monte Carlo simulation elimination was removing the simulation not from the affected spin but from all spins (bug #12416, https://gna.org/bugs/?12416). * Fix for the failure of the value.write() user function in all analysis types (bug #12418, https://gna.org/bugs/?12418). ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.3.
This is a major bugfix and feature release. Support for the programs Dasha, Modelfree and OpenDX has returned and XEasy and NMRView peak lists can now be read. Upgrading to this version is highly recommended as it fixes a number of very important bugs. Some of these are include faulty error analysis when performing relaxation curve-fitting, results.write() failure, model selection failure if spins were deselected, diffusion tensor optimisation failure, and internal PDB reader problems. 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: * Dasha can be run from within relax again. * Art Palmer's Modelfree can be run from within relax again. * OpenDX execution and control is once again supported. * NMRView peak lists are now supported. * XEasy peak lists are again supported. Changes: * Internal relax cleanups by the addition of the specific model_loop() method - this should eliminate a series of potential hidden bugs. * 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. * Fixes and improvements to much of the API documentation. Bugfixes: * A failure of the minimisation set() function has been fixed. * The reset() user function now works again. * Fixes to the relax data store methods add(), to_xml() and from_xml(). * Many fixes for the support of Art Palmer's Modelfree program. * The mapping of the global parameter space (diffusion tensor, etc.) for visualisation in OpenDX has been fixed. * state.save() no longer fails after running state.load() (bug #12437, https://gna.org/bugs/?12437). * Sparky peak lists with the assignment '?-?' are now handled properly (bug #11913, https://gna.org/bugs/?11913). * Error analysis in relaxation curve-fitting was incorrectly implemented with standard deviation rather than variance averaging (bug #12456, https://gna.org/bugs/?12456). * A number of fixes for the LaTeX table generating sample script. * Fixes for the teeing and logging via the -l and -t command line arguments (bug #12489, https://gna.org/bugs/?12489). * Fix for when XH bond vector data from a PDB file is missing for a spin system (bug #12487, https://gna.org/bugs/?12487). * Many fixes for when structural data is missing. * The relax script is no longer overwritten if the log or tee file is not specified on the command line (bug #12498, https://gna.org/bugs/?12498). * Missing RelaxError failure in the sequence handling code (found when trying to solve bug #12582, https://gna.org/bugs/?12582). * A failure in the results.write() user function has been fixed (bug #12582, https://gna.org/bugs/?12582). * Model selection no longer fails if no model is ever selected. * Model selection was failing if spins were deselected (bug #12591, https://gna.org/bugs/?12591). * The directory name can now be part of the file name argument to results.read() (bug #12588, https://gna.org/bugs/?12588). * Optimisation of only the diffusion tensor after calling fix() was failing if some spins were deselected (bug #12607, https://gna.org/bugs/?12607). * The internal PDB reader was failing when the PDB file contained CONECT records (bug #12637, https://gna.org/bugs/?12637). ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.4.
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 use
Announcing the bmrblib project (https://gna.org/projects/bmrblib/).
This is a short message to introduce a new software project named bmrblib (https://gna.org/projects/bmrblib/). This project was spun out of the relax BMRB branch and will be a relax dependency for BMRB data deposition. The project is an interface, currently with only a Python front end - though C and other language interfaces can later be added, for reading and writing the NMR-STAR formatted files of the BioMagResBank (http://www.bmrb.wisc.edu/). It was written to allow relax (http://www.nmr-relax.com/) to produce NMR-STAR formatted files for deposition of model-free dynamics data (and to read the data downloaded from the BMRB for downstream research). It ships with Jurgen F. Doreleijers' pystarlib (http://code.google.com/p/pystarlib/) code, slightly modified, to read and write the basic STAR tags, but provides a much higher level infrastructure abstracting the "saveframe supergroup - saveframe - tag category - tag" hierarchy used by the BMRB. Data is passed into *.add() functions as floats, strings, or lists, and returned by *.loop() functions in the same format. The API provided means that almost no knowledge of the NMR-STAR dictionary is required to read and write BMRB NMR-STAR files. For compatibility, bmrblib supports the different NMR-STAR format versions. It is currently limited to data required for NMR relaxation and model-free experiments, but can easily be extended by any interested parties. Regards, Edward ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.5.
This is a major feature release consisting of over a year's worth of improvements and bug fixes, with close to 2000 code changes. All users are recommended to upgrade to this newest version. New features include the ability to determine the stereochemistry of flexible organic molecules, expansion of the frame order theory, better support for RDCs and PCSs, 2D Grace plot improvements, and many new rotation_matrix module conversion functions. 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 the frame_order.ref_domain() user function to specify the alignment of different domains. * Converted the reduced J(w) mapping sample script to the relax 1.3 design to make it functional. * Created the 'rigid' frame order model. * Made the profile module optional, removing the dependency on the Python development packages. * Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function. * Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function. * Created the maths_fns.rotation_matrix.R_to_quaternion() function. * relax save files are now by default XML formatted rather than the pickle format (for better compatibility with future relax versions and between different systems). * Added a force flag to the state.load() user function. * Redesign and improvement of the frame order grid search. * Added a script for creating Molmol macros to represent the model-free motions. * Created the structure.delete() user function for deleting all structural information. * Spun out the automatic model-free protocol code from the full_analysis.py script. The simplified script now simply sends in user supplied data to an automatic analysis API. * Expansion of the rotation_matrix module with the addition of many new conversion functions. * Added support for using methyl pseudo-atom RDCs. * Created the structure.get_pos() user function for extracting atomic positions. * The atomic position can now be directly supplied to pcs.centre(). * Addition of a sample script for the determination the relative stereochemistry of organic molecules. * Large improvements for the creation of 2D Grace plots. * Anisotropic cone PDB representations can now be created. * The diffusion tensor within the PDB frame can now be specified, avoiding the 2304 different Euler angle conventions for a rank-2 symmetric tensor. * PyMOL is now being executed as a python module, if available, instead of being launched on the command line and remotely controlled. * Addition of the rdc.display() and rdc.write() user functions. * Addition of the pcs.display() and pcs.write() user functions. * Implemented dfunc_tensor_opt() and d2func_tensor_opt() allowing all optimisation algorithms to be used for the N-state model. * Creation of the rdc.corr_plot() and pcs_corr_plot() user functions for creating correlation plots of measured vs. back-calculated RDCs and PCSs. * Added the -i or --info option to relax. Changes: * Test suite fixes for Python 2.5. * Epydoc docstring improvements/fixes for the API documentation. * Many updates using 2to3 preparing for a transition to Python 3.x. * Renamed the pipe.list() user function to pipe.display(). * Created a base class for the user function classes. More user function back end simplifications. * Addition of many new RelaxError classes for the user function interface. * Removal of many unused Python module imports. * Redesign of the RelaxError classes. * Simplified all the argument RelaxError classes using BaseArgError. * Added a check for the unimplemented constraints in the frame order code. * Rearrangement of the handling of frame order models. The tensor rotation Euler angles are now model independent, the 'rigid' model is better supported, and a clear isolation of the isotropic cone model has been made. * Shifted the current data pipe to __builtin__.cdp so that it is accessible as 'cdp' in all of relax - including user scripts (and removal of 484 calls to generic_fns.pipes.get_pipe()). * Specific architecture and optimisation details are now printed if the frame order system tests fail. * Added a function for converting the frame order matrix to the rotational superoperator. * Improved and expanded the output of the print_frame_order_2nd_degree() function. * Function renaming and argument order changes in the maths_fns.rota
relax version 1.3.6.
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
relax version 1.3.8.
This is a minor bugfix release in preparation for the impending merger of relaxGUI. New features include a sample script for creating CSV files from model-free results for import into spreadsheet programs, extensive system testing of all model-free models, fixes for a system test on 32-bit GNU/Linux, and a fix for running scripts with certain versions of Python. 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: * Created a sample script to create a CSV file of model-free results for reading into spreadsheets, based on the LaTeX table generation script. * Extensive system tests for all the model-free models have been introduced. Changes: * Loosened the te check in value_check() so that the test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149() model-free system test would pass on 32-bit Linux. * Renamed the model-free results LaTeX table generation script. * Created a test-suite module to aid in the back-calculation of relaxation data from model-free parameters independent of relax. * Updates for Python 3.0 using 2to3. Bugfixes: * Fix for running scripts in certain versions of python - if a file with the same name as the script lies in one of the paths in sys.path, then that file will be executed rather than the script. ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.9.
This is a major feature release which introduces the new graphical user interface written by Michael Bieri. This GUI provides easy access to a sub-set of relax's features - the R1 and R2 relaxation rate curve-fitting, NOE calculations, and the fully automatic model-free analysis of the dauvergne_protocol module (d'Auvergne and Gooley, 2008, JBNMR, 40, 121). 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: * The addition of Michael Bieri's graphical user interface - relaxGUI. Changes: * Improvements to the HTML version of the user manual (http://www.nmr-relax.com/manual/1.3/relax.html). Bugfixes: N/A All developmental details can be seen in the SVN logs of the bieri_gui branch (http://svn.gna.org/viewcvs/relax/branches/bieri_gui/?pathrev=12386), or by typing: $ svn log -v --stop-on-copy http://svn.gna.org/svn/relax/branches/bieri_gui@r12386 | less ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.10.
This is a major feature release which introduces support from reading Bruker Protein Dynamics Centre (PDC) files. It also fixes a bug in the N-state model Q factor values when run in combination with Monte Carlo simulations for error analysis. 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: * Support for the reading of relaxation data out of the Bruker Protein Dynamics Centre (PDC) files. Changes: * Updates for 2 model-free system tests for a new system which again shows optimisation differences. Bugfixes: * Fix for a bug in the N-state model - the Q-factors and back calculated RDCs and PCSs were set to that of the last Monte Carlo simulation. * Fix for the N-state model error returning method for when errors are not present. ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.11.
This is a major feature release - all users are recommend to upgrade to this version. The major features include the integration of relax and the BMRB via the reading and writing of the BMRB NMR-STAR format files for model-free analyses, support for reading the XYZ 3D structure files used in organic chemistry, significant GUI improvements, and better support for the Bruker Protein Dynamics Centre (PDC) files. In addition a large number of bugs have been resolved. All together, this is a large release consisting of just under 2000 individual changes. 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: * Integration of relax and the BioMagResBank (BMRB, http://www.bmrb.wisc.edu). * Support for the creation of NMR-STAR version 3.1 files for BMRB deposition of model-free analysis results. * Support for the reading of all versions of NMR-STAR files containing model-free or relaxation data from the BMRB. * Use of the new bmrblib library for BMRB integration support (http://gna.org/projects/bmrblib). * Activated the PDC peak intensity type reading. * Added the Bruker PDC to the exp_info.software_select user function back end. * Implemented the value.set user function in the GUI. * Redesign of how relaxation data is handled within relax so that the data is identified via ID strings rather than relaxation type and frequency strings. * Added two sample scripts for determining the populations of an ensemble of small molecules. This uses RDCs and PCSs with the N-state model to study the dynamics of small organic molecules (http://dx.doi.org/10.1002/chem.201100854). * The GUI can now be resized. * Big clean up and simplification of the GUI code resulting in a more regularised GUI on all operating systems. * Added initial support for determining protein connectivities in the internal structural reader. This is currently only for intra-residue connectivities in the protein backbone. * Support for the reading of the organic chemistry XYZ 3D structure file format. Changes: * Removed the Numeric module from the --info print out as it is completely unused now. * Added the Bruker PDC software info to the exp_info module. * The pdc.read user function back end is now reading the PDC version information. * Added a catch for the "worst case per peak scenario" option in the PDC. This will now throw a RelaxError, telling the user to go back to the PDC and use the other option. * Converted the pdc.read user function back-end to use the \t delimitation of the PDC file for parsing. * The R1 value and error are now being read directly from the PDC file. * Added wrapper methods to the relaxation curve-fitting specific code for the new C modules. These allow the parameter numpy array from minfx to be converted into a Python list prior to sending it into the C module. * Added a check for the runpy Python module. * Scripts can now be run again under Python versions 2.4 or lower (by avoiding the runpy module). * The auto_analyses package modules are now imported by __init__ to force their existence. * The relax_data.back_calc user function arguments no longer need to be supplied. * Shifted all of the model-free sample scripts into the new subdirectory sample_scripts/model_free. * Added copyright headers to all of the sample scripts, and updated the introduction text. This allows users to determine the age of the scripts. * Updated the OpenDX mapping sample scripts from the relax 1.2 to the 1.3 design. * Added a sample script for creating plots of experimental verses back calculated relaxation data. * Deleted the incomplete and useless N_state_model.py sample script. * Created a sample script subdirectory called n_state_model. * Added a sample script for the unsuccessful two domain N-state model optimisation. * Deleted the ancient TODO file, as it is no longer relevant. * Deleted the SRLS analysis type - there is no incentive to develop this part of relax. * Removed 'relax_disp' from the VALID_TYPES data pipe type array. This is supported in the relaxation dispersion 'relax_disp' branch and not in the main line. * The RDC and PCS Q factor user functions now do nothing when data is missing rather than failing. A warning is given and the function now simply returns rather than raising an error. * The grace file created by the pcs.corr_plot user function now separates each element into its own graph. * Converted the
relax version 1.3.12.
This is a major feature release which adds the ability to run relax on clusters or grids of computers via the MPI protocol. This merges in Gary Thompson's multi-processor branch which was started all the way back in 2007. The 'multi' package introduces two processor fabrics, the standard uni-processor mode and the mpi4py mode for using the MPI protocol with Python. The model-free analysis code has been parallelised to take advantage of the multi-processor modes, significantly speeding up calculations on clusters with near perfect scaling efficiency. The flexible 'multi' package can easily be extended for other multi-processor modes such as additional MPI implementations using different Python libraries (pypar, etc.), the use of ssh tunnels for parallel programming, use of the twisted framework for communication, or the parallel virtual machine (PVM) via pypvm. For more information on how to use this, see https://mail.gna.org/public/relax-devel/2007-05/msg0.html. 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: * The multi-processor capabilities of Gary Thompson's multi package including both uniprocessor and mpi4py modes. Changes: N/A Bugfixes: N/A ___ relax (http://nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.14.
This is a major bug fix release focusing on memory usage, performance, and IO. The parallised model-free optimisation code (for running on clusters/grids using the multi-processor package) was causing relax to crash on 32-bit systems due to the system running out of virtual memory. The new version should only require about a third of the memory of relax 1.3.13 (see https://mail.gna.org/public/relax-users/2012-03/msg00037.html). The parts of relax dealing with atomic or spin specific data (reading of spin systems from PDB files, reading and writing of spin specific data, etc.) have been rewritten for efficiency and should now be many orders of magnitude faster for certain work loads. There have also been large improvements to the multi-processor framework, specifically the creation of a public API and a reference implementation. In addition there are improvements for IO capture on both the uni-processor and mpi4py-processor fabrics for relaying slave messages back to the master, better integration with the GUI and compatibility with the logging and teeing command line flags. Other changes include expansion of the relax information print out, support for numpy data structures in save files, and the addition of the rdc.delete and pcs.delete user functions. Feel free to upgrade if you would like the benefits of this new version. The new relax versions can be downloaded from either http://www.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, http://www.nmr-relax.com/manual/index.html). The full list of changes is: Features: * An expanded system information printout (from 'relax -i'). * Improvements to the multi-processor implementation, including creation of a public API and a reference implementation. * Overhaul of the multi-processor stream capture design - the slave IO streams are now properly redirected to the master processor and the master no longer overrides stream capture by the relax user interfaces. * Numpy data structures are now supported in relax save files. * Implemented the rdc.delete and pcs.delete user functions. * Speed ups of a number of user functions involved in looping over atomic or spin specific data - this can be significant if a lot of structural operations are performed, or a large number of structures are required. * Redesigned how spin parameters are handled in the specific analyses (which includes parameter name changes). Changes: * The MS Windows text wrapping width has been changed from 80 to 79 - this now fits the cmd prompt. * The program intro print out and prompt UI help system is using the new Status.text_width variable to wrap text. * The model-free constraint matrix A is now of numpy.int8 type - this is to decrease virtual memory usage and increase the scaling efficiency on clusters. * Changed all relax website links to http://www.nmr-relax.com for consistency. * The setup.py script can now be imported for the epydoc API documentation system. * The extern and minfx.scipy_subset relax packages are excluded form the API documentation. * Added the ability to skip scripts in the package __all__ list unit test checks. * Added some code to detect the bit version of MS Windows in the information print out (to better distinguish 32 vs. 64-bit versions). * Added some documentation about master processors on Linux 2.6 eating 100% of one CPU core (in the mpi4py multi-processor fabric). * Added a reference implementation to the multi-processor package - this is to demonstrate to users of the package how an implementation is created via the public API. * Elimination of all relax dependencies from the multi-processor package. * Added support for the memory size on MS Windows to the relax info print out. * Updated the value.set user function unknown parameter error message to list the known ones. * For Unix and GNU/Linux systems, the relax info printout now shows the ram and swap size. * Expansion and improvement of the information printed out by 'relax --info'. * Expansion of the multi-processor API documentation. * Expansion of the multi-processor package documentation with a step by step usage guide - this should increase the usability of the package by clarifying how one should use it. * Expansion and improvements to the multi-processor package and module docstrings. * The finish button in the new analysis wizard has been renamed to "Start". * Created a special Verbosity singleton for controlling the multi-processor package print outs. * Future proofed the relax codebase by replacing all ''' with """ in the docstrings.
A call for help to all Mac users!
Dear all, If you are a Mac OS X user, I would like to ask if you could help with relax's support for Mac OS X? I have created a special relax application which targets 10.5, 10.6, and 10.7 systems and which is a 3-way universal binary build for ppc, i386, and x86_64 systems. It is using a full Python 2.7 framework and the wxWidgets used to create the graphical user interface is using Cocoa. Unfortunately I do not have access to enough test systems covering all these OS versions and CPU architectures to be able to comprehensively test the Mac support. I have now successfully tested on real hardware (Intel x86_64) with both Lion and Snow Leopard, but more testing would be useful, especially if you have an old PPC system lying around. I have created a special relax version 1.3.15_rc1 release just for Mac users. This can be found on the download page at http://download.gna.org/relax/. This is a DMG file containing the relax app. If you could download this 130 Mb file and see if relax will simply open, taht would be very useful information. I have more instructions below for performing full analyses using the data in the relax test-suite, if are interested in helping to improve Mac OS X support for relax. Any help would be appreciated! Cheers, Edward P. S. Here are some instructions for extensively stress-testing relax, which is also useful for learning how to use relax The data from the test-suite is all truncated, and sometime randomised, but can be used for a full analysis. 1) Testing relax via analyses. If some value is not give below, then it can be invented without consequence. All the data is in the relax.app/Contents/Resources/test_suite folder. 1a) NOE analysis. There are two Sparky peak lists in ./test_suite/shared_data/peak_lists/ called 'ref_ave.list' and 'sat_ave.list'. To load the spin systems for these lists into relax, the PDB file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb can be used. This is sufficient for a full analysis. 1b) R2 analysis. A full set of Sparky peak lists for R2 data can be found in ./test_suite/shared_data/curve_fitting/. The relevant sequence data can be extracted from the test_suite/shared_data/Ap4Aase.seq file. You can invent the delay times of these data sets for fun. 1c) Model-free analysis. One of the many examples from the model-free shared data directories is for a synthetic spherical diffusion model. The data can be found at ./test_suite/shared_data/model_free/sphere. The PDB file and relaxation files are all there, no other files are required. 2) Stress testing. For this type of testing, randomly clicking everywhere and anywhere in any order would be useful. Or throwing in any random data or files. If relax responds with an error that is not a special 'RelaxError', then this is a bug. The nastier you can break relax, the better! 3) relax information Before reporting any problems, a copy of the relax information print out would be incredibly useful (assuming you can open relax to start with). You will find this under the Tools->System Information menu. The output will go to the relax controller, and this text can be copied and pasted. 4) Reporting problems. If you notice any problems, could you please report this as a bug report (https://gna.org/bugs/?func=additem&group=relax). Please try to report all steps required to reproduce the problem, Include the information print out, and copy and paste all error messages (including most of the information before the error occurred). Note that any strange behaviour outside of what you would expect is to be considered a bug. Any suggestions would also be appreciated (though if it involves months worth of work, it may not happen straight away ;). Thank you very much! ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 1.3.15
This is a major feature release focusing on more complete Mac OS X support and prettifying all of the user interfaces (UIs). The new features include full Mac OS X support via fink and the Mac application DMG file (for Leopard, Snow Leopard and Lion with PPC, i386 and x86_64 CPUs), coloured terminal output in the prompt/script UI modes, the ability to run the full relax test suite within the GUI mode, general improvements throughout the GUI, support for wxPython 2.9, faster program start up, improved formatting of the HTML version of the user manual, and expansion of the multi-processor framework. Many additional changes are listed below. If you are a Mac OS X user, you are affected by one of the bugs listed below, or you would like to use the new features, then I would recommend upgrading to this new version. The new relax versions can be downloaded from either http://www.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, http://www.nmr-relax.com/manual/). The full list of changes is: Features: * Large improvements to the HTML user manual (http://www.nmr-relax.com/manual/index.html). * The full test suite, including GUI tests, can now be run successfully from the GUI. * The Mac OS X binary distribution file now supports Leopard, Snow Leopard and Lion as well as the PPC, i386 and x86_64 CPU architectures. * The prompt and script output to a terminal is now coloured. * Faster program startup by only importing the test suite and GUI packages if they are actually needed. * Files selected via the GUI user functions can now be previewed. * Redesign of the spin loading wizard of the spin viewer window to be more intuitive. * Expansion of the system information print out. * Advances in the multi-processor framework including the pre-sending of data to slaves. * Support for wxPython 2.9. Changes: * Changed all of the maths in the HTML user manual page titles, the latexonly and htmlonly environments are now being used to produce different section titles with and without maths respectively. * The latex2html configuration script now allows for more maths in the HTML user manual with the HTML_VERSION math extension. * The section numbers are now removed from the HTML user manual pages to allow for more static webpages for the user functions which do not disappear as new user functions are added. * The title page of the HTML user manual has been renamed to "The relax user manual". * Updated the ancient COMMITTERS file which has not been changed in over 4 years! * The pipe editor window is no longer centred, now matching the behaviour all other windows. * All open relax windows are now closed prior to running the test suite within the GUI. * Exiting the GUI now only warns about data loss only if there is data to loose. * The relax controller can now not be closed while the test suite is running. * During the GUI tests from the GUI, the relax controller is now modal preventing users from interfering with the tests. * The relax controller now stays on top of all windows when the GUI tests are being run improving the running of the tests on Mac OS X and MS Windows. * The GUI tests now work in the GUI thanks to a lot of GUI black magic. The tests' tearDown() method now carefully deconstructs the GUI element prior to the next test being run. In the normal 'relax --gui-test' mode, the GUI object is destroyed and recreated for each test however, when run from the GUI, the GUI object is always there and must remain intact. The deconstruction includes deletion of each analysis tab and selective destruction of all non-main windows (excluding the controller which shows the test suite progress). The relax data store GUI object is also reconstructed in the tearDown() method, and all wx events flushed at the very end to prevent clashes with the next GUI test. * The relax mode (i.e. prompt, script, GUI, test suite, etc.) is now stored in the status object - this is used to activate and deactivate certain parts of the GUI tests within the GUI and normal test suite modes. * The ds.relax_gui GUI data object is now a permanent feature of the relax data store. * The 'Tools->Test suite' menu item has been converted into a sub-menu with entries for running all tests or the individual test categories. * Created the _det_install_path() status singleton method for better determining the install path - this is used for the Mac OS X applications whereby the current logic of using sys.path[0] fails miserably! * Prepared the multi-processor package for the import mechanisms of Python 3 - this new mechanism is present in Pyt
relax version 1.3.16.
This is mainly a documentation release. The relax user manual has been significantly updated - changes include the expansion and completion of the model-free analysis chapter, addition of graphical user interface (GUI) screenshots and descriptions, a description of Gary Thompson's multi-processor framework, and general updates and improvements throughout. Fro those who install relax using the scons 'install' target, the *.pyc and *.pyo files are now properly created for faster startup. The Bruker Protein Dynamics Centre user function class 'pdc' has been renamed to 'bruker' because of Bruker's absorption of the PDC into the Bruker Dynamics Centre. These user functions, as well as the BMRB user functions, have been added to the menu system in the GUI. Finally a test suite bug triggered in the Fink relax installation has been eliminated. If you would like improved documentation or would like to use any of the other changes, please update to this version. The new relax versions can be downloaded from either http://www.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, http://www.nmr-relax.com/manual/). The full list of changes is: Features: * The scons 'install' target now creates both *.pyc and *.pyo files during installation - this should result in faster relax startup times. * The test suite now passes on the Fink relax installation on Mac OS X as the ancient and very dead PyXML module is now being detected and worked around. * Renamed the 'pdc' user function class to 'bruker' and removed all references to 'protein' - this is due to the Bruker absorption of the Protein Dynamics Centre into the Bruker Dynamics Centre announced at https://mail.gna.org/public/relax-users/2012-04/msg00011.html (Message-id: <4f7ae13b.6010...@bruker.de>) by Dr. Klaus-Peter Neidig (peter dott neidig att bruker-biospin dott de). * Updates and improvements throughout the relax user manual. * Added a new section to the introduction chapter of the user manual for Gary Thompson's multi-processor framework. * Added screenshots and descriptions of the graphical user interface (GUI) to the introduction and all of the analysis chapters of the relax user manual. * The GUI and logging/teeing modes are now compatible with each other. * Expansion and completion of the model-free chapter of the relax user manual. Changes: * Improved debugging of the observers in the status singleton object. * Changed the behaviour of the arg_check module so that the functions can return answers. * The Bmrb.test_bmrb_rw GUI test now uses the base execute_uf() method for the pipe.create call - this is part of the simplification of the user function interfaces. * A number of the pipe GUI user function front ends now use the wizard page element_*() methods to simplify the code base. * The wizard page element_string_list() method can now create the special Combo_list objects. * Created the wizard page ResetChoices() method for resetting the list of values in a ComboBox. * Created a Clear() wizard page method for clearing a specific GUI element. * The wizard page element_string() GUI element creator read_only flag now defaults to False. * The read_only=True flag to wizard_elements.Base_value now sets a TextCtrl to the background colour. * The wizard_elements.Base_value.SetValue() method now works properly with the ComboBox. * The wizard_elements.Base_value class now can set the element to be read only. * Created generic_fns.pipes.PIPE_DESC_LIST which is the PIPE_DESC as a list, sorted by VALID_TYPES (to be used in the GUI user functions). * Better ComboBox support in wizard_elements.Base_value class - now strings and data are separate (if the data is supplied), and the GetValue() method now returns the client data rather than the string value. * Modified the wizard_elements.Base_value base GUI element class to handle combo boxes. * The Bmrb.test_bmrb_rw GUI test now uses the new execute_uf() method for the bmrb.citation user function. * Created the GUI test base method execute_uf() for executing a user function. * The bmrb.citation GUI user function now uses the new wizard page element_*() methods for the GUI elements. * Created a new wizard element for inputting integers. * Created a new wizard element for inputting strings. * Created the Bmrb.test_bmrb_rw GUI test. * Completed the GUI interface for the bmrb.citation user function. * Created a new wizard GUI element for lists of lists of strings. * Abstracted out most of the String_list wizard element into the List base class.
relax version 2.1.0.
This major feature release introduces the new concept of a container for data linking two atoms or spins - the interatomic data design. This is for NMR data such as the magnetic dipole-dipole interaction between two spins (including relaxation and RDC data) and NOESY data. This design significantly extends relax's flexibility and opens up new analysis type possibilities. As this is a highly invasive change, touching almost all of the relax analysis types and modifying the GUI, the minor version number has been incremented and all of the 2.0.x version numbering has been skipped. Additional features and changes include the update of the relax copyright license to GPLv3, support for absolute or signless RDCs has been added, and elimination of many GUI bugs in MS Windows. Due to the large number of improvements, changes, and bug fixes, all users are recommended to upgrade. 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). The full list of changes is: Features: * Update of relax to the GNU General Public License version 3. * Introduction of the interatomic data container design for NMR data such as the magnetic dipole-dipole interaction between two spins (including relaxation and RDC data) and NOESY data. * Support for absolute or signless RDC values. * Creation of a fast molecule, residue and spin data lookup framework using private metadata. Changes: * Updated the journal reference for the published lactose conformational search scripts. * Shifted some of the sample scripts into the analysis specific sub-directories. * Increased the size of the test suite warning dialog for MS Windows. * Improvements to the skipped test printout from the test suite. Now all test categories (system, unit and GUI) are printed if a module/package is missing. This allows for better debugging. * Shifted all of the observer registration and unregistration to observer_setup() in the pipe editor. * Improved debugging print outs for the observer objects. The method name is now stored and included in all the observer 'debug>' printouts. * Removed the notebook tab deletion from the GUI tests tearDown() method. This should be performed when a relax reset happens, so it is not needed in the tearDown() method just before the reset() call. * Merger of the absolute RDC branch (absolute_rdc). * Added support for the absolute or signless RDCs to the N-state model. This simply propagates the absolute flags into the maths_fns.rdc module functions whereby the absolute RDC values and gradients can be returned. * The rdc.read user function backend is now storing the absolute value flag in interatom.absolute_rdc. * Converted the N-state model absolute_rdcs.py system test script to the interatomic data design. * Created an absolute value version of the synthetic CaM RDC file for the test suite. * The rdc.read user function backend now accepts the 'absolute' argument. This is used to signal that the RDCs are signless absolute values. * Created an initial system (and GUI) test for the absolute RDC concept. * Added the 'absolute' keyword arg to the rdc.read user function definition. This will be used to mark RDCs as being unsigned. * Merger of the interatomic data container branch (interatomic). * Added a new screenshot of the GUI model-free auto-analysis, as it is now quite different. * Added a wizard graphic (SVG form) for the 13C-1H dipole-dipole pair. * A number of the generic_fns.mol_res_spin functions now accept the pipe argument. These include name_spin(), set_spin_element(), and set_spin_isotope() and this allows the functions to operate on any data pipe. * The dipole_pair.define user function backend now can handle the pipe argument. This allows it to operate on an alternative data pipe. * The State.test_old_state_loading() GUI test now checks the loaded data to a small extent. * Better backwards compatibility of old relax results and state XML files for the interatomic design. The MoleculeContainer._back_compat_hook() method has been shifted into the Relax_data_store._back_compat_hook() method. This allows the spin containers with attached protons to be converted (with new spin containers for the attached protons added) after loading of the XML state. * A small speed up for the model-free duplicate_data() function. This is used in model selection. * The generic_fns.mol_res_spin.index_molecule() function now handles no molecule name given. If no name is given and only a single molecule
relax version 2.1.1.
dow problems.
* Created the User_functions.test_structure_pdb_read GUI test
for checking the sequence editor window. This new user function GUI
testing class is to be used for testing out the special GUI elements
not invoked within the unit testing. The test_structure_pdb_read()
test specifically shows a number of failures of the sequence editor
window.
* Modified the operation of the sequence GUI element to have
access to the sequence editor window. This is to allow this GUI
element to be blasted within the test suite.
* Improvements to the descriptions of the structure.read_xyz
user function arguments.
* Improvements to the descriptions of the structure.read_pdb
user function arguments.
* Added @HE1 to the spin ID list of the structure.load_spins
user function. This is only seen in the GUI.
* Created the new generic_fns.result_files for standardising
the handling of results files. This fixes the bug where results files
are repetitively added to the list. All of the code touching
cdp.result_files now uses this module instead.
* Updated the scripting section of the intro chapter of the
user manual for non-technical users.
* Expanded the spin ID list for the structure.load_spins user
function. This now includes the spins "@N", "@NE1", "@C", "@H", "@O",
"@P", ":A@C2", ":A@C8", ":G@N1",":G@C8", ":C@C5", ":C@C5", ":U@N3",
":U@C5", ":U@C6".
* Changed the RelaxError for missing relaxation times in the
relaxation curve-fitting analyses.
* Modified the test_bug_20152_read_dc_file() GUI test to catch
the RelaxError. This error is because of the old PDC format.
* Created the test_bug_20152_read_dc_file() GUI test for
catching bug #20152 (https://gna.org/bugs/?20152). This includes
truncated data taken from the bug report (with data for only the first
3 residues).
* Set up the Bruker Dynamics Center system tests as GUI tests.
This is in preparation for catching bug #20152
(https://gna.org/bugs/?20152).
* Re-added Dominique Marion's solvent suppression to the
NMRPipe script in the curve-fitting chapter.
* A few small edits of the relaxation curve-fitting chapter.
This is to reinforce the exact time of the relaxation time period.
* Added some text to explain why test only J(0) is discussed
whereas the script also calculated F_R2 and F_eta. This was suggested
by Edward d'Auvergne in a post
at:https://mail.gna.org/public/relax-devel/2012-09/msg00044.html.
* Big clean up of the Bibtex bibliography file for the relax
user manual.
* Small edits of the consistency testing figure caption in the
relax user manual.
* Editing and a number of fixes/cleanups for the consistency
testing chapter of the user manual.
* Editing of the "Values, gradients, and Hessians" chapter of
the user manual to make it fit better. The context of this chapter
has been specified by changing the title to "Optimisation of
relaxation data -- values, gradients, and Hessians" and the intro text
has been updated. As this chapter is no longer straight after the
model-free chapter, this is needed.
* Made a small correction to a reference such that a
superscript is correctly displayed.
* Added the bounding box and a centerline command to the code
for the figure for consistency testing. This follows two remarks by
Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00030.html and
https://mail.gna.org/public/relax-devel/2012-09/msg00032.html.
* Added more text to describe the consistency testing
approach. Also includes a very basic point by point protocol for
consistency testing. This was proposed by by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00028.html. This
also follows a discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Added some text to describe the consistency testing example
figure. This follows a discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Added a modified version of Figure 1 from Morin and Gagne
(JBNMR, 2009 (http://dx.doi.org/10.1007/s10858-009-9381-4)). File
formats are .agr (xmgrace), eps (gzipped), and png. This follows a
discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Added a directory for placing consistency testing graphics.
This follows a discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Corrected the bibliography entries whih were still in plain
text and not as a Latex \cite call. Also renamed the MorinGagne09
entry to MorinGagne09a as there is now also MorinGagne
relax version 2.1.2.
This is the Python super-compatibility release - relax will now run on Python 2.3 all the way to Python 3.3, a span of over 9 years of Python development. Some exceptions are Python 3.0 as numpy and scipy are not compatible with that release, the execution of external programs in Python 2.3 not being supported, and the GUI currently not available on Python 3 due to the wxPython project not being compatible with this new Python design yet. A number of important bug fixes are also included. For more details please see below. 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). The full list of changes is: Features: * Python 2.3 to 3.3 support, including large changes throughout the code to be able to run on Python 3. * Improvements to the GUI tutorial in the model-free chapter of the relax manual. * A number of bugfixes. * Small improvements overall. Changes: * The scons 'clean' target now removes the Python 3 __pycache__ directories. * Small edit to the installation chapter of the user manual. * Decreased the Python version dependency from 2.5 to 2.3 in the installation chapter of the user manual. * More error checking for the associate_auto() method of the data pipe editor window. * Added data pipe bundle error checking for the GUI pipe editor window associate_auto() method. * Added some error checking for the data pipe bundle in the auto model-free analysis GUI code. * Added some special RelaxErrors for data pipe bundles. * Added some bug catching code for the observer objects. In some rare cases a registered method's key was set to None. This is now caught and a RelaxError thrown to prevent later indecipherable errors. * The setup.py application building script now complains if the Python setuptools are not installed. * Updated the relax prompt mode figure in the intro chapter of the user manual to the more modern prompt. * Improvements to the API documentation compilation. The excluded files and directories, as well as hidden ones, are no longer included in the list of files/directories to add to the documentation. * Added a file with the relax user functions used for the prompt screenshots. This is for the manual and the website. * Added the public domain LaTeX nth.sty style file for the user manual. Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing the PDF manual to compile on more systems. * Fixes for weird print statements with double brackets generated by the 2to3 Python conversion script. * Removed a debugging printout. * Python 3 fixes for one of the test data scripts - print statement with function call replacements. * Python 3 fixes for non-used Python code - converted print statements to function calls. * Python 3 fixes for the script for generating plots of magnetic field lines. * Another print statement to function Python 3 fix for the user manual. * The Python print statements in the user manual are now function calls to be Python 3 compatible. * Python 3 fix for the generic_fns.structure.geometric.angles_regular() function. Integer divisions no longer produce integers. * Better formatting of the test suite summary. * The text relax controller log is no longer cleared when a reset occurs. This allows the test suite results to still be presented in GUI mode. * Even cleaner exiting of the GUI - the interpreter thread is terminated by the exit_gui() method. * The GUI is now cleanly exited with a call to wx.App.ExitMainLoop rather than wx.Exit. * Python 3 fix for the compat module - the Queue2 object needs to always be defined. * Added support for Python 2.2 and earlier for the compilation of the C modules. * Removed an unused import of the Queue module from the multi-processor. * Python 3 fix for the ScientificPython PDB reader unit tests. The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to comparison. * Redesigned the reset user function backend. This now no only clears out the relax data store, but it also resets the GUI if present. Some of the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI window are closed and the relax controller gauges are set to zero and the log window text cleared. These changes should allow GUI tests after an error or failure to pass, something which is currently problem
MARC archives for the relax mailing lists.
This message is to announce that the relax mailing lists are now being archived in the MARC database (the Mailing list ARChives, http://marc.info). This supplementary archive has a number of advantages over the current Gna!, The Mail Archive, and GMANE systems, for example having a simple but very fast interface. See http://marc.info/?q=about for more details and http://www.nmr-relax.com/communication.html for the links to the other archives. You can find the archives for the various mailing lists at: http://marc.info/?l=relax-announce&r=1&w=2 http://marc.info/?l=relax-users&r=1&w=2 http://marc.info/?l=relax-devel&r=1&w=2 http://marc.info/?l=relax-commits&r=1&w=2 Regards, Edward ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 2.2.0.
This is a major feature and bugfix release which marks the completion of the N-state model analysis implementation. The N-state model allows single structures or ensembles of static structures to be analysed and compared using residual dipolar couplings (RDCs), pseudo-contact shifts (PCSs), distance restraints via NOEs. In addition to alignment tensors, the populations or probabilities of each state can be optimised as well as the position of the paramagnetic centre when PCSs are used. 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). The full list of changes is: Features: * Implementation of the rdc.copy and pcs.copy user functions. * Improved printouts from the model_selection, pipe.display, rdc.read user functions. * Implemented the interatomic.copy and interatomic.create user functions * Added the 'units' argument to the frq.set user function to allow values other than Hz to be input. * Added the 'empty' flag to the sequence.copy user function to allow all the spin contents to be copied. * Implemented the pcs.structural_noise user function. This is used to determine the PCS error due to structural noise via simulation, and adds the error via variance addition to the experimental PCS error. * The N-state model grid search optimises each tensor separately when only tensors are optimised. This massively collapses the grid search size from inc**(5*N) to N*inc**5, where inc are the number of increments per dimension and N is the number of alignments, making a grid search possible. * Implemented the rdc.set_errors and pcs.set_errors user functions. * Added Monte Carlo simulation support for the paramagnetic centre for PCSs in the N-state model. * The paramagnetic centre position for the PCS can now be optimised using algorithms other than simplex, such as BFGS, as the gradients of the PCS equations have been implemented. This allows for huge speedups as the simplex optimiser is not suited to such a problem. * The probabilities and paramagnetic position can now be simultaneously optimised in the N-state model. Such a combination would have previously failed to unpack the parameters correctly. * Constraints are now allowed for the paramagnetic position optimisation in the N-state model. This is because the gradients are implemented and functional. Changes: * The relax HTML user manual footer has been modified to remove the name of the person who compiled it. This is for http://www.nmr-relax.com/manual/index.html, and now contains links for relax (http://www.nmr-relax.com), the manual (http://www.nmr-relax.com/manual) and the PDF version of the manual (http://download.gna.org/relax/manual/relax.pdf). * Small syntax fix in the release checklist document. * Added the MARC archive links to the development chapter of the relax user manual. These links are: http://marc.info/?l=relax-announce&r=1&w=2, http://marc.info/?l=relax-users&r=1&w=2, http://marc.info/?l=relax-devel&r=1&w=2, and http://marc.info/?l=relax-commits&r=1&w=2. * The model-free overfit deselection algorithm now fails with a RelaxError when no spins are selected. This is to avoid situations such as bug #20277 (https://gna.org/bugs/?20277). * The pipe.display user function now uses relax_io.write_data() for better output formatting. * Created the N_state_model.test_data_copying system test for the rdc.copy and pcs.copy user functions. These user functions do not exist yet, but this test will be used to implement them. * Reactivated the rdc.copy and pcs.copy user function front-ends. The backends are missing, so relax is currently broken. * Created the RelaxNoAlignError error class for use by rdc.copy and pcs.copy. * Created the RelaxAlignError error class for use by the rdc.copy and pcs.copy user functions. * Implemented the rdc.copy and pcs.copy user function backends. This code is copied from the relax_data.copy user function and has been tailored to the different data types. * Modified the RDC and PCS data copying system test script to check overwriting. The rdc.copy and pcs.copy user function should support the overwriting of existent values. * The rdc.copy and pcs.copy user functions now support overwriting pre-existing data. * Removed some debugging printouts. * The N_state_model.test_data_copying system test now checks the spin RDC and PCS data. * The model_selection user function is now using relax_io.write_data() for its printouts. This allows for clean formatting when data pipes have long nam
relax version 2.2.1.
This is a quick bugfix release solving a number of issues uncovered since the release of relax 2.2.0 last week. Upgrading to this newest version is highly recommended. 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). The full list of changes is: Features: N/A Changes: * Replaced a reference to freshmeat with Freecode in the Release checklist document. Freshmeat no longer exists and is now called Freecode (http://freecode.com/projects/nmr-relax). * Created the Mf.test_bug_20464_missing_ri_data system test to catch bug #20464. The data comes from the bug report submitted by Stanislava Panova (stpanova att gmail dot com) at https://gna.org/bugs/?20464. * Created the Structure.test_bug_sr_2998_broken_conect_records system test. This is to catch the bug reported as service request #2998 (https://gna.org/support/?2998) and is for corrupted PDB files with broken CONECT records. * Created the Structure.test_bug_20469_scientific_parser_xray_records system test. This is to catch bug #20469 (https://gna.org/bugs/?20469). * Created the Structure.test_bug_20470_alternate_location_indicator system test to catch bug #20470. This report is at https://gna.org/bugs/?20470. * Created the Structure.test_alt_loc_missing system test. This is to test that the internal relax PDB reader raises an error when a PDB file is encountered with alternate location indicators but the alt_loc argument has not been specified. * Created the Bmrb.test_bug_20471_structure_present to catch bug #20471 (https://gna.org/bugs/?20471). * Modified the bmrb.read documentation to make it clearer that the data pipe must be empty. Bugfixes: * Python 3 fix for a print statement in the metal_pos_opt.py N-state model system test script. * Python 3 fix for the part of ScientificPython distributed with relax (for the PDB parser). * Python 3 import fixes for the GUI. * Python 3 fixes for the list sort() method - this has been replaced by the builtin sorted() function. * Fix for bug #20464 (https://gna.org/bugs/?20464) - the model-free analysis failure with missing relaxation data. The problem was the previously missing data had a value of None whereas now the dictionary element can be missing. Checks have been added to make sure the spin specific relaxation data structures have the key corresponding to the data. * Fix for the N_state_model.test_monte_carlo_sims system test. On certain systems, the chi2 check is too stringent. * Fix for the bug reported as the support request #2998 (https://gna.org/support/?2998). CONECT records pointing to non-existent atoms can now be handled. * Fix for bug #20469 (https://gna.org/bugs/?20469). This is the Failure in reading X-ray PDB files using the ScientificPython parser. The ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra imports in the Geometry.TensorModule in newly used code paths have been fixed as well. * Fix for bug #20470 (https://gna.org/bugs/?20470). The structure.read_pdb user function now accepts the alt_loc argument for specifying the alternate location indicator to read. This is used by the internal PDB reader. The bug was caught by the Structure.test_bug_20470_alternate_location_indicator system test. * Fix for bug #20471 (https://gna.org/bugs/?20471) - the is_empty() AttributeError when reading BMRB files. The problem was that the data pipe is_empty() method was not handling structural data correctly. The is_empty() method now belongs to the MolContainer objects rather than cdp.structure, and the object cdp.structure is not always present. ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 2.2.2.
This is a minor bug fix release which resolves an important issue, introduced somewhere within the last few relax releases, whereby missing relaxation data is not handled properly in a model-free analysis. A number of other small bugs have also been fixed - please see below for details. If you plan on performing a new model-free analysis, upgrading to this version is recommended. 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). The full list of changes is: Features: * Improvements to the relax API documentation (http://www.nmr-relax.com/api/). Changes: * Updated the release checklist to include the devel_scripts/log_converter.py script usage. * Modified the relax manual subtitle as this is no longer only for relaxation analysis. * Docstring fix for the maths_fns.vectors.random_unit_vector() function (this is for the API documentation at http://www.nmr-relax.com/api/). * Epydoc docstring fix for the dfunc_standard() N-state model target function (this is for the API documentation at http://www.nmr-relax.com/api/). * Epydoc docstring fixes for the diffusion tensor objects of the relax data store. * Added and edited a number of module docstrings. * Module and package docstrings additions/improvements for the SCons scripts. * Lots of module and package docstring updates for the analysis specific code. * Module docstring additions and improvements for the relax data store modules. * Addition of the generic_fns package docstring. * Added a module docstring for the main relax module. * Created the State.test_bug_20480 system test to catch bug #20480, the failure to load a saved relax model-free state in the GUI (https://gna.org/bugs/?20480). This bug was reported by Stanislava Panova (https://gna.org/users/stacy). * Created the Mf.test_bug_20479_gui_final_pipe GUI test to catch bug #20479, the model-free analysis failure in the GUI after setting the protocol mode to local tm. (https://gna.org/bugs/?20479). This bug was reported by Stanislava Panova (https://gna.org/users/stacy). * Added a printout to the GUI test case base check_exceptions() method to explain what is happening. * Large expansion of the Mf.test_bug_20479_gui_final_pipe GUI test. Instead of loading the bug #20480 state file, now the entire GUI analysis starting from scratch and using the relaxation data files is performed remotely by the test. This is necessary because the result of the bug is present in the state file. * Added spherical diffusion to the optimisation in the Mf.test_bug_20479_gui_final_pipe GUI test. * Added a global model print out to the Mf.test_bug_20479_gui_final_pipe GUI test. This is to help identify where failures occur. * Proper handling of the dipole interaction wizard in the Mf.test_bug_20479_gui_final_pipe GUI test. This was causing the subsequent GUI tests to fail as the observer objects from the wizard were not all being unregistered. * Added skips for some GUI tests when wxPython version '2.9.4.1 gtk2 (classic)' is used. There are a number of bugs in this version which cannot be worked around in certain GUI tests, so they must be skipped. * More wxPython version '2.9.4.1 gtk2 (classic)' bug avoidances in the GUI tests. Now the auto-analyses do not check the gauges in the relax controller at the end of the auto NOE, Rx, and model-free analyses, as reading gauge values is faulty in this version. The Rx test is no longer skipped for this wxPython version. * Improved the printout from the align_tensor.matrix_angles user function. The relax_io.write_data() function is being used and the tensors are now identified by name rather than index. * Improved the printouts from the align_tensor.svd user function. * The relax program introduction now includes the revision number for subversion checked out copied. This allows for better identification of the code base being used. * Fixes for the Pcs.test_structural_noise system test. As this is based on random functions, sometimes, though rarely, the test fails. Now the simulation accuracy has been increased and the tests are less rigorous. * Spacing fixes as identified by the Python 2to3 conversion program. Bugfixes: * Epydoc documentation fix - a circular import in the GUI code paths has been broken. This affects the API documentation at http://www.nmr-relax.com/api/. * Fix for the failed loading of states in the GUI. This problem was caught by the State.test_bug_20480 GUI test. If the loading of a state file fails,
relax version 2.2.3.
This relax version is a major feature and bugfix release. It adds the new structure.add_model, structure.rmsd and structure.web_of_motion user functions, enhances the structure.load_spins and structure.find_pivot functions, and PDB support for the internal structural object has been improved and updated. The new 'lib' package is introduced which will, in the future, be extensive collection of functions and special objects for all types of molecular dynamics analyses. The relax controller in the relax GUI has been improved with line wrapping to allow all messages to be seen. And some major bugs affecting the model-free auto-analysis and PDB file creation have been fixed. All users are recommended to upgrade. 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). The full list of changes is: Features: * Added the mol_name_target argument to the structure.load_spins user function. This allows spins from different molecules to be placed together in the same molecule container in the relax data store. * Addition of two new user functions - structure.add_model and structure.rmsd. * Created the structure.web_of_motion user function. This is used to create a special PDB file which represents the atomic motions between different structural models. Identical atoms of the selected models are concatenated into one model, within a temporary internal structural object, and linked together using PDB CONECT records. * Better PDB support in the internal structural object with: Improvements and fixes in reading/writing, an update of the format to version 3.30, and faster PDB parsing. * Creation of two new modules for better PDB support - generic_fns.structure.pdb_read and generic_fns.structure.pdb_write. * Improvements to the structure.find_pivot user function including the addition of the func_tol argument to better control the simplex optimisation and the use of the logarithmic barrier function to prevent the pivot from heading to infinity when the solution is a line. * Initialised a new package called 'lib' - this will in the future be an extensive collection of functions, methods, classes, objects, etc. useful for the study of all types of molecular dynamics. * Line wrapping has been turned on in the relax controller in the GUI so that all text is visible. Changes: * The relax intro text now includes the repository URL for checked out code. This is for preserving better debugging and logging information, so that it is clear where the code comes from. * Created the Structure.test_load_spins_mol_cat system test. This will be used to test a new 'mol_name_target' argument to the structure.load_spins user function. * Created the Structure.test_delete_multi_pipe system test. This is to check that the structure.delete user function is operating on a single data pipe. * Updated the Freecode instructions in the release checklist document. * Created the simple Structure.test_delete_empty system test. This is to demonstrate a failure of the structure.delete user function when no structural data is present. * Added a printout to structure.delete for when no structures are present. * Created the Structure.test_rmsd system test. This test checks the currently unimplemented structure.add_model and structure.rmsd user functions. * The structural API num_molecules() method can now handle no data being present. * Implemented the structure.add_model user function. * Added some more checks to the Structure.test_rmsd system test. * Modified the structure.add_model calls in the Structure.test_rmsd system test to include model nums. * Added the 'model_num' argument to the structure.add_model user function. * Modified the structure.add_atom user function to allow the position argument to be a rank-2 array. This allows a different coordinate for each model to be specified. * Spun out the atomic_rmsd() and calc_mean_structure() functions into their own module. They were previously in the generic_fns.structure.superimpose module but are now in the new generic_fns.structure.statistics module. * Added checks for the atomic information to the Structure.test_rmsd system test. This demonstrates a failure of structure.add_atom user function when specifying different positions for the different models. * Docstring addition for the generic_fns.structure.statistics.atomic_rmsd() function. * Implemented the structure.rmsd user function. * Fixes for the Structure.test_rmsd system test - it now passes. * Created a
relax version 2.2.4.
This is a major bugfix release. System and unit test bugs in the Mac OS X application have been eliminated, the RMSD related functions for systems with old Numpy versions installed have been fixed, the system information printout when the relax path contains spaces now works, Python 3 fixes have been made throughout, problems with the last steps of the model-free auto-analysis under certain conditions have been resolved, and the value.write and value.display user functions no longer present a list of zero values when very small number are encountered (for example the field-strength independent Rex values from a model-free analysis). Upgrading is recommended. 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). The full list of changes is: Features: * Creation of the structure.create_rotor_pdb user function for creating representations of the rotor frame order model. Changes: * Updated the release checklist document to include the correct instructions for minfx and bmrblib. These are the packages bundled with relax (http://gna.org/projects/minfx/ and http://gna.org/projects/bmrblib/) * Improvements for Python 2 and 3 compatibility. Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and different Python 3 version compatibility, code has been shifted into the compat module. The different parts of relax now import from the compat module for modules/packages with different import semantics for different Python versions. In addition the different handling of the bz2 and gzip module for reading and writing files has been shifted from 'relax_io' into 'compat'. * Updated the 2to3 checklist document to include multiple threads for faster operation. * Eliminated the os.devnull import flag dep_check.devnull_import. This is not needed as the compat relax module defines os.devnull for Python <= 2.3. The devnull module is no longer part of the relax information printout. * Added a more informative error message if the platform module is missing. This is for Python <= 2.2. The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can simply be copied into the lib/pythonX.X/ directory to fix this. * Slight change to the message printed if the platform module is missing. * Modified the script for running the relax test-suite on multiple Python versions. The pre-2.2 Python versions are now commented out as well as the abortive Python 3.0. * Created the Mf.test_bug_20613_auto_mf_diff_tensor_pdb system test to catch bug #20613. This was reported by Angelo Miguel Figueiredo at https://gna.org/bugs/?20613. This test is a direct copy of the Mf.test_bug_20563_missing_ri_error system test. The only change is that the local tm global model results file (in the local_tm/aic/ directory) has been modified. This results were read into relax, the file test_suite/shared_data/structures/Ap4Aase_res1-12.pdb loaded into the data pipe, and the results saved again. This triggers the bug as the problem is the presence of structural data with the local tm global model being selected in the auto-analysis. * Shifted all of the model-free specific analysis class documentation variables to the top. This is simply for better organisation of the code. * Created the model-free write_doc class variable talking about the field strength independent Rex value. This has been added to the value.display and value.write user functions to explain that Rex values are very small and that the user needs to scale them up. * Shifted all of the documentation variables to the top of the specific API_base class. This is for better organisation. * Added the write_doc class variable to the specific analysis API class as a empty string. This is to fix the unit tests. * Created the front end for the new structure.create_rotor_pdb user function. This will be used to create a PDB representation of a rotor motional model. * Added file, directory and overwrite force arguments to the structure.create_rotor_pdb user function. * Started to implement the backend of the structure.create_rotor_pdb user function. * The internal structural object MolContainer.add_atom() method now returns the index of the new atom. * Created the internal structural object MolContainer.last_residue() method. * Fully implemented the structure.create_rotor_pdb user function. For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created. Bugfixes: * Fix for the system tests in the Mac OS X application binary. The
relax version 2.2.5.
This is a minor feature release. Improvements include the creation of Rex value files scaled to all spectrometer frequencies for the model-free auto-analysis and some new capabilities in the structural API. Feel free to upgrade if you wish to use these new features. 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). The full list of changes is: Features: * The files created by the value.write user function now include a header describing the parameter. * The relax internal structural object now supports the merger of molecules. This can be useful if different domains of one system are in two PDB files or are split in the one file. * The structure.delete user function can now be used to delete parts of molecules down to the level of individual atoms. * Helix and sheet information from PDB files are now stored in the internal structural object as metadata. The structure.read_pdb and structure.write_pdb user functions will preserve this information. * The numbers output by the value.display and value.write user functions can now be scaled. * The model-free auto-analysis now generates field strength dependent Rex files for each field present. Changes: * Added a comment to the output from value.display and value.write to describe the parameter. This idea is discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428. The idea is to take the parameter description from the specific analysis API and add it to the top of the file or output. This is to help understand what the Rex value are. For example for the Rex parameter the first line would be: "# Parameter description: Chemical exchange relaxation (sigma_ex = Rex / omega**2)." * Created the Structure.test_read_merge system test to test a new concept - merging of structures. The idea is to add the merge argument to the structure.read_pdb user function to allow two different structures in two PDB files to be merged. This is useful if structures of individual domains have have been solved separately and are located in two PDB files. Then with the merge flag, you will not need to use and external program or hand edit PDB files to join them. * Added the merge flag to the structure.read_pdb user function. This currently does nothing. * The merge flag for the structure.read_pdb user function is now propagated to the pack_structs() method. This structure API method calls the ModelList.merge_item() method which is yet to be implemented. * The MolList.add_item() structural API method now returns the added molecule container. This is used by the pack_structs() method to alias the molecule, and will be required when structure merging is implemented. * Whitespace fixes - replaced many instances of the tab character '\t' with 4 spaces. * Implemented the merging of structural objects. This allows the merge flag of the structure.read_pdb user function to work. * The printouts from the structure.read_pdb user function are now different with the merge flag set. The text now says that the molecules are being merged rather than added. * Sections of molecules can now be deleted using the structure.delete user function. The atom ID argument has been added and this is now propagated into the internal structural object. This ID string can be used to delete subsets of the 3D structural data in the relax data store. * Created the Structure.test_read_write_pdb_1UBQ system test. This is for checking the use of the structure.delete user function with the atom ID argument. * The Structure.test_read_write_pdb_1UBQ system test now checks for HELIX and SHEET records. This is not implemented yet, but the idea is that the structure.read_pdb and structure.write_pdb should preserve the helix and sheet information present in the original PDB and that the internal structural object should store this information. * Created the internal structural object _pdb_chain_id_to_mol_index() method. This will be used to convert PDB chain IDs, which are used to indicate different molecules in the PDB, into molecule indices for the internal structural object. * HELIX PDB records are now read, stored, and written out by the internal structural object. This affects the structure.read_pdb and structure.write_pdb user functions. The helix is stored as a metadata type object - its elements do not correspond to the atoms in the structural object. * SHEET PDB records are now read, stored, and written out by the internal structural object. This affects the structure.read_pdb and structure.write_pdb user f
relax version 3.0.1.
This version is a minor feature and bugfix release. The handling of peak lists has been enhanced and chemical shifts can now be read into relax, there are a number of improvements throughout the GUI, and a number of minor bugs have been solved. If these changes affect you, please upgrade to this latest version. 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). Features: * Improved handling of peak lists. * Simplification of the user function GUI elements for those associated with the free file format. * Support for the reading of chemical shifts into the relax data store with the new chemical_shift.read user function. * Improvements to the appearance of the GUI by using more unicode. * Redesign of the model list GUI element used in the model-free analysis. Changes: * The font size is no longer set for the latex2html compiled user manual. * A number of updates and improvements to the document explaining how to setup a Mac OS X framework. This Framework Python setup is used to build the binary distribution files. * Updated the Mac Framework testing script to handled 4-way binaries (ppc74 included). * Better support for 4-way binaries in the Mac OS X Framework detection script. * Added support for the 'current ar archive random library' file type in the Mac OS X Framework testing script. * Added py2app to the Mac OS X Framework setup instructions. * Shifted code from pipe_control.spectrum to the new lib.spectrum.peak_list relax library module. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/3972/focus=4347. * Added a special script for locating all Python versions and printing out the installed modules. * Large change to the free file format GUI element for the user functions. The GUI element used in the user function wizard windows has been modified to have both a 'default' form, which is the previous design, and a 'mini' form which is now used for the user functions. This mini form only uses 1 row, rather than the default of 6 or 8. It is a read only text element with a button that launches the free file format window. The amount of space saved is huge. * Improved the text for the mini free file format GUI element. * Updated all of the user function GUI window sizes for the 'mini' free file format GUI element. This allows much more text of the description to be displayed. * Updated the Mac Framework setup document to help with scipy compilation problems. * Improved the Python seeking and module version print out script for symlinks. This should now be much more capable of finding all Python versions on a system. * Added support for the Mac OS X Modelfree4 binary results to the Palmer.* system tests. The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In the Mac binaries, the results are instead written out to 4 significant figures. Therefore the number of decimal places are much less than the Linux results. * Syntax error fix for one of the unused scripts in the relax test suite shared data directories. This problem was encountered by Jack Howarth and communicated in a private message. The issue was found by fink. This script is never used and will never be used again - it is only there for reference. * Modification of the spectrum.read_intensities user function front end. The heteronuc and proton arguments have been eliminated. Instead the new dim argument is used to associate the data with the spins of any dimension in the peak list. * Replaced the 'heteronuc' and 'proton' arguments of the spectrum.read_intensities user function backend with 'dim'. * Created the new lib.spectrum.objects module. This will hold temporary data structures for representing peak lists and other spectral data. The module currently contains the Peak_list class which is used to hold peak list data. * Started to shift the spectrum.read_intensities user function backend to use lib.spectrum.peak_list. * The pipe_control.spectrum.read_intensities() function now works with the Peak_list object. * The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function. * The lib.software.sparky.read_list_intensity() function now operates on the Peak_list object. * Changed the spectrum.read_intensities dim argument default to w2 and improved the long description. * Fix for the assignm
relax version 3.0.2.
This version is a minor feature and bugfix release which includes better pseudo-atom support, support of the value.write user function to allow model information to be written to file, improvements to the 2D Grace plots, and fixes for missing log messages when running on a cluster using OpenMPI. 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). Features: * Much better pseudo-atom support, including not requiring tetrahedral geometry. * The value.write user function can now create files with non-numeric data, such as the models for each spin. * Improvements to the 2D Grace plotting from the grace.write user function including full support for multiple graphs and the setting of the axes to the zero point. Changes: * Updated the Release Checklist document rsync instructions to allow resumed uploads. This is needed if the internet connection has been cut, as uploading can take a long time. * The test_suite.clean_up.deletion() function can now handle the case of missing files and directories. This problem was occurring in the relax_disp branch for some of the system tests. * Created the is_int() and is_num() functions for the lib.check_types module. * The value.write user function can now properly handle non-numeric data types. This allows the spin specific model name to be written to file, or any other string defined in the specific analysis PARAMS data object. * The multi-processor section of the manual is now labelled in the correct position. * Created a special GUI analysis element for floating point numbers. This allows for user input of floating point numbers into one of the GUI analysis tabs. If the input is not a number, the original value will be restored. * Created the new pipe_control.spectrum.add_spectrum_id() function. This is used to handle the creation of spectrum ID strings in the data store. This way new spectrum IDs can be created from different parts of relax in a controlled way. * Created the pipe_control.spectrometer.check_frequency() function to standardise this check. * Created the pipe_control.spectrometer.get_frequency() function for returning the frequency for a given ID. * The pipe_control.spectrum.add_spectrum_id() function now returns silently if the ID already exists. * Improvements to the pymol.view and molmol.view user functions for finding the PDB files. Now the possibility that this is being run from a results subdirectory is taken into consideration. If the file cannot be found, the os.pardir parent directory is added to the start of the relative path and the file checked for. * The rdc.read user function will now skip all lines of the RDC file starting with '#'. To include molecule identifiers at the start of the line will now require quotation marks. * Shifted the RDC and PCS assembly methods from the main class to the data module for the N-state analysis. * Created the pipe_control.mol_res_spin.is_pseudoatom() function to simplify pseudo-atom handling. * Created the pipe_control.mol_res_spin.pseudoatom_loop() function. This is used to loop over the spin containers corresponding to a given pseudo-atom. * Added a PDB file and RDC values (and absolute J+D and J) for propylene carbonate. This will be used for testing of pseudo-atoms in the N-state model analysis. * Renamed the propylene carbonate files to the correct name of pyrotartaric anhydride. * Created two new system tests based on the new pyrotarctic anhydride long range (1J, 2J & 3J) RDC data. The first (N_state_model.test_pyrotartaric_anhydride_rdcs) optimises an alignment tensor using long range signed RDC data. The second (N_state_model.test_pyrotartaric_anhydride_absT) optimises an alignment tensor using long range absolute T (J+D) data. Both test long range data together with methyl group pseudo-atom data. * Added all of the pyrotartaric anhydride RDC generation scripts and files. This is simply for reference and reproducibility. * Modifications for the pyrotartaric anhydride system test script. The grid search now is much quicker, and the RDC correlation plots are now sent to DEVNULL. * Added the return_id argument to the pipe_control.mol_res_spin.pseudoatom_loop() function. This will then yield both the spin container and spin ID string. This mimics the spin_loop()function. * Added proper pseudo-atom support for the RDCs in the N-state model analysis. This involves a number of changes. The pseudo-atom specific functions ave_rdc_tensor_pseudoatom() and ave_rdc_tensor_pseudoa
relax version 3.1.1.
This is a major feature and bugfix release which adds support for
reading 3D structures of organic molecules from Gaussian log files,
the new lib.periodic_table and lib.nmr modules, the 'NS MMQ 3-site
linear', 'NS MMQ 3-site', 'NS R1rho 3-site linear', and 'NS R1rho
3-site' relaxation dispersion models, R1rho dispersion data sets where
multiple offsets and multiple spin-lock fields have been collected for
each spin, the loading of spins directly from peak lists, and the
reading of NMRPipe seriesTab files. Due to the improvements and the
bugs fixed in the relaxation dispersion analysis, all users are
recommended to upgrade to this version.
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).
The full list of changes is:
Features:
* Support for reading 3D structures of organic molecules from
Gaussian log files using the new structure.read_gaussian user
function.
* Addition of the lib.periodic_table module for storing
information about the periodic table.
* Addition of the lib.nmr module for basic NMR related
functions. It currently has functions for converting between ppm, Hz,
and rad.s^-1 units.
* Many improvements to the relaxation dispersion chapter of
the user manual.
* The 'NS MMQ 3-site linear' numeric model - the model for
3-site exchange using 3D magnetisation vectors linearised with kAC =
kCA = 0 with the parameters {R20, ..., pA, pB, dw_AB, dw_BC, dwH_AB,
dwH_BC, kex_AB, kex_BC}.
* The 'NS MMQ 3-site' numeric model - the model for 3-site
exchange using 3D magnetisation vectors with the parameters {R20, ...,
pA, pB, dw_AB, dw_BC, dwH_AB, dwH_BC, kex_AB, kex_BC, kex_AC}.
* The 'NS R1rho 3-site linear' numeric model - the model for
3-site exchange using 3D magnetisation vectors linearised with kAC =
kCA = 0 with the parameters {R1rho', ..., pA, pB, dw_AB, dw_BC,
kex_AB, kex_BC}.
* The 'NS R1rho 3-site' numeric model - the model for 3-site
exchange using 3D magnetisation vectors with the parameters {R1rho',
..., pA, pB, dw_AB, dw_BC, kex_AB, kex_BC, kex_AC}.
* More model nesting in the relaxation dispersion
auto-analysis ('CR72' and 'MMQ CR72', 'LM63' and 'LM63 3-site').
* Large speed up of the 'TP02' and 'NS R1rho 2-site'
dispersion models by minimising repetitive calculations.
* Support for the loading of spins directly from peak lists.
* Support for the reading of peak intensities from NMRPipe
seriesTab formatted files (*.ser).
Changes:
* Small improvement for the devel_scripts/log_converter.py
script for detecting commit boundaries.
* Added many small details to the release checklist document.
This is for the formatting and editing of the CHANGES file, which is
used for the release announcements. Some additional details about the
API documentation at http://www.nmr-relax.com/api have been added too.
* Added sectioning printouts for the relaxation dispersion
auto-analysis. This simply tells the user which part of the protocol
is currently being performed.
* Setup for testing the
sample_scripts/relax_disp/R1rho_analysis.py sample script. The script
was copied into the
test_suite/shared_data/dispersion/r1rho_off_res_tp02/ data directory
where it will be tested on real data. The 'fake_sequence.in' and
'unresolved' files have been created to allow the script to run. And
the script itself has been heavily debugged.
* All of the relaxation dispersion auto-analysis options are
now exposed by the sample scripts. This included the pre_run_dir
argument for specifying a directory of results from a non-clustered
analysis and the flag for running MC simulations for all models.
* Added the DATA_PATH variable to the cpmg_analysis.py
dispersion sample script. This allows the user to more easily specify
a different directory for the files.
* Docstring improvement for the
test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1rho_analysis.py
script.
* Synchronised the
test_suite/shared_data/dispersion/Hansen/relax_disp.py with the sample
script. This script now matches very closely with the
sample_scripts/relax_disp/cpmg_analysis.py sample script. This is for
sample script debugging purposes.
* Created a base data pipe for Flemming Hansen's truncated
CPMG data for testing out missing data. The :4 spin is missing just a
few data points, whereas the :71 spin is missing all 800 MHz data.
* Created the
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test.
This is used to demonstrate a failure in the 'R2eff' model when some
data is missing.
* Expansion and fixes for the
Relax_disp.test_hansen_cp
relax version 3.1.2.
This relax version is a minor bugfix release which repairs a number of icons on newer operating systems and a solves a problem caused by accidentally setting an incorrect spectrometer frequency. 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). The full list of changes is: Features: N/A Changes: * The average_intensity() dispersion function now accepts the offset argument. This is for better support of combined offset and spin-lock varied R1rho-type data. The argument is then passed into the find_intensity_keys() function. * Improved the DPL94 dispersion model description in the manual. * Copied a Sparky peak list to be modified to be a Sparky file without intensity column. * Modified the Sparky file to have no columns with intensity values. * Implemented to read spins from a SPARKY list, when no intensity column is present. Addition to Support Request #3044, (https://gna.org/support/index.php?3044) - load spins from Sparky list. * Created the Relax_disp.test_bug_21460_disp_cluster_fail system test. This is to catch bug #21460 (https://gna.org/bugs/?21460) reported by Min-Kyu Cho. The save file added to the repository consists solely of the data for the first residue. * Speed ups for the Relax_disp.test_bug_21460_disp_cluster_fail system test. The optimisation precision is not important for demonstrating this bug. * Updated the main copyright notice for 2014. * Fix for the main copyright notice. * Updated the copyright notice visible to the user to 2014. * Updated the copyright for the relax GUI splash screen for 2014. * Improvement for the relax test suite printout with the --time command line argument flag. The tests printed out now have the package and module names removed, so that one the test name remains. This removes a large amount of text, simplifying the printout. Bugfixes: * Partial fix for bug #21338 (https://gna.org/bugs/?21338) - the bad sRGB profile in some PNGs. This is only partial as some files are still to be converted (the original Bruker logo, and the 16x16, 22x22 and 32x32 sized Bruker icons). * Fix for bug #21460, the failure of relaxation dispersion due to incorrect spectrometer information. This is the bug https://gna.org/bugs/?21460, reported by Min-Kyu Cho. There was only one place in the dispersion analysis which failed due to a spectrometer frequency not containing any relaxation data - in the insignificance testing in the auto-analysis. * Loosened the chi2 check in the Relax_disp.test_korzhnev_2005_15n_mq_data system test. This is to allow the test to pass on a 32-bit Linux (Mageia 1) test system. ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 3.1.3.
This is a minor documentation release which includes small improvements to the documentation of the relaxation dispersion analysis in the manual as well as the API documentation for the lib.dispersion package. As the manual is available from http://download.gna.org/relax/manual/relax.pdf, installing this newer version of relax is not necessary. 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). The full list of changes is: Features: N/A Changes: * Fix for the parameters listed for the IT99 dispersion model in the manual. * Improvements and addition of many links to the lib.dispersion.cr72 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html. * Spacing fix for the lib.dispersion.cr72 module docstring. * Improvements and addition of many links to the lib.dispersion.dpl94 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html. * Improvements and addition of many links to the lib.dispersion.it99 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html. * Improvements and addition of many links to the lib.dispersion.lm63_3site API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html. * Improvements and addition of many links to the lib.dispersion.lm63 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html. * Improvements and addition of many links to the lib.dispersion.m61b API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html. * Improvements and addition of many links to the lib.dispersion.m61 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html. * Improvements and addition of many links to the lib.dispersion.mmq_cr72 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html. * Improvements and addition of many links to the lib.dispersion.mp05 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html. * Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_3d API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html. * Epydoc URL simplifications. * Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_expanded API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html. * Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_star API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html. * Added the 'NS CPMG 2-site 3D full' model to the lib.dispersion.ns_cpmg_2site_3d module docstring. * Improvements and addition of many links to the lib.dispersion.ns_mmq_2site API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html. * Improvements and addition of many links to the lib.dispersion.ns_mmq_3site API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html. * Improvements and addition of many links to the lib.dispersion.ns_r1rho_2site API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html. * Improvements and addition of many links to the lib.dispersion.ns_r1rho_3site API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html. * Small docstring edit for the lib.dispersion.mp05 module. * Improvements and addition of many links to the lib.dispersion.tap03 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html. * Improvements and addition of many links to the lib.dispersion.tp02 API documentation. This is for the API documentation at http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html. * Epydoc URL simplifications in the lib.dispersion.mp05
relax version 3.1.4.
This is a minor feature and bugfix release which has improvements for the handling of structural data involving multiple molecules or models and improved support in the NOE analysis for replicated spectra. Included are fixes for the failure of the structure.create_diff_tensor_pdb user function for non-spherical diffusion tensors when no Monte Carlo simulations are present and for the failure of the rdc.write user function for back calculated RDC data. Full details are given below. 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). The full list of changes is: Features: * The structure.write_pdb user function now supports multiple molecules being present. * Large speed optimisations for the internal structural object when multiple models are present. * Improved support for replicated spectra in the NOE analysis. Changes: * Created the Frame_order.test_generate_rotor2_distribution system test. This is to test the Frame Order distribution generating base script, used for creating the synthetic Frame Order test data, and to demonstrate a failure in handling back-calculated RDC data. To implement this, the test_suite/shared_data/frame_order/cam/ path has been converted into a Python package (with the addition of the __init__.py files). The base data generation script test_suite/shared_data/frame_order/cam/generate_base.py has also been modified to use the absolute path for the data files and its run() method now accepts the save_path argument to allow the files to be saved into a temporary directory. * Fixes for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script now saves the program state files into the self.save_path directory, preventing the system test from attempting to save files into the relax test suite directories. * Another fix for the Frame_order.test_generate_rotor2_distribution system test. The test_suite/shared_data/frame_order/cam/generate_base.py script no longer prints its progress indicator to sys.__stderr__ but to sys.stderr instead. This avoids the progress text from appearing during the relax test suite execution. * Created the Structure.test_bug_21522_master_record_atom_count system test. This is designed to catch bug #21522 (https://gna.org/bugs/?21522), the structure.write_pdb user function creating an incorrect MASTER record. This hence also catches bug #21520 (https://gna.org/bugs/?21520), the failure of the structure.write_pdb user function when creating the MASTER record due to too many ATOM and HETATM records being present. The test simply creates two structural models, adds one atom, and writes out a PDB file, checking its contents. * The structure.write_pdb user function can now handle a file instance for the file argument. This is for the Structure.test_bug_21522_master_record_atom_count system test, to allow a dummy file object to be used. This can also be useful for power users. * Created the lib.geometry.vectors.unit_vector_from_2point() function. This is used to quickly calculate the unit vector between two points. * The lib.structure.represent.rotor.rotor_pdb() function can now handle multiple rotors. Previously this function would fail if called twice with the same structural object. * Added the has_molecule() method to the relax internal structural object. This is used to quickly check if a molecule name already exists in the structural object. * More improvements for handling multiple rotors in the lib.structure.represent.rotor.rotor_pdb() function. The atom numbering is now better handled. * Better support for the writing out of multiple molecules by the structure.write_pdb user function. This is for the internal structural object write_pdb() method. Now each molecule is assigned a different chain ID in the PDB file, and the chain IDs loaded into the structural object are ignored. The chain IDs should however be preserved when using structure.read_pdb followed by structure.write_pdb, without storing the ID. A number of the Structure system tests had to be updated, as now the relax generated PDB files will always write out a chain ID. * Large speed up for the internal structural object for when many models are present. The new ModelList.current_models object keeps track of all the models already present in the structural object. This simplifies the checks of the pack_structs() internal structural object method by removing expensive looping. This allows the loading of PDB files to continue to be fast even with many tens or hundreds of thousa
relax version 3.1.5.
This is a major bugfix release which fixes the complete failure of the NOE analysis for most users, a bug introduced in the last relax release (https://gna.org/forum/forum.php?forum_id=2433). All users of relax 3.1.4 should upgrade to this version. 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). The full list of changes is: Features: N/A Changes: * Updated the interatom.unit_vectors user function description to add the text '3D structure'. This is in response to the http://thread.gmane.org/gmane.science.nmr.relax.user/1547 relax-users mailing list message and the change is to clarify the usage of the user function. * Created the Noe.test_bug_21591_noe_calculation_fail system test. This is to catch bug #21591 (https://gna.org/bugs/?21591) submitted by Martin Ballaschk (https://gna.org/users/mab). This is the complete failure of the NOE analysis. The peak lists attached to the bug report have been included in the test suite to create the system test. * Improvements for the steady-state NOE analysis overfit_deselect() method. The spin deselection which occurs at the start of the calc user function call, used to calculate the NOE, is now clearer. Each deselection condition is now explained in detail and the text is now far more informative. In addition, the special condition of all spins being deselected is now caught. If this happens, a RelaxError is raised to prevent the user from going forwards. This should remove confusion as to why the output file is empty. Bugfixes: * Fix for bug #21591 (https://gna.org/bugs/?21591), the complete failure of the NOE analysis. This bug was reported by Martin Ballaschk (https://gna.org/users/mab). The issue was introduced in the fix for bug #21562 (https://gna.org/bugs/?21562). The problem is that the overfit_deselect() method was deselecting all spins with two data points or less rather than one or less. ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 3.1.6.
This is a major feature and bugfix release. A comprehensive tutorial has been added to the relaxation dispersion chapter of the manual which shows, step-by-step, the dispersion analysis in the GUI using screenshots. Other changes include improved PDB chain ID support, a new mode for running a relax script and then entering the prompt UI mode, multiple file reading by the spectrum.read_intensities user function, and improvements to the relaxation dispersion analysis. A number of major bugs in the dispersion analysis concerning different relaxation delay times for different experiments and for improved handling of the offset have also been fixed. A number of important GUI bugs have also been fixed. All users are recommended to upgrade to this version of relax. 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). The full list of changes is: Features: * Full support for PDB chain IDs in the internal structural object. * Improvements for the devel_scripts/python_seek.py for finding all installed Python versions and modules. Individual modules can now be specified on the command line. * The pedantic command line option -p, --pedantic has been renamed to -e, --escalate. * The new prompt command line option -p, --prompt causes the relax prompt mode to launch after running a script to allow relax to be inspected interactively. * Better organisation of the relax command line options into groups, as shown by running 'relax -h'. * A tutorial for using the relaxation dispersion analysis in the GUI has been added to the manual. This includes step-by-step instructions with many screenshots. * Improvements to the manual including better and consistent line breaking for the GUI menu item text, user functions, file and directory paths, and Python module paths. * The spectrum.read_intensities user function can now load multiple files simultaneously, allowing for simplified use in the GUI. * Addition of a new GUI window element for loading multiple files. * Improvements to the sequence data input GUI window including the item count being displayed and a 'Delete' button to remove the last element. * Improvement for the relaxation dispersion auto-analysis - the names of the automatically created data pipes are now unique by appending the name of the data pipe bundle to the end. This allows multiple dispersion auto-analyses to exist simultaneously in the GUI or within one relax state file. * The relaxation dispersion analysis now handles deselected spins. * Improved colour coding of relax log messages in the relax manual. * The relaxation dispersion auto-analysis now creates the chi2.out text file. This is for more easily comparing the chi-squared values between analyses. Changes: * Converted the chain ID list in the internal structural object to the CHAIN_ID_LIST module variable. * The internal structure object method _pdb_chain_id_to_mol_index() now uses the CHAIN_ID_LIST string. This allows for the full PDB chain ID range to be supported. * Small improvement for the devel_scripts/python_seek.py script. The list of detected Python binaries files are now sorted prior to determining the installed modules. * Updated the N_state_model.5_state_xz system test to allow it to complete on i586 Linux systems. The optimisation would continue for a huge amount of time on a test system (Mageia 4 i586 VM) and would make it appear as though the test suite has hung. By limiting the maximum number of iterations in the optimisation to 1000, the test will complete successfully and the parameters optimised to the same precision. * Loosened the checks for the Frame_order.test_korzhnev_2005_15n_zq_data system test. This is to allow the test to pass on a 32-bit test system (Mageia 4 i586 VM). * Decreased the accuracy of the Relax_disp.test_korzhnev_2005_15n_dq_data system test. This is to allow the test to pass on a 32-bit test system (Mageia 4 i586 VM). * Decreased the precision of the Relax_disp.test_hansen_cpmg_data_auto_analysis system test. This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1 (Mageia 4i586 VM). * Decreased the precision of the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test. This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1 (Mageia 4i586 VM). * Decreased the precision of the Relax_disp.test_hansen_cpmg_data_to_cr72 system test. This is to allow the test to pass on a 32-bit test system using Python 2.5 and Python 3.1
relax version 3.1.7.
This is a minor feature and bugfix release which includes improvements to the relaxation dispersion chapter of the manual and the addition of new infrastructure for R1rho data handling in the dispersion analysis. More details are given below. 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). The full list of changes is: Features: * Large amounts of new infrastructure for the R1rho relaxation dispersion analysis type. * More hardware information printed out when using the '--info' command line option. * The user function relax_disp.write_disp_curves now produces text files of R2eff verses the rotating frame tilt angle theta. * Small improvements for the relaxation dispersion GUI tutorial and citation chapter of the relax manual. Changes: * Added text file for the articles reference values from the global fit in Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. This is from optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. This uses the data from Kjaergaard's paper at DOI: http://dx.doi.org/10.1021/bi4001062. * Replaced "_" with "-" in text file with global fit residues. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Sorted the reference values in residue order. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Added reference data and guess data for a global fit R1rho analysis. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. This system test is setup comparison with paper values, and will be turned off later to prevent long running time. * Redid dict() keys for unit test of find_intensity_keys(), to pass on Python 3.2 and 3.3. Work in progress for Bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. This is a response to message: http://thread.gmane.org/gmane.science.nmr.relax.devel/5132. * Added ":" to dictionary keys to match return from spin_loop in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Removed model 'No Rex' to be tested in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Aliased spins in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Set opt_func_tol = 1e-15 and opt_max_iterations = 10 to run system test Relax_disp.test_r1rho_kjaergaard faster. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Re-ordered code lines in system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Assigned guess values for system test Relax_disp.test_r1rho_kjaergaard. Regarding bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Added a section at the start of the dispersion GUI analysis tutorial about 'computation time'. This is for the dispersion chapter of the manual. * Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard. Work in progress for Bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. * Added fitted R1 values from paper to system test Relax_disp.test_r1rho_kjaergaard. Regarding sr #3124, (https://gna.org/support/?3124) - Grace graphs production for R1rho analysis with R2_eff as function of O
relax version 3.2.1
This is a major bugfix release which includes the equations for the "B14" and "B14 full" relaxation dispersion models, from Baldwin 2014 and introduced with relax version 3.2.0, now being calculated correctly, the 'NS CPMG 2-site expanded' model correctly handling edge cases where no exchange is expected, and the structure.delete user function correctly operating when multiple models are loaded into the data store. 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). The full list of changes is: Features: * N/A Changes: * Punctuation fixes throughout the CHANGES document. * Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models. System test was renamed from test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to reflect which model create the data and which model fits the data. * Modified cpmg_synthetic script to first create all time structures before doing back-calculation. Bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models. The numerical models need all time points which are defined in setup to be present when calculating. * Renamed system test to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster. The model that creates the data has been changed to numerical model. Bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models. * Implemented system test Relax_disp.test_cpmg_synthetic_ns3d_to_b14. Bug #22021: (https://gna.org/bugs/?22021) model B14 shows bad fitting to data. This is to catch model B14 showing bad fitting behaviour. * Parameter precision increase for system test Relax_disp.test_baldwin_synthetic. The correct implementation of the trigonometric functions allow for higher precision. Bug #22021: (https://gna.org/bugs/?22021) model B14 shows bad fitting to data. Duplicate line codes were also removed. * Code cleanup in system test Relax_disp.test_baldwin_synthetic_full. Bug #22021: (https://gna.org/bugs/?22021) model B14 shows bad fitting to data. The precision could also be increased by 1 digit. * Code cleanup in system test Relax_disp.test_baldwin_synthetic. Bug #22021: (https://gna.org/bugs/?22021) model B14 shows bad fitting to data. Removing many unnecessary lines of code. * Added 7 unit tests demonstrating edge case 'no Rex' failures of the 'NS CPMG 2-site expanded' model. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. These tests cover all parameter value combinations which result in no exchange: dw = 0.0; pA = 1.0; kex = 0.0; dw = 0.0 and pA = 1.0; dw = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; dw = 0.0, pA = 1.0, and kex = 0.0. Such tests should be replicated for all dispersion models. * Created the Structure.test_bug_22069_structure_delete_helix_attribute system test. This is to catch bug #22069 (https://gna.org/bugs/index.php?22069), the failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'". * Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test. This is to catch bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the structure.superimpose user function after deleting atoms with structure.delete. * Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test. These tests reveal the real problem - that the atoms of the second model have not been removed by the structure.delete user function. * Added git-svn support for the relax version information module. This allows the subversion revision number and repository URL to be displayed on program startup, so that it is stored in log files. This is very useful for debugging purposes. * Improvements for the git-svn support in the relax version module. Python 3 is now correctly handled and the URL is properly extracted from the git repository. * Improvement for the unit test printouts when run with the --time command line option. The full unit test name is now printed out, reverting to the old behaviour. However the shortened test names are preserved for the other test suite categories. * Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test. This is a demonstration, showing the 'NS CPMG 2-site expanded' model with no exchange when kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used for all dispersion m
relax version 3.2.3.
This is a major bugfix release and the first requiring numpy >= 1.6 to allow for faster calculations for certain analyses. There have been improvements to the GUI user functions, the ^[[?1034h escape code is finally suppressed on Linux systems, and the structure.com user function has been added. Bugfixes include the proper handling of R20A and R20B parameters in the relaxation dispersion models, the 'IT99' dispersion model tex parameter was incorrectly handled, the 'LM63 3-site' dispersion models had a fatal mistake in its equations, files with multiple extensions (for example *.pdb.gz) are now correctly handled, and closing the free file format window in Mac OS X systems caused the GUI to freeze. Full details can be found below. For this release, the Mac OS X framework used to build the universal 3-way (ppc, i386, x86_64) binaries for the stand-alone relax application has been updated. The relax application now bundles Python 2.7.8, numpy 1.8.1, scipy 0.14.0, nose 1.3.3, wxPython 2.9.3.1 osx-cocoa (classic), matplotlib 1.3.1, epydoc 3.0.1, mpi4py 1.3.1 and py2app 0.8.1. This should result in better formatted relax state and results files and give access to more advanced packages for power users to take advantage of. 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). The full list of changes is: Features: * Improvements for a number of GUI elements used in the user function windows. * The ^[[?1034h escape code should now no longer be emitted by GNU readline on Linux systems. * Created the very basic structure.com user function for calculating the centre of mass. This is to simply allow an easy interface to the pipe_control.structure.mass.pipe_centre_of_mass() function. * Expansion of the REMARK section of the PDB file created for the internal structural object. This is visible when using the structure.write_pdb user function, as well as the many other user functions which create PDB files. The relax version as well as the file creation date are now recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK section improve the formatting. Changes: * Added proper sectioning to the release checklist document. * Added the upload script to the release checklist document. * Modified the Sequence GUI input element used for the user function list arguments. The first column is now of fixed with when titles are supplied. Previously when supplying titles, the width would be tiny and no text would be visible. * Added titles for all 3D coordinate user function arguments. This is for the Sequence GUI input element, and affects the frame_order.average_position, n_state_model.CoM and paramag.centre user functions. * The compilation of the C modules now respects the user defined environment. This is the patch from Justin (https://gna.org/users/jlec) attached to bug #22145 (https://gna.org/bugs/?22145). It has been modified to include a comment and remove a double empty line. * Bug fix for the compilation of the C modules now respects the user defined environment. The problem was that on Mac OS X (as well as other systems), that these environmental variables were not defined and hence the scons commands would all fail with a KeyError and traceback. Now the keys in the os.environ dictionary are being searched for before they are set. * Fix for the wxPython link in the installation chapter of the manual. This was pointing to the scipy website for some reason. * Changed the Python readline link for MS Windows in the installation chapter of the manual. This now points to https://pypi.python.org/pypi/pyreadline as the iPython link is broken. * Implemented system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models. * Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for B14 full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: (https://gna.org/bugs/?22146) Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models. * Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for NS CPMG 2SITE 3D full model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. Bug #22146: (https://gna.org/b
relax version 3.3.1.
Write a Python class for the repeated analysis of dispersion data. * Turned on minimisation in system test Relax_disp.test_repeat_cpmg(). Task #7826 (https://gna.org/task/index.php?7826): Write a Python class for the repeated analysis of dispersion data. * The lib.spectrum.nmrpipe module has been made independent of the relax source code. This was discussed at http://thread.gmane.org/gmane.science.nmr.relax.scm/23357/focus=7103. The change allows the software verification tests pass. The dep_check module cannot be used in the relax lib package. Only modules from within lib are allowed to be imported into modules of lib. The fix now allows the full test suite to pass and hence new relax releases are once again possible. * Created a document which explains how missing copyrights can be found. * Even more improvements to the shell command for finding missing copyrights. * Updated the copyright notice for 2014 for all files changed by Edward d'Auvergne. These were identified using the command in the find_missing_copyrights document. * Added numdifftools to the extern package __all__ list. * Updated the find_missing_copyrights document. The matching is now more precise and skips all svnmerge operations. * Added the 2014 copyright notice for Troels Linnet to many relax source files. These were identified as being edited by Troels using the command listed in the find_missing_copyrights document. The changes include adding "Copyright 2014 Troels E. Linnet" to many files not containing Troels' copyright notice, and extending the 2013 copyright to 2014. * Implemented correlation plot of minimisation values. Task #7826 (https://gna.org/task/index.php?7826): Write a Python class for the repeated analysis of dispersion data. * Changed the missing package/module/software table in the test suite. This is to allow all names to fit and to update the column titles for software packages. * Decreased the accuracy of a check in the Relax_disp.test_estimate_r2eff_err_auto system test. This is to allow the test to pass on my Windows 7 VM. * Added Troels E. Linnet to the COMMITTERS file, which has not been updated in almost 3 years. * Created the Structure.test_get_model system test. This demonstrates that the internal structural object get_model() method is not working as it should. * Added a few more checks to the Structure.test_get_model system test. * Created the Structure.test_collapse_ensemble system test. This is used to test a planned feature of the internal structural object. The collapse_ensemble() method will be created to remove all but one model in the structural ensemble. * Modified the Structure.test_collapse_ensemble system test to check the initial values. This is for sanity reasons as the test coverage of the structure.add_atom user function is poor. * Implemented the internal structural object collapse_ensemble() method. This allows the Structure.test_collapse_ensemble system test to pass. * Created a basic text based progress meter in the new lib.text.progress module. This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py. * Modifications to the User_functions.test_structure_add_atom GUI test. As lists of lists are now accepted by the structure.add_atom user function, the operation in the GUI is now significantly different. Therefore many checks have been removed from the GUI test. * Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the dep_check module. This newest version handles infinite target function values preventing optimisation from continuing forever (https://gna.org/forum/forum.php?forum_id=2477). The 1.0.10 version is also useful as there is full support for gradients and Hessians in the log-barrier constraint algorithm (https://gna.org/forum/forum.php?forum_id=2475). * Shifted the specific_analyses.relax_disp.variables module into lib.dispersion. This is both to minimise circular dependencies, as previously the specific_analyses.relax_disp modules import from target_functions.relax_disp and vice-versa, and to allow the relax library functions to have access to these variables. This follows from a similar change to the frame order analysis in the frame_order_cleanup branch. * Dependency fix for the auto_analyses.relax_disp_repeat_cpmg module. This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused relax to not start if scipy was not installed. This was detected by testing relax with PyPy. * Implemented writing out of particular correlation plots to file. Task #7826 (https://gna.org/task/index.php?7826): Write a Python class for the repeated analysis of dispersion data. * Created a special internal structural object selection object. This will be used for massively spe
relax version 3.3.2
This is a minor feature and bugfix release. It includes improvements to the readability of the HTML version of the manual (http://www.nmr-relax.com/manual/index.html), improved printouts throughout the program, numerous GUI enhancements, and far greater Python 3 support. Please see below for a full listing of all the new features and bugfixes. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.2. 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). The full list of changes is: Features: * Many improvements for the HTML version of the manual at http://www.nmr-relax.com/manual/index.html. * Improved sectioning printouts in the model-free dauvergne_protocol auto-analysis. * Significant improvements for the relax controller window. * All wizards and user functions in the relax GUI now have focus so that keyboard is active without requiring a mouse click. * The ESC key will now close the relax controller window and all user function windows. * The structure.load_spins user function can now load spins from multiple non-identical molecules and merge them into one molecule allowing missing atoms and differential atom numbering to be handled. * Improvements to the printouts for many user functions. Changes: * Updated the minfx version in the release checklist document to version 1.0.11. * Updated the relax version in the release checklist document to be more modern. * Spelling fixes for the CHANGES file. * Updates for the release checklist document. This is mainly because the main release notes are now the relax wiki, for example for the current version at http://wiki.nmr-relax.com/Relax_3.3.1. * Spelling fixed throughout the CHANGES document. * Removed a few triple spaces in the CHANGES document. * Added periods to the end of all items in the CHANGES document. * Fix for an 'N/A' in the CHANGES document. * Converted a number of single spaces between sentences to double spaces in the CHANGES document. * More updates for the announcement section of the release checklist document. * The HTML version of the manual is now compiled with Unicode character support. This is for the manual at http://www.nmr-relax.com/manual/index.html. It allows Greek symbols, for example, to be represented as text rather than LaTeX generated PNG images. This fixes titles and massively decreases the number of images required by the HTML pages. * Removal of many dual LaTeX and latex2html section titles in the manual. As the HTML manual (http://www.nmr-relax.com/manual/index.html) is now compiled with Unicode support, the Greek characters in the titles are now supported. Therefore in the model-free and the values, gradients, and Hessians chapters, the dual LaTeX and latex2html section titles could be collapsed to the standard LaTeX section title. This will result in better formatting of the manual and its links. * Added instructions and a build script for creating a useful version of latex2html. This version is essential for building the HTML version of the manual at http://www.nmr-relax.com/manual/. The build script downloads the Debian latex2html-2008 sources as well as all Debian patches for latex2html. It then applies a number of patches for fixing and improving the relax documentation. The program is then compiled and can be installed as the root user into /usr/local/. * Extended the number of words used in the HTML webpage file names. This is to hopefully prevent files from being overwritten by multiple files having the same name. * Added the write out of parameters and chi2 values, when creating a dx_map. Task #7860 (https://gna.org/task/index.php?7860): When dx_map is issued, create a parameter file which maps parameters to chi2 value. * Created system test Relax_disp.test_dx_map_clustered_create_par_file, which must show that relax is not able to find the local minimum under clustered conditions. When creating the map, the map contain chi2 values, which are lower than the clustered fitted values. This should not be the case. Running a larger map with larger bounds and more increments, which should show that there exist a minimum in the minimisation space with a lower chi2 value. Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() does not calculate chi2 value for clustered residues. Task #7860 (https://gna.org/task/index.php?7860): When dx_map is issued, create a parameter file which maps parameters to chi2 value. * Renamed test scripts a
relax version 3.3.3.
This is a major feature and bugfix release. It fixes a failure when
loading relaxation data and adds Python 3 support for using the
NMRPipe showApod software. Features include a large expansion for the
align_tensor.matrix_angles and align_tensor.svd user functions to
support the standard inter-matrix angles, the unitary 9D vector
notation {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}, and the
irreducible spherical tensor 5D basis set of {A-2, A-1, A0, A1, A2}
for correctly calculating the inter-tensor angles, singular values and
condition numbers.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.3.
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).
The full list of changes is:
Features:
* Implemented the lib.geometry.vectors.vector_angle_atan2()
relax library function. This is for calculating the inter-vector
angle using the more numerically stable atan2() formula.
* Implemented the lib.geometry.vectors.vector_angle_acos()
relax library function. This is used to calculate the inter-vector
angle using the arccos of the dot product formula. The function has
been introduced into the relax library as the calculation is repeated
throughout relax.
* Expanded the basis sets for the align_tensor.matrix_angles
user function to allow the correct inter-tensor angles to be
calculated. This includes the standard inter-matrix angles via the
arccos of the Euclidean inner product of the alignment matrices in
rank-2, 3D form divided by the Frobenius norm of the matrices,
irreducible spherical tensor 5D basis set {A-2, A-1, A0, A1, A2}, and
the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}
(all of which produce the same result).
* Expanded the basis sets for the align_tensor.svd user
function to allow the correct singular values and condition number to
be calculated. This includes the irreducible spherical tensor 5D
basis set {A-2, A-1, A0, A1, A2} and the unitary 9D basis set {Sxx,
Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} (both of which produce the
same result).
* Added the angle_units and precision arguments to the
align_tensor.matrix_angles user function to allow either degrees or
radians to be output and the number of decimal points to be specified.
* Added the precision argument to the align_tensor.svd user
function to allow the number of decimal points for the singular values
and condition number to be specified.
* Updated the align_tensor.display user function to output the
irreducible spherical harmonic weights. This is the alignment tensor
in the {A-2, A-1, A0, A1, A2} notation.
Changes:
* Basic Epydoc fix for the data_store.exp_info module.
* Epydoc fix for the name_pipe() method of the relaxation
dispersion auto-analysis for repeated data.
* Fixes for the HTML user manual compilation. The index.html
file was not being created as the main page has changed from
'relax_user_manual.html' to 'The_relax_user_manual.html'.
* Added a line to the release checklist document about
updating the wiki release links. These are for the combined release
notes pages at http://wiki.nmr-relax.com/Relax_releases,
http://wiki.nmr-relax.com/Relax_release_descriptions,
http://wiki.nmr-relax.com/Relax_release_metadata,
http://wiki.nmr-relax.com/Relax_release_features,
http://wiki.nmr-relax.com/Relax_release_changes,
http://wiki.nmr-relax.com/Relax_release_bugfixes,
http://wiki.nmr-relax.com/Relax_release_links.
* Updates for the release announcement section of the release
checklist document.
* Created a system test to catch a rare relaxation data loading problem.
* Created the Mf.test_dauvergne_protocol_sphere system test.
This catches bug #22963 (https://gna.org/bugs/?22963): Using '@N*' to
define the interatomic interactions for a model-free analysis fails
when using non-backbone 15N spins.
* Set more reasonable default values for the
lib.structure.pdb_write functions atom() and hetatm(). The occupancy
now defaults to 1.0 instead of '', and the temperature factor to 0.0
instead of ''. This avoid painful errors when using these functions,
as these arguments must be floating point numbers at all times, hence
the default value of '' causes a TypeError.
* Updated the PDB file in the
test_suite/shared_data/model_free/sphere/ directory. The relax
library is now being used to create the PDB file. Additional TER and
CONECT records are now being created so the result is a more correct
PDB file.
* Converted all ATOM records to HETATM in the sphere.pdb file.
* Renamed vector_angle() to vector_angle_n
relax version 3.3.4.
the model type. * Fix for the Rx.test_r1_analysis GUI test. A click on the relax_fit.select_model user function button is now being simulated. * Created a directory for holding synthetic inversion recovery R1 data. * Copied synthetic inversion recovery Sparky peak lists from Sébastien Morin's inversion-recovery branch. * Created a system test script for the inversion-recovery function. This is based on a copy of the script 'relax_fit_exp_2param_neg.py'. * The 3-parameter curve fitting test script now uses the corresponding peak lists. * Prepared the "exp_3param" test for inclusion of artificial data. * Added missing delays in the list. The duplicates had been omitted... * Manually fix the script based on changes made during branch updating. This is as discussed by Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-01/msg1.html. * Updated Séb's relax_fit_exp_3param_inv_neg.py system test script to work with the current relax design. * Added a script for calculating the expected peak intensities for an inversion recovery curve. This is based on the values used by Sébastien Morin in his inversion-recovery branch, as the check_curve_fitting_exp_3param_inv_neg() function of the test_suite/system_tests/relax_fit.py file. * Increased the precision of the printout from the calc.py script of the last commit. * Changed the peak intensities for Gly 4 in the synthetic inversion recovery Sparky lists. The values have been changed to match that determined from the calc.py script. The replicate spectra intensities are simply the calculated intensity +/-1, to preserve the average. * Created the Relax_fit.test_inversion_recovery system test. This simply calls Sébastien Morin's relax_fit_exp_3param_inv_neg.py system test script, ported from the inversion-recovery branch, and then checks the parameter values for the single optimised spin. * Updated the manual_c_module.py C module compilation development script for the recent changes. The exponential_inv.c and exponential_sat.c files need to be compiled as well. * Python 3 fix for the relax_fit_exp_3param_inv_neg.py system test script. The xrange() function does not exist in Python 3, so was replaced by range(). * Updated the memory_leak_test_relax_fit.py development script for the C module changes. This is only the docstring description which changed. * Epydoc docstring fixes for the lib.io module - keyword arguments were not correctly identified. These were identified by Troels in the post at http://thread.gmane.org/gmane.science.nmr.relax.scm/24565/focus=7384. * Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test. This is to catch bug #23017 (https://gna.org/bugs/?23017), the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files. This test checks a rank-2 float64 numpy array stored in the current data pipe against what the IEEE 754 int list should be for it. * Grammar fix for a warning from the pymol.display user function. Bugfixes: * Bug fix for the pymol.view user function for when no PDB file exists. The pymol.view user function would fail with an AttributeError when the currently loaded data does not exist as a PDB file. This is now caught and the non-existent PDB is no longer displayed. A better solution might be to dump all the current structural data into a temporary file and load that, all within a try-finally statement to be sure to delete the temporary file. This solution may not be what the user is interested in anyway. * Simple fix for bug #23017 (https://gna.org/bugs/?23017). This is the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files. The problem was a relatively recent regression caused by a change to the is_float_matrix() function of the lib.arg_check module. It was simply that the default dims keyword argument value was changed from None to (3, 3). Therefore any call to the function without supplying the dims argument would fail if the matrix was not of the (3, 3) shape. ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 3.3.5.
This is a major feature and bugfix release. It fixes an important bug in the Monte Carlo simulation error analysis in the relaxation dispersion analysis. Features include improvements to the NMR spectral noise error analysis, expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments, the implementation of Needleman-Wunsch pairwise sequence alignment algorithm using the BLOSUM62, PAM250 and NUC 4.4 substitution matrices for more advanced 3D structural alignments via the structure.align and structure.superimpose user functions as well as any of the other structure user functions dealing with multiple molecules, conversion of the structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a new pipes/models/molecules/atom_id design to allow the user functions to operate on different data pipes, different structural models and different molecules, addition of the displace_id argument to the structure.align and structure.superimpose user functions to allow finer control over which atoms are translated and rotated by the algorithm, large improvement for the PDB molecule identification code affecting the structure.read_pdb user function, creation of the lib.plotting package for assembling all of the data plotting capabilities of relax, implementation of the new structure.atomic_fluctuations user function for creating text output or Gnuplot graphs of the correlation matrix of interatomic distance, angle or parallax shift fluctuations, the implementation of ordinary least squares fitting, and improvements for the pcs.corr_plot and rdc.corr_plot user functions. Many more features and bugfixes are listed below. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.5. 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). The full list of changes is: Features: * Improvements to the NMR spectral noise error analysis. * Addition of the new spectrum.error_analysis_per_field user function to quickly perform a per-NMR field spectrum error analysis. * Added spectrum.sn_ratio user function to calculate the signal to noise ration for all spins, and introduced the per-spin sn_ratio parameter for the NOE, relaxation curve-fitting and relaxation dispersion analyses. * Added the new select.sn_ratio and deselect.sn_ratio user functions to change the selection status of spins according to their signal to noise ratio. * Expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments. * Conversion of the structure.align, structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a standardised pipes/models/molecules/atom_id argument design to allow the user functions to operate on different data pipes, different structural models and different molecules simultaneously and to restrict operation to a subset of all spins. This is also used by the new structure.atomic_fluctuations user function. * Addition of the displace_id argument to the structure.align and structure.superimpose user functions to allow finer control over which atoms are translated and rotated by the algorithm independently of the align_id atom ID for selecting atoms used in the superimposition. * Large improvement for the PDB molecule identification code affecting the structure.read_pdb user function allowing discontinuous ATOM and HETATM records with the same chain ID to be loaded as the same molecule. * Creation of the lib.plotting package for assembling all of the data plotting capabilities of relax into a unified software independent API. * Implementation of the new structure.atomic_fluctuations user function for creating text output or Gnuplot graphs of the correlation matrix of interatomic distance, angle or parallax shift fluctuations, measured as sample standard deviations, between different molecules. * The implementation of ordinary least squares fitting. * And improvements for the pcs.corr_plot and rdc.corr_plot user functions. * The implementation of Needleman-Wunsch pairwise sequence alignment algorithm using the BLOSUM62, PAM250 and NUC 4.4 substitution matrices for more advanced 3D structural alignments via the structure.align user function. The Needleman-Wunsch algorithm is implemented as in the EMBOSS software to allow for gap opening and extension penalties as well as end
relax version 3.3.6.
This is a minor feature and bugfix release. It includes the addition of the new structure.sequence_alignment user function which can use the 'Central Star' multiple sequence alignment algorithm or align based on residue numbers, saving the results in the relax data store. The assembly of structural coordinates used by the structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and structure.web_of_motion user functions has been redesigned around this new user function. It will use any pre-existing sequence alignments for the molecules of interest, use no sequence alignment if only structural models are selected, and default to a residue number based alignment if the structure.sequence_alignment user function has not been used. Bug fixes include a system test failure on Mac OS X, and I∞ parameter text files and Grace graphs are now produced by the relaxation curve-fitting auto-analysis for the inversion recovery and saturation recovery experiment types. Many more details are given below. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.6. 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). The full list of changes is: Features: * The Needleman-Wunsch sequence alignment algorithm now calculates an alignment score. * Implementation of the central star multiple sequence alignment (MSA) algorithm. * Implementation of a reside number based multiple sequence alignment (MSA) algorithm. * Large speed up of the molecule, residue, and spin selection object, affecting all parts of relax. * Sequence alignments are now saved in the relax data store. * Important formatting improvement for the description in the GUI user function windows, removing excess empty lines after lists. * Creation of the structure.sequence_alignment user function. The MSA algorithm can be set to either 'Central Star' or 'residue number', the pairwise sequence alignment algorithm to 'NW70' for the Needleman-Wunsch algorithm, and the substitution matrix to one of 'BLOSUM62', 'PAM250', or 'NUC 4.4'. * More advanced support for different numpy number types in the lib.xml relax library module. This allows numpy int16, int32, float32, and float64 objects to be saved in the relax data store and retrieved from relax XML save and results files. * Merger of structure.align into the structure.superimpose user function. * The assembly of common atomic coordinates by the structure user functions now takes sequence alignments into account. The logic is to first use a sequence alignment from the relax data store if present, use no sequence alignment if coordinates only come from structural models, or fall back to a residue number based alignment. This affects the structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and structure.web_of_motion user functions. * Large improvements in the memory management for all parts of the GUI. Changes: * Spelling fixes for the CHANGES document. * Created the Structure.test_align_molecules2 system test. This is to demonstrate a failure condition in the structure.align user function. * Large simplification of the atomic coordinate assembly code in the internal structural object. This is in the lib.structure.internal.coordinates.assemble_coord_array() function. The logic of the function has recently changed due to the introduction of the pairwise sequence alignments. This caused a lot of code to now be redundant, and also incorrect in certain cases. This simplification fixes the problem caught by the Structure.test_align_molecules2 system test. * Fix for the Structure.test_displacement system test - the molecule IDs needed updating. * Created the Structure.test_align_molecules_end_truncation system test. This is to demonstrate a failure of the common residue detection algorithm using multiple pairwise alignments in the backend of the structure.align and other multiple structure based user functions. * Created empty unit test infrastructure for testing the lib.structure.internal.coordinates module. * Created the Test_coordinates.test_common_residues unit test. This is from the _lib._structure._internal.test_coordinates unit test module. The test shows that the lib.structure.internal.coordinates.common_residues() function is working correctly. However the printout, which is not caught by the test, is
relax version 3.3.7.
This is a major feature and bugfix release. New features include the statistics.aic and statistics.model user functions, plotting API advancements, huge speed ups for the assembly of atomic coordinates from a large number of structures, the sorting of sequence data in the internal structural object for better structural consistency, conversion of the structure.mean user function to the new pipe/model/molecule/atom_id design, and improvements to the rdc.copy and pcs.copy user functions. Bugs fixed include the incorrect pre-scanning of old scripts identifying the minimise.calculate user function as the old minimise user function, Python 3 fixes, and the failure in reading CSV files in the sequence.read user function. Many more features and bugfixes are listed below. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.7. 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). The full list of changes is: Features: * Creation of the statistics.aic and statistics.model user functions for calculating and printing out different statistics. * Addition of new infrastructure for future support for plotting data using Veusz (http://home.gna.org/veusz/). * Huge speed up for the assembly of atomic coordinates from a large number of structures. * Sequence data in the internal structural object can now be sorted for better structural consistency. * The structure.read_pdb user function now skips water molecules, avoiding the creation of hundreds of new molecules when reading X-ray structures. * Conversion of the structure.mean user function to the new pipes/models/molecules/atom_id design and the addition of the set_mol_name and set_model_num arguments to allow the mean structure to be stored alongside the other molecules. * The monte_carlo.setup user function now raises a RelaxError if the number of simulations is less than 3, avoiding subsequent errors. * Expanded the functionality of the rdc.copy and pcs.copy user functions, allowing for the operation on two data pipes with different spin sequences, skipping deselected spins and interatomic data containers, printing out all copied data for better feedback, and copying all alignment metadata. * The sequence.attach_protons user function now lists all the newly created spins. * Clarification of the RDC and PCS Q factors with the printouts and XML file variable names modified to indicate if the normalisation is via the tensor size (2Da^2(4 + 3R)/5) or via the sum of data squared to allow for clearer RDC vs. PCS comparisons. * Expansion of the align_tensor.copy user function to allow all tensors to be copied between different data pipes. * Huge speed up for loading results and state files with Monte Carlo simulation alignment tensors. * Improvements for the rdc.weight and pcs.weight user functions. The spin_id argument can now be set to None to allow all spins or interatomic data containers to be set. * Improvements for the pcs.structural_noise user function. The check for the presence of PCS data for points to skip now includes checking for PCS values of None. And the output Grace file now also includes the spin ID string as a string or comment value which can be displayed in the plot when desired. Changes: * Created the N_state_model.test_statistics system test. This system test will be used to implement the new statistics user function class consisting of the structure.model and structure.aic user functions for calculating and storing the [chi2, n, k] parameters and Akaike's Information Criterion statistic respectively. * Added the structure.align user function to the renaming translation table. This is so relax identifies structure.align user functions in scripts to raise an error saying that the structure.superimpose user function should be used instead. * Added the office-chart-pie set of Oxygen icons for use in the new statistics user function class. * Created the empty statistics user function class. This adds the infrastructure for creating the statistics user functions. * Small fix for the structure.add_model user function description. * Created the frontend for the statistics.model user function. * Created a wizard graphic for the statistics user functions. This is based on a number of Oxygen icons, as labelled in the SVG layer names. * The statistics.model user function now uses the new statistics wizard graphic. * Created the empty pipe_control.statistics module. This will be used for the backend of all of the st
relax version 3.3.8.
This is a minor bugfix release which allows the relax GUI to be used on screens with the low resolution of 1024x768 pixels. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.8. 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). The full list of changes is: Features: N/A Changes: * Fix for the pipe_control.reset.reset() function when resetting the GUI in non-standard contexts. This is mainly for debugging scripts when simulating a GUI and hence the GUI reset() method does not exist. * Created a GUI memory management debugging script for the align_tensor.init user function. This repetitively calls the reset, pipe.create and align_tensor.init user functions, and opening the GUI element for setting alignment tensor elements (the Sequence window). The pympler muppy_log file shows no memory leaks for these user functions on Linux systems. Bugfixes: * Resized all fixed-sized GUI wizards to fit on 1024x768 pixel wide displays. The problem was reported by Lora Picton in the thread starting at http://thread.gmane.org/gmane.science.nmr.relax.user/1813. Both the spin loading wizard of the spin viewer window and the relaxation data loading wizard used currently in the model-free analysis tab and BMRB export page were fixed. These both had the y-dimension set to 800 pixels, hence parts of the window would be out of view. ___ relax (http://www.nmr-relax.com) This is the relax-announce mailing list relax-announce@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-announce
relax version 3.3.9.
This is a minor feature release with improvements to the automatic relaxation dispersion protocol for repeated CPMG data, support for Monte Carlo or Bootstrap simulating RDC and PCS Q factors, a huge speedup of Monte Carlo simulations in the N-state model analysis, and geometric mean and standard deviation functions added to the relax library. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.9. 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). The full list of changes is: Features: * Improvements to the automatic relaxation dispersion protocol for repeated CPMG data. * Support for Monte Carlo or Bootstrap simulating the RDC and PCS Q factors. * Huge speedup of Monte Carlo simulations in the N-state model analysis. * Geometric mean and standard deviation functions added to the relax library. Changes: * Wrote a method to store parameter data and dispersion curves, for the protocol of repeated CPMG analysis. This is to prepare for analysis in other programs. The method loops through the data pipes, and writes the data out. It then writes a bash script that will concatenate the data in an matrix array style, for reading and processing in other programs. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Added to write out a collection script for chi2 and rate parameters. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * In the collection bash script, removes spins which have not been fitted. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Fix for use of " instead of ' in bash script. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Adding option to minimise class function, to perform Monte Carlo error analysis. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Printout when minimising Monte Carlo simulations. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Added additional test to system test Relax_disp.test_bug_23186_cluster_error_calc_dw() to prove that Bug #23619 is invalid. Bug #23619: (https://gna.org/bugs/index.php?23619): Stored chi2 sim values from Monte Carlo simulations does not equal normal chi2 values. * Small fix for the shell script to collect data files, and not use the program "column" in the end. The line width becomes to large to handle for column. Task #7826 (https://gna.org/task/?7826): Write an Python class for the repeated analysis of dispersion data. * Added a unit test that triggers the bug. Test added in test_delete_spin_all, and can be accessed with: relax -u _pipe_control.test_spin. Bug #23642 (https://gna.org/bugs/index.php?23642): When deleting all spins for a residue, an empty placeholder is where select=True. * Added sample data and analysis script, that will eventually show that there is not much difference in the sample statistics used for comparing the output of two very similar datasets. This is a multiple comparison test with many T-tests at once, where the familywise error is controlled by the Holm method. Even if the values are close to equal, and within the standard deviation, this procedure will reject up to 20% of the null hypothesis. This is not deemed as a suitable method. Bug #23644 /https://gna.org/bugs/?23644): monte_carlo.error_analysis() does not update the mean value/expectation value from simulations. * Added Monte Carlo simulations to the N_state_model.test_absolute_T system test. This is to demonstrate a failure of the simulations in certain N-state model setups. * Added a missing call to monte_carlo.initial_values in the N_state_model.test_absolute_T system test. This fixes the N_state_model.test_absolute_T system test, showing that there is not a problem with the Monte Carlo simulations. * Added Monte Carlo and Bootstrap simulation support for the RDC and PCS Q factor calculations. The pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions have been modified to support Monte Carlo and Bootstrap simulations. The sim_index argument has been added to allow the Q factor for the given simulation number to be calculated. All of the Q factor data structures in the base data pipe now have *_sim equivalents for permanently storing the simulation values. For t
relax version 4.0.1.
This is a major feature and bugfix release. Features include the new
structure.pca user function for performing a principle component
analysis (PCA) of a set of structures, handling of replicated R2eff
data points in the dispersion analysis, improvements in the handling
of PDB structures, the protection against numpy ≥ 1.9 FutureWarnings
for a number of soon to change behaviours in numpy, and addition of a
deployment script for the Google Cloud Computing. Bugfixes include an
error when loading relaxation data, the CSA constant equation in the
manual, missing information in the relax state and results files,
loading of certain state files in the GUI, running relax with no
graphical display and using matplotlib, BMRB export failure when a
spin container is missing data or parameters.
For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.1 .
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).
The full list of changes is:
Features:
* Many improvements for the compilation of the HTML version of
the relax manual (http://www.nmr-relax.com/manual/index.html).
* Updated relax to eliminate all FutureWarnings from numpy ≥
1.9, to future-proof relax against upcoming numpy behaviour changes.
* Ability to handle replicated R2eff data points by the
relax_disp.r2eff_read user function, but adding 0.001 to the frequency
value for the replicated point.
* A new sample script for loading a model-free results file
and back-calculating relaxation data.
* Improvements for the handling of PDB structural data.
* Implementation of the structure.pca user function for
performing principle component analyses (PCA) of an ensemble of
structures.
* Addition of a script for rapid deployment on the Google
Cloud Computing infrastructure.
Changes:
* Fix for the rigid frame order model 2nd degree frame order
matrix in the manual. The wrong symbol was being used.
* Removed the newparagraph and newsubparagraph definitions
from the LaTeX manual. These were causing conflicts with latex2html,
preventing the HTML version of the manual at
http://www.nmr-relax.com/manual/index.html from being compiled. These
definitions are unnecessary for the current set up of the sectioning
in the manual.
* Modified the short captions in the new frame models chapter
of the manual. The runic ᛞ character has been replaced simply by
'Daeg'. This is due to incompatibilities with latex2html which
prevents the HTML manual at http://www.nmr-relax.com/manual/index.html
from being compiled.
* Removal of the definition of a fixed-width table column from
the LaTeX manual preamble. This is required as the definition breaks
latex2html compatibility, causing a corruption in the figure numbering
resulting in the images in the HTML to be essentially randomised.
* Removal of the accents package to allow the HTML manual to
be compiled. The 'accents' LaTeX package is not compatible with
latex2html, so the easiest fix is to eliminate the package.
* Manually rotated the frame order matrix element EPS manual
figures, for latex2html compatibility. The '90 rotate' command has
been deleted and the bounding box permuted as 'a b c d' -> 'b -c d
-a'. This allows the angle argument in the \includegraphics{} command
to be dropped, as latex2html does not recognise this. It allows the
figures to be visible in the HTML version of the manual at
http://www.nmr-relax.com/manual/index.html .
* Redesign of the frame order parameter nesting table in the
manual for latex2html compatibility. The table uses the tikz package,
which is fatal for latex2html, even if not used. Therefore the table
in the docs/latex/frame_order/parameter_nesting.tex file has been
converted into a standalone LaTeX document to create a cropped
postscript version of the tikz formatted table. A compilation script
has been added as well. The resultant *.ps file is now included into
the PCS numerical integration section, rather than this section
creating the tikz table. All tikz preamble text has been removed to
allow latex2html to run.
* Workaround for latex2html not being able to handle the
allrunes package or associated font. In the preamble 'htmlonly'
environment, the frame order symbols are redefined using the text
'Daeg' instead of the runic character ᛞ.
* Fixes for sub and superscripts throughout the manual. This
introduces {} around all sub and superscripted \textrm{} instances.
This is not needed for the PDF version of the manual as the missing
bracket problem is avoided, but it affects the HTML version of the
manual
relax version 4.0.2
This is a minor feature and bugfix release. The new user functions system.cd and system.pwd have been added to allow the working directory to be changed and displayed. The time and sys_info user functions have been renamed to system.time and system.sys_info. The structure.delete_ss user function has been created to remove the helix and sheet information from the internal structural object. For bugs, the R2eff dispersion model can now handle missing peaks in subsets of spectra, and the structure.read_pdb can now handle multiple structures and multiple models with the merge flag set. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_4.0.2 . 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). The full list of changes is: Features: * Addition of the new user functions system.cd and system.pwd to allow the working directory to be changed and displayed. * Addition of the structure.delete_ss user function to remove the helix and sheet information from the internal structural object. Changes: * Improved formatting for the \yes LaTeX command for the HTML manual (www.nmr-relax.com/manual/). This now inputs the raw HTML character for a tick. * The replicate title finding script now processes short titles as well. This shows that the Frame_order.html file will be conflicting and overwritten. * Avoidance of a replicated title in the frame order chapter of the manual. * Added some unicode characters for improved formatting of the CHANGES file. * A number of updates for the release checklist document. This should make it easier to replicate the full release process. * Update the release checklist document. The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release. * Added a check for the total argument for the frame_order.distribute user function. The maximum value is , as the PDB format cannot accept more models. * Creation of the structure.delete_ss user function. This simply resets the helices and sheets data structures in the internal structural object to []. * Updated the copyright notices for 2016. * Created a short Info_box copyright string for displaying in the main GUI window. This shows the full range of copyright dates. * Added the spin_num boolean argument to the structure.load_spins user function. Setting this flag to False will cause the spin number information to be ignored when creating the spin containers. This allows for better support of homologous structures but with different PDB atom numbering. The default flag value is True, preserving the old behaviour. * Added support for concatenating atomic positions in the structure.load_spins user function. Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering. The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions. * Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument. * In the GUI the user functions sys_info and time are now grouped into a "system" subclass. This is to prepare for other system related functions. * Added a new 16x16 icon for the oxygen folder-favorites icon. * Adding a new file at lib/system.py. This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. * In /lib/__init__.py, adding the filename for system.py. * Renaming the folder-favorites icon. * Deleting the old folder-favorites icon. * Adding a new graphics variable: WIZARD_OXYGEN_PATH, to use oxygen icons with size of 200px. * Adding the new user function system.cd. This is to change the current working directory. * Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image. * Adding a user function translation for: This is to catch the new naming of these functions. * Adding a new lib.system.pwd() function, to print and return the current working directory. * Adding a new user function system.pwd() to print/display the current working directory. * Adding new 16x16
relax version 4.0.3.
This is a minor feature and bugfix release. The structure.rmsd user function can now calculate per-atom RMSDs, structure superimposition is now orders of magnitude faster, the relax deployment scripts have been improved and expanded to cover other GNU/Linux systems, OpenMPI system testing scripts have been added, and the relax information printout has been improved. Bugfixes include that the structure.rmsd user function now correctly calculates the RMSD value, and the inversion recovery relaxation curve-fitting equations are now correct. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_4.0.3 . 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). The full list of changes is: Features: * Per-atom RMSD calculation by the structure.rmsd user function. * Much faster superimposition of structures. * More relax deployment scripts for Google Cloud for different GNU/Linux distributions. * Addition of OpenMPI testing scripts. * Improved relax information printout. Changes: * Addition of the atomic boolean argument to the structure.rmsd user function front end. This will be used to enable the calculation of per-atom RMSDs. * Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation. This is for the new option in the structure.rmsd user function. * Implemented the per-atom RMSD calculation for the structure.rmsd user function. * Fixes for the Relax_fit.test_inversion_recovery system test. The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files. The script and Sparky files have been updated. And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative. * Huge speed up for the superimposition of a large number of structures. The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object. This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times. Therefore selection() method no longer calls validate_models(). This may speed up quite a number of internal structure object methods when large numbers of structures are present. * Copying deployment script of Ubuntu to a Fedora version. This is a response to bug #25084 (https://gna.org/bugs/?25084). * Moving fedora to redhat. Google Cloud does not offer fedora images. * Adding deploy script for RHEL 6. * Added initial script for testing OpenMPI. * Making a redhat 6 deploy script, which will upgrade Python from 2.6 to 2.7 The normal installation through yum will have Python 2.6 and only numpy 2.4. This is not good. * Moved deploy scripts. There would probably have to be a deploy script for each system. * Renamed the Ubuntu deploy script. * Adding scripts to test OpenMPI installation and deploy in redhat. * Change to pip install command, to source Python first. * Adding installation of matplotlib to Redhat 6, Python 2.7. * More changing to deploy scripts. * Small change to deploy script to build wxPython. * More changing to deployment scripts. * Moving test script of OpenMPI to bash version. * Made a copy of OpenMPI test script for tcsh shell. * Again small changes to deployment scripts. * Changed more to OpenMPI script. * Altering test OpenMPI script to an alias function. * Change to bash OpenMPI test script. * Last changes to testing of OpenMPI. * Small change to test OpenMPI script for bash * Back to function in bash script for OpenMPI. * Made a deployment script for CentOS 6. * Scons on CentOS finds python2.6 instead of python2.7 * Try to make the script for tcsh and OpenMPI working on all versions of tcsh. * Added the MPI version information to the mpi4py information printout. * Windows scons C module compilation now defaults to 32-bit. This is because the default Python downloads are 32-bit. And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit. Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do. * Added support in the information prin
