This release includes a major overhaul of the relax user manual with
the addition of new chapters and tutorials for all analyses and major
expansions and improvements overall. It also includes a major set of
bug fixes to re-enable the NOE, R1 and R2 analyses of multiple spin
types (e.g. the Trp sidechain indole NH), window ordering fixes for
the GUI, and numerous other small bug fixes. More details are given
below. All users are recommended to upgrade to this newest 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:
* Creation of extensive tutorials for both the script and GUI
modes for the NOE, R1 and R2, model-free chapters with screenshots in
of the GUI in operation.
* Restored support for multiple spin types in the NOE, R1 and
R2 analyses allowing, for example, tryptophan sidechain indole NE1
data to be analysed.
* The activation and expansion of the consistency testing
chapter to the user manual.
* The completion of the reduced spectral density mapping
chapter of the user manual.
* Improvements to the user function section of the user manual
with better visual separation and the inclusion of the icons used in
the GUI.
* Creation of the relax data model chapter of the user manual
to explain how to set up data in relax in all UI modes (with
screenshots in the GUI mode).
* Creation of the citations chapter of the user manual to help
users properly cite the parts of relax that they use.
* A complete rewrite of the relaxation curve-fitting chapter
of the relax manual.
* General improvements and expansions throughout the user
manual (the manual is now 15 Mb compared to 4.3 Mb for relax 2.1.0).
Changes:
* Modified the model-free optimisation final printout to be
more multi-processor friendly. The message saying that the optimised
chi2 is an improvement or not now includes the spin ID string if
present. This is more informative for the multi-processor mpi4py
printouts.
* Added the use of the program 'nice' to the model-free GUI
tutorial in the user manual.
* Removed the out of date and useless README file for the HTML
version of the user manual.
* Added a BMRB section to the end of the model-free chapter of
the user manual.
* Massive expansion of the model-free chapter of the user
manual including script and GUI tutorials. The model-free chapter now
has step-by-step tutorials for both the prompt/script mode and GUI
mode for the new automated model-free protocol (the d'Auvergne
protocol). This includes a large set of screenshots for the GUI mode.
* Created the User_functions.test_value_set GUI test
demonstrating the failure of the value.set user function.
* Modified the dauvergne_protocol sample script to handle
tryptophan indole NE1 data.
* The graphics.fetch_icon() function argument 'format' can now
be set to None. This will return the file path without the extension.
* Improvements to the duplicate user manual title finding script.
* Created a simple shell script to find duplicate titles in
the relax user manual. This is important for the HTML version of the
manual as duplicated titles causes HTML pages to be overwritten. For
example all chapters, sections and subsections titled "Introduction"
will load the introduction.html file which will contain the text of
the last section with that title!
* Additions to the scripting section of the relaxation
curve-fitting chapter of the user manual.
* A small edit to the intro chapter for the multi-processor
operation and logging.
* Added some labelling to the infrastructure chapter of the
user manual for referencing.
* A number of updates and edits to the intro chapter of the
user manual. The model-free GUI screenshot has been shifted to the
intro chapter in preparation for a full tutorial with screenshots in
the model-free chapter.
* Updated the data model chapter of the user manual to cover
the handling of protons. This change includes the modification of the
PDB reading screenshot to demonstrate the reading of a specific model
and the naming of the molecule.
* All of the GUI strings and text are now formatted with a
small sans serif font in the user manual. This is because in the GUI,
a sans serif font is almost always used be default.
* Modified the User_functions.test_structure_pdb_read() GUI
test to catch another bug. This is a bug recently introduced with the
fixes to the other sequence editor GUI window 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 MorinGagne09b. This was
proposed by Edward d'Auvergne in a post at
https://mail.gna.org/public/relax-devel/2012-09/msg00025.html.
* Added the DOI to reference Morin11 and fixed indentation
(10.1016/j.pnmrs.2010.12.003). This follows a comment by Edward
d'Auvergne at https://mail.gna.org/public/relax-devel/2012-09/msg00022.html.
* Deletion of the relax version LaTeX file - this is
automatically created anyway.
* Added text to detail the usage of the consistency testing
script. This text was modified from the corresponding text for
jw_mapping. This follows a discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Added some text and a reference to the consistency testing
chapter. This follows a discussion started by Edward d'Auvergne at
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Editing of the nmrPipe script in the Rx curve-fitting
chapter of the manual.
* Some editing of the NOE chapter of the relax user manual.
* The old R1 and R2 analysis screenshots have been shifted to
the intro chapter.
* Editing of the relax data model chapter of the user manual.
* Large expansion and lots of editing of the relaxation
curve-fitting chapter of the user manual. The GUI section has been
added which includes step-by-step instructions on how to use
relax,illustrated with screenshots at each step. There has been
general editing of the whole of the chapter as well.
* Added a tonne of GUI screenshots of an R1 analysis. These
will be used in the relaxation curve-fitting chapter of the user
manual.
* Added some Grace plots from an NOE analysis for use in the
user manual.
* Small edits of the relax data model chapter of the user manual.
* Editing of the relaxation curve-fitting and NOE chapters of
the user manual. This is to synchronise the format of the two
chapters, and includes the swapping of text between them.
* Added trp indole NH loading into the relaxation
curve-fitting sample script.
* Large edits of the consistency testing chapter of the user manual.
* Activated the consistency testing chapter of the user manual.
* Added a LaTeX label to the J(w) mapping chapter.
* Added the other consistency testing references to the
citation chapter of the manual.
* Added the Fushman et al., 1998 reference.
* Fix for the Farrow et al., 1995 DOI number.
* Changed the order of the Rx curve-fitting and NOE chapters
in the relax manual. This is because the NOE chapter references
passages from the Rx curve-fitting chapter, so it's more logical to
have the Rx curve-fitting chapter first.
* Clean up of a paragraph of the data model chapter of the user
manual.
* Improved the consistency in the user manual by using the new
LaTeX commands. These changes are throughout the manual and affect
all the text of user functions, menu items, prompt examples, GUI
elements, files, directories, etc.
* Removed some '()' text from the end of the user functions in
the user function documentation.
* Added some more LaTeX functions for formatting consistency.
* Defined a new set of LaTeX commands for prompt/script/GUI
strings and elements for the user manual. These will be used to
regularize the text throughout the manual, as this is currently quite
mixed up.
* More rearrangements of data model and NOE chapters of the
relax manual. The GUI spin deselection part of the NOE chapter has
been shifted into the data model chapter. And the GUI loading of
spins from a sequence file section has been completed.
* Added screenshots of the spin viewer spin loading wizard
sequence.read page.
* Redesign of the data model chapter of the user manual. This
includes the moving of all of the spin viewer window text and
screenshots from the NOE chapter.
* Shifted the spin viewer screenshots into their own directory.
* Changed the "View->Spin view" menu item to "View->Spin viewer".
* Created a directory for screenshots of the spin viewer
window operation.
* The NOE auto-analysis GUI test now checks the support for
Trp indole N data as well.
* The spectrum.read_intensities user function now prints out a
list of the intensities read in. This is for better user feedback as
to what the user function has actually done.
* Created the GUI wizard _apply() method for executing the
current page's _apply() method. This is for the GUI tests to simulate
a click on the 'Apply' button.
* Removed a debugging print out.
* Modified the NOE system test to catch bug #20120
(https://gna.org/bugs/?20120).
* Lots of editing of the NOE chapter of the user manual.
* Significant update of the NOE chapter of the user manual.
The sample script used in this chapter was incredibly out of date.
* Modified the NOE system test to test the usage of Trp indole
15N data. This is to catch bug #20119
(https://gna.org/bugs/index.php?20119).
* Added some Trp peak data (backbone and indole N) to the
Sparky steady-state NOE peak lists. This is in preparation for the
modification of the NOE system test to catch bug
#20119(https://gna.org/bugs/index.php?20119).
* Modified the NOE sample script to include Trp indole NH data.
* Added a step-by-step tutorial for the GUI NOE auto-analysis
to the user manual. This includes 22 screenshots of all the steps.
* Added a section label.
* Added some Sparky info to the Rx curve-fitting chapter of
the user manual.
* Allowed the raggedbottom LaTeX setting as this is better for
the screenshot layout in the user manual.
* Added the nth package for the user manual LaTeX compilation.
* The NOE chapter now points to the recommendations in the Rx
fitting chapter.
* Added a new section called 'From spectra to peak
intensities' to the Rx fitting chapter of the manual. This adds a
number of recommendations for high quality relaxation rates.
* Added the Viles et al., 2001 reference.
* Small description edit for the relax_data.temp_control user
function.
* Added a LaTeX label to the NOE chapter of the user manual.
* Added a paragraph to the model-free chapter of the user
manual explaining the J(w) equation forms.
* Added a label to the data model chapter of the user manual.
* Created an initial rough version of the RSDM chapter of the
user manual.
* Better figure layout in the NOE chapter of the user manual.
* The relax data model chapter of the user manual now uses the
higher quality graphics.
* Some more high quality graphics.
* Added more high resolution graphics for use in the relax user
manual.
* Expanded the size of the specific analysis graphics - mainly
for use in the relax user manual.
* Added the specific analysis graphics to the start of each
chapter of the relax user manual.
* Small edit of the 'Citations' chapter of the relax user manual.
* Added EPS versions of the specific analysis graphics for use
in the user manual.
* Added the Fushman et al., 1999 reference for consistency
testing to the intro chapter of the user manual.
* More chapter cross referencing in the relax user manual.
* Added the Horne 2007 paper to the 'Citations' chapter of the
user manual. Whitespace has also been cleaned up, and a chapter label
added.
* Added the Horne 2007 paper to the 'Supported NMR theories'
subsection of the user manual intro.
* Shortened the Literature subsection of the intro chapter to
point to the citations chapter. This part of the user manual is now
redundant.
* Small edits of the relax user manual.
* Edits to the abbreviations chapter of the relax user manual.
* Added another abbreviation.
* Expansion of the abbreviations chapter of the relax user manual.
* Added a tonne of DOI numbers to the relax user manual
bibliography. This will simplify accessing these references for the
user.
* Added and fixed DOI numbers for many bibliographic entries.
* The LaTeX bibliography style for PhD theses now includes the
DOI hyperlink. This is for the user manual.
* Slight modification of the DOI hyperlink formatting
bibliography style for the user manual.
* Modified the relax LaTeX bibliography style file relax.bst
to convert DOI numbers to hyperlinks. This is to add links to the
references within the relax user manual.
* Created the new 'Citations' chapter of the relax user
manual. This is to clearly outline to the user the citations required
for the various components of relax.
* Added the Fushman 1999 reference and a few formatting fixes
in other references.
* Improvements to the 'Supported NMR theories' section of the
user manual introduction. This includes the addition of the Morin and
Gagne 2009 reference.
* Added the Morin and Gagne 2009 reference for the consistency
testing.
* Added some more abbreviations to the relax user manual.
* Created a new chapter for the relax user manual titled 'The
relax data model'.
* Fix for the pipe editor window screenshot width in the relax manual.
* Converted some more wizard graphics to the EPS format for
the user manual.
* Updates and small expansion of the intro chapter of the
relax user manual.
* The user manual now specifies the repository revision if a
non-tagged version is built. This enables easier tracking and editing
of the manual.
* Updates to the generic_fns.mol_res_spin.id_string_doc
documentation structure.
* Updated the screenshot of the pipe editor window.
* Created EPS versions of a number of wizard graphics for use
in the user manual.
* Removed some now useless whitespace from the top of each
user function subsection of the manual.
* Redesigned the formatting of the user function chapter of
the relax manual. The fetch_docstrings.py now forces each user
function to start in a new column. This increases the size of the
manual, but makes the reading of the user function documentation much
easier. The user function class and function icons (128x128 format)
are now placed between the top bar and the subsection title and are
left and right justified. This prettification simply allows the user
functions to be more quickly identified.
* Large expansion of the relax icon set. All 128x128 versions
of the icons used by the user functions have been added as both PNG
and gzipped EPS files. A few gzipped SVG and non-sized icons have
been added as well.
* Large expansion of the Oxygen icons within relax. All
128x128 versions of the icons used by the user functions have been
added as both PNG and gzipped EPS files. A number of gzipped SVG
icons has been added as well.
* Modified the graphics.fetch_icon function to return
different file formats. This will be used for the relax manual where
eps.gz files are required.
* Improvements to the final section of the relaxation
curve-fitting chapter. The Xmgrace screenshot and page references for
the user functions have been added.
* Added screenshots of Xmgrace displaying relaxation curves.
* The fetch_docstrings.py now adds LaTeX labels to each user
function section. This has the form of 'uf: ' followed by the user
function name, and is for referencing purposes within the main text.
* Rewrote the relaxation curve-fitting chapter of the relax
manual. This chapter was quite out of date and was of no use to
modern relax versions.
* Redesign of how the GPL license is presented to the user.
The old prompt.gpl module with the version 2 of the license has been
deleted. Now the text form the docs/COPYING file is passed through
pydoc.pager for the './relax --licence' and the prompt mode GPL
object, and is simply printed to STDOUT for the GUI help system.
* Import clean ups for the N-state model specific module.
* Added the 'unit' argument to the dipole_pair.read_dist and
dipole_pair.set_dist user functions. This is to allow distances in
Angstroms to be read into relax and converted to meters.
Bugfixes:
* Fix for bug #20189 (https://gna.org/bugs/?20189). The
Sequence GUI element can not handle values of None.
* The citations chapter is now included in the HTML version of
the user manual. For some reason, a file named 'cite.tex' cannot be
handled by latex2html.
* The latex2html compilation of the user manual now ignores
the \bibitem{} commands. This is needed for the HTML version of the
user manual.
* Fixed a section titled 'Introduction' clashing with the
intro chapter of the user manual.
* Fixes for the user function icons in the HTML version of the
user manual. These icons are now placed on the correct HTML page.
* Removed the text '.eps.gz' from all of the LaTeX included
graphics in the user manual. This allows latex2html to select and use
the PNG images instead, producing much better graphics for the online
manual (http://www.nmr-relax.com/manual/index.html).
* Fix for the graphics.fetch_icon() function for when no file
format is specified.
* Elimination of all duplicated chapter, section and
subsection titles in the user manual. This fixes bug #20185
(https://gna.org/bugs/?20185).
* The HTML files for the user manual now have longer names -
this is needed for removing the duplicates.
* Fix for the duplicate title finding script - the LaTeX and
HTML mode alternatives are no longer mixed up.
* Fix for bug #20177 (https://gna.org/bugs/?20177). This was
simply a lower precision OS/Python/numpy combination causing a test
suite failure - there are no practical effects and only the precision
of the system/GUI test has been lowered.
* Another bug fix for the sequence GUI editor window. This
bug was being triggered by the
User_functions.test_structure_pdb_read() GUI test which now passes.
* Small fix for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20184 (https://gna.org/bugs/?20184). The
behaviour of the gui.string_conv.gui_to_int() and related functions
has changed in the last few months and the Sequence_window() GUI
element has not changed to match. This has been fixed and the
User_functions.test_structure_pdb_read() GUI test now passes.
* Fixes for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20183 (https://gna.org/bugs/?20183) - the
failure of the sequence editor window. The problem was that fields
which could be either single values or lists (or tuples) of values
were not properly handled.
* Fix for bug #20182 (https://gna.org/bugs/?20182) - the
sequence element window ordering issue. The sequence element window
now has the parent wx.Window element set. This prevents the main
relax window from being set as the parent and hence coming to the
front after the sequence element window is launched from a user
function window.
* Fix for bug #20181 (https://gna.org/bugs/?20181) - the GUI
sequence editor window TypeError problem.
* Window ordering bug fix for the user function windows
launched from the spin viewer window. The spin viewer window no
longer hides behind the main relax window after the launch of the user
function.
* Bug fix for the repetition of Monte Carlo simulations in the
relaxation curve-fitting analyses. This is in the specific analysis
API, so will allow all analysis types to repeat Monte Carlo
simulations for error analysis.
* MS Windows fix - the NOE system and GUI tests are now less
strict in checking the errors.
* Proper bug fix for storing the execution status of wizard
and user function pages. This allows the test suite to pass again.
The execution status is now properly returned from the wizard pages
run synchronously (and always set to True for asynchronous calls).
* Fix for bug #20173 (https://gna.org/bugs/?20173). The
palmer.create user function should have been checking that the
diffusion tensor had been initialised. This is now being performed.
* Bug fix for the execution of wizard pages - the execution
status is now observed. This fixes bug #20152
(https://gna.org/bugs/?20152). The problem was that the execution
status was being lost in the protected_exec() function. However as
relax errors are caught in the GUI interpreter anyway and the status
is returned normally, the protected_exec() wrapper was removed.
* Bug fix for the creation of the user function GUI pages -
the (a)synchronous arg is now observed. This argument was being
ignored, which in some wizards was causing user function calls to be
asynchronous. This can result in racing related crashes.
* The bruker.read user function now throws a RelaxError when
old PDC files are detected. This is a partial fix for bug #20152
(https://gna.org/bugs/?20152).
* Fixed the newlines in the sample script in the consistency
testing chapter.
* Fixed the bounding box for the consistency testing figure
and also fixed some Latex unfriendly code. Problems were spotted by
Edward d'Auvergne in a post at
https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.
* Fixed a bibliography entry label problem. This was spotted
by Edward d'Auvergne in a post
at:https://mail.gna.org/public/relax-devel/2012-09/msg00040.html.
* Bug fix for the creation of 2D graphs via grace.write for
when many data sets exist. The algorithm for setting the Grace symbol
number to be between 1 and 10 was broken!
* Fix for bug #20133 (https://gna.org/bugs/?20133) - this was
simply a missing import.
* Fix for the spin.create user function documentation - the
prompt examples were wrong.
* Bug fix for the generic_fns.grace.get_data() function. This
was just recently introduced and was triggered by the
Relax_fit.test_bug_12670_12679 system test.
* Fix for bug #20120 (https://gna.org/bugs/?20120), the bad
Grace plots with multiple spin types. The grace data assembly
function was not setting the correct index for when a spin type
changes to a preexisting type.
* Bug fix for the reading of Sparky peak lists. Spin names
with numbers at the end were not being correctly identified. This fix
allows Trp indole NE1-HE1 data to be loaded.
* Bug fix for the loading of peak intensities via
spectrum.read_intensities. The user function could not be applied
twice, preventing the loading of data from different spin systems such
as Trp indole NH data.
* Another fix for the relax_data.temp_control description.
* Fix for the incomplete relax_data.temp_control user function
description.
* Spell fix for the relax_data.temp_calibration user function
description.
* Fixes for the referencing in the J(w) mapping chapter of the
user manual.
* Fixed some citations in the newly introduced model-free J(w)
paragraph.
* Fixed a bunch of links in the development chapter of the user
manual.
* Small fix for the sample script in the relaxation
curve-fitting chapter of the relax manual.
* Small fix for the sample script in the NOE chapter of the
relax manual.
* Bug fix for the RDC Q factor calculations for when the
dipolar constants are not all the same. Now instead of a RelaxError,
a warning is given and the Q factor normalised by 2Da^2(4 + 3R)/5 is
skipped. This allows long range and mixed nuclear pairs to be
supported.
* Import additions to fix the epydoc import of the
'sconstruct' script for the API documentation.
* Epydoc docstring fixes for the API documentation.
* Import fix for the epydoc building of the API documentation.
relax version 2.1.1.