Merged revisions 17391-17538 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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r17391 | bugman | 2012-08-30 11:02:04 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a paragraph to the model-free chapter of the user manual explaining the J(w) equation forms.
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r17392 | bugman | 2012-08-30 11:03:23 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixed some citations in the newly introduced model-free J(w) paragraph.
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r17393 | bugman | 2012-08-30 11:13:54 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a LaTeX label to the NOE chapter of the user manual.
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r17394 | bugman | 2012-08-30 11:14:21 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixes for the referencing in the J(w) mapping chapter of the user manual.
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r17395 | bugman | 2012-08-30 16:40:40 +0200 (Thu, 30 Aug 2012) | 3 lines
Small description edit for the relax_data.temp_control user function.
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r17396 | bugman | 2012-08-30 16:42:48 +0200 (Thu, 30 Aug 2012) | 3 lines
Spell fix for the relax_data.temp_calibration user function description.
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r17397 | bugman | 2012-08-30 16:49:41 +0200 (Thu, 30 Aug 2012) | 3 lines
Fix for the incomplete relax_data.temp_control user function description.
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r17398 | bugman | 2012-08-30 16:50:46 +0200 (Thu, 30 Aug 2012) | 3 lines
Another fix for the relax_data.temp_control description.
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r17399 | bugman | 2012-08-30 17:43:09 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the Viles et al., 2001 reference.
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r17400 | bugman | 2012-08-30 18:07:51 +0200 (Thu, 30 Aug 2012) | 5 lines
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.
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r17401 | bugman | 2012-08-30 18:11:27 +0200 (Thu, 30 Aug 2012) | 3 lines
The NOE chapter now points to the recommendations in the Rx fitting chapter.
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r17402 | bugman | 2012-08-30 18:11:49 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the nth package for the user manual LaTeX compilation.
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r17403 | bugman | 2012-08-31 22:05:56 +0200 (Fri, 31 Aug 2012) | 6 lines
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.
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r17404 | bugman | 2012-08-31 22:16:37 +0200 (Fri, 31 Aug 2012) | 6 lines
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.
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r17405 | bugman | 2012-08-31 23:35:22 +0200 (Fri, 31 Aug 2012) | 3 lines
Allowed the raggedbottom LaTeX setting as this is better for the screenshot layout in the user manual.
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r17406 | bugman | 2012-08-31 23:36:07 +0200 (Fri, 31 Aug 2012) | 3 lines
Added some Sparky info to the Rx curve-fitting chapter of the user manual.
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r17407 | bugman | 2012-08-31 23:36:17 +0200 (Fri, 31 Aug 2012) | 3 lines
Added a section label.
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r17408 | bugman | 2012-08-31 23:42:01 +0200 (Fri, 31 Aug 2012) | 5 lines
Added a step-by-step tutorial for the GUI NOE auto-analysis to the user manual.
This includes 22 screenshots of all the steps!
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r17409 | bugman | 2012-08-31 23:53:41 +0200 (Fri, 31 Aug 2012) | 3 lines
Modified the NOE sample script to include Trp indole NH data.
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r17410 | bugman | 2012-09-01 10:09:08 +0200 (Sat, 01 Sep 2012) | 6 lines
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).
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r17411 | bugman | 2012-09-01 10:17:30 +0200 (Sat, 01 Sep 2012) | 5 lines
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).
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r17412 | bugman | 2012-09-01 10:18:22 +0200 (Sat, 01 Sep 2012) | 5 lines
Significant update of the NOE chapter of the user manual.
The sample script used in this chapter was incredibly out of date!
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r17413 | bugman | 2012-09-01 11:05:16 +0200 (Sat, 01 Sep 2012) | 3 lines
Lots of editing of the NOE chapter of the user manual.
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r17414 | bugman | 2012-09-01 11:20:30 +0200 (Sat, 01 Sep 2012) | 3 lines
Modified the NOE system test to catch bug #20120 (https://gna.org/bugs/?20120).
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r17415 | bugman | 2012-09-01 11:21:54 +0200 (Sat, 01 Sep 2012) | 3 lines
Removed a debugging print out.
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r17416 | bugman | 2012-09-01 11:27:10 +0200 (Sat, 01 Sep 2012) | 6 lines
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.
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r17417 | bugman | 2012-09-01 13:13:01 +0200 (Sat, 01 Sep 2012) | 6 lines
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.
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r17418 | bugman | 2012-09-01 14:58:49 +0200 (Sat, 01 Sep 2012) | 5 lines
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.
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r17419 | bugman | 2012-09-01 15:13:43 +0200 (Sat, 01 Sep 2012) | 5 lines
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.
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r17420 | bugman | 2012-09-01 15:14:32 +0200 (Sat, 01 Sep 2012) | 3 lines
The NOE auto-analysis GUI test now checks the support for Trp indole N data as well.
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r17421 | bugman | 2012-09-03 10:19:35 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the spin.create user function documentation - the prompt examples were wrong.
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r17422 | bugman | 2012-09-03 10:23:39 +0200 (Mon, 03 Sep 2012) | 3 lines
Created a directory for screenshots of the spin viewer window operation.
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r17423 | bugman | 2012-09-03 10:48:57 +0200 (Mon, 03 Sep 2012) | 3 lines
Changed the "View->Spin view" menu item to "View->Spin viewer".
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r17424 | bugman | 2012-09-03 11:11:48 +0200 (Mon, 03 Sep 2012) | 3 lines
Shifted the spin viewer screenshots into their own directory.
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r17425 | bugman | 2012-09-03 11:16:01 +0200 (Mon, 03 Sep 2012) | 5 lines
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.
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r17426 | bugman | 2012-09-03 11:28:42 +0200 (Mon, 03 Sep 2012) | 3 lines
Added screenshots of the spin viewer spin loading wizard sequence.read page.
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r17427 | bugman | 2012-09-03 11:43:36 +0200 (Mon, 03 Sep 2012) | 6 lines
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.
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r17428 | bugman | 2012-09-03 12:06:00 +0200 (Mon, 03 Sep 2012) | 6 lines
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.
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r17429 | bugman | 2012-09-03 12:16:00 +0200 (Mon, 03 Sep 2012) | 3 lines
Added some more LaTeX functions for formatting consistency.
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r17430 | bugman | 2012-09-03 13:29:09 +0200 (Mon, 03 Sep 2012) | 3 lines
Removed some '()' text from the end of the user functions in the user function documentation.
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r17431 | bugman | 2012-09-03 14:13:37 +0200 (Mon, 03 Sep 2012) | 6 lines
Improved the consistency on 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.
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r17432 | bugman | 2012-09-03 14:22:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Clean up of a paragraph of the data model chapter of the user manual.
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r17433 | bugman | 2012-09-03 14:24:13 +0200 (Mon, 03 Sep 2012) | 6 lines
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.
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r17434 | bugman | 2012-09-03 14:51:11 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the Farrow et al., 1995 DOI number.
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r17435 | bugman | 2012-09-03 15:03:36 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the Fushman et al., 1998 reference.
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r17436 | bugman | 2012-09-03 15:06:25 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the other consistency testing references to the citation chapter of the manual.
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r17437 | bugman | 2012-09-03 15:06:52 +0200 (Mon, 03 Sep 2012) | 3 lines
Added a LaTeX label to the J(w) mapping chapter.
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r17438 | bugman | 2012-09-03 15:13:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Activated the consistency testing chapter of the user manual.
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r17439 | bugman | 2012-09-03 15:13:38 +0200 (Mon, 03 Sep 2012) | 3 lines
Large edits of the consistency testing chapter of the user manual.
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r17440 | bugman | 2012-09-03 17:37:14 +0200 (Mon, 03 Sep 2012) | 3 lines
Added trp indole NH loading into the relaxation curve-fitting sample script.
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r17441 | bugman | 2012-09-03 22:34:03 +0200 (Mon, 03 Sep 2012) | 6 lines
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.
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r17442 | bugman | 2012-09-03 23:07:07 +0200 (Mon, 03 Sep 2012) | 3 lines
Small edits of the relax data model chapter of the user manual.
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r17443 | bugman | 2012-09-04 11:52:07 +0200 (Tue, 04 Sep 2012) | 3 lines
Added some Grace plots from an NOE analysis for use in the user manual.
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r17444 | bugman | 2012-09-04 16:51:24 +0200 (Tue, 04 Sep 2012) | 5 lines
Added a tonne of GUI screenshots of an R1 analysis.
These will be used in the relaxation curve-fitting chapter of the user manual.
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r17445 | bugman | 2012-09-04 16:51:25 +0200 (Tue, 04 Sep 2012) | 7 lines
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.
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r17446 | bugman | 2012-09-04 16:52:00 +0200 (Tue, 04 Sep 2012) | 3 lines
Editing of the relax data model chapter of the user manual.
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r17447 | bugman | 2012-09-04 16:52:34 +0200 (Tue, 04 Sep 2012) | 3 lines
The old R1 and R2 analysis screenshots have been shifted to the intro chapter.
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r17448 | bugman | 2012-09-04 16:53:06 +0200 (Tue, 04 Sep 2012) | 3 lines
Some editing of the NOE chapter of the relax user manual.
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r17449 | bugman | 2012-09-04 17:11:43 +0200 (Tue, 04 Sep 2012) | 3 lines
Fix for bug #20133 (https://gna.org/bugs/?20133) - this was simply a missing import.
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r17450 | bugman | 2012-09-05 12:12:02 +0200 (Wed, 05 Sep 2012) | 3 lines
Editing of the nmrPipe script in the Rx curve-fitting chapter of the manual.
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r17451 | semor | 2012-09-05 13:52:36 +0200 (Wed, 05 Sep 2012) | 6 lines
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
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17452 | bugman | 2012-09-05 13:52:45 +0200 (Wed, 05 Sep 2012) | 5 lines
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!
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r17453 | semor | 2012-09-05 14:16:17 +0200 (Wed, 05 Sep 2012) | 8 lines
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
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17454 | bugman | 2012-09-05 14:18:38 +0200 (Wed, 05 Sep 2012) | 3 lines
Deletion of the relax version LaTeX file - this is automatically created anyway.
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r17455 | semor | 2012-09-05 14:20:52 +0200 (Wed, 05 Sep 2012) | 8 lines
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
(Message-id: <CAED9pY-ikjPvGaRPADHRJpLGFGnoeu+yNp5D1hLLm1U70maAwA@...>)
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r17456 | semor | 2012-09-05 14:25:48 +0200 (Wed, 05 Sep 2012) | 3 lines
Made some corrections to the formatting of math symbols in Latex.
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r17457 | semor | 2012-09-05 14:48:42 +0200 (Wed, 05 Sep 2012) | 8 lines
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
(Message-id: <CAED9pY9uKUd_OesCvDLqv2fGPoLDHB4ftrbW1-y6df4oQtbWyg@...>)
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r17458 | semor | 2012-09-05 15:08:57 +0200 (Wed, 05 Sep 2012) | 6 lines
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
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17459 | semor | 2012-09-05 15:23:32 +0200 (Wed, 05 Sep 2012) | 10 lines
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
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17460 | semor | 2012-09-05 15:33:12 +0200 (Wed, 05 Sep 2012) | 6 lines
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
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17461 | semor | 2012-09-05 16:00:48 +0200 (Wed, 05 Sep 2012) | 12 lines
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
(Message-id: <CAED9pY_YTDj8SX8crQu9on4LqA=pLzQwwyaz9kMLWD96xg-d0g@...>)
This also follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id: <CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@...>)
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r17462 | semor | 2012-09-05 17:02:41 +0200 (Wed, 05 Sep 2012) | 12 lines
Reverted r17456.
This follows a remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00029.html
(Message-id: <CAED9pY9jMXUyUsRv_FDcoen-_3SOu3oyrYK_egyw89dgH5-ESQ@...>)
The command used was:
svn merge -r17456:17455 .
Then, the file was manually adjusted since there were apparently conflicts with svn...
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r17463 | semor | 2012-09-05 17:09:25 +0200 (Wed, 05 Sep 2012) | 13 lines
Added the bounding box and a centerline command to the code for the figure for consistency testing...
This follows two remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00030.html
(Message-id: <CAED9pY_DzNvTcCjD0NzzkW_Zy-xdHrUe4q6ooqrSF17ySnj_Tg@...>)
and
https://mail.gna.org/public/relax-devel/2012-09/msg00032.html
(Message-id: <CAED9pY-aymMGvmo=JMC_nWYSeLd-HAsCirv7so5P3OhJBNFY5Q@...>)
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r17464 | semor | 2012-09-05 17:15:23 +0200 (Wed, 05 Sep 2012) | 3 lines
Made a small correction to a reference such that a superscript is correctly displayed.
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r17465 | semor | 2012-09-05 21:07:58 +0200 (Wed, 05 Sep 2012) | 7 lines
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
(Message-id: <CAED9pY-pvtpE69tqXqb30fj9aWL1_wU8yaM4u44rMXY1LEQbag@...>)
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r17466 | semor | 2012-09-05 21:11:24 +0200 (Wed, 05 Sep 2012) | 6 lines
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
(Message-id: <CAED9pY9pucoVrGzDvKs0u6hdUb94-Db8ixvno7MFN1QZsQDonA@...>)
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r17467 | bugman | 2012-09-06 08:17:08 +0200 (Thu, 06 Sep 2012) | 3 lines
Fixed the newlines in the sample script in the consistency testing chapter.
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r17468 | bugman | 2012-09-06 10:59:01 +0200 (Thu, 06 Sep 2012) | 7 lines
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.
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r17469 | bugman | 2012-09-06 11:19:43 +0200 (Thu, 06 Sep 2012) | 3 lines
Editing and a number of fixes/cleanups for the consistency testing chapter of the user manual.
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r17470 | bugman | 2012-09-06 11:30:04 +0200 (Thu, 06 Sep 2012) | 3 lines
Small edits of the consistency testing figure caption in the relax user manual.
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r17471 | bugman | 2012-09-06 11:47:49 +0200 (Thu, 06 Sep 2012) | 3 lines
Big clean up of the Bibtex bibliography file for the relax user manual.
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r17472 | semor | 2012-09-06 11:48:22 +0200 (Thu, 06 Sep 2012) | 6 lines
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
(Message-id: <CAED9pY9U46ga6_j245peX1ETNZc_Lw0f5cz+5xx5rGVhee29YA@...>)
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r17473 | bugman | 2012-09-06 16:07:04 +0200 (Thu, 06 Sep 2012) | 5 lines
A few small edits of the relaxation curve-fitting chapter.
This is to reinforce the exact time of the relaxation time period.
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r17474 | bugman | 2012-09-06 17:14:43 +0200 (Thu, 06 Sep 2012) | 3 lines
Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.
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r17475 | bugman | 2012-09-07 08:59:17 +0200 (Fri, 07 Sep 2012) | 5 lines
Set up the Bruker Dynamics Center system tests as GUI tests.
This is in preparation for catching bug #20152 (https://gna.org/bugs/?20152).
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r17476 | bugman | 2012-09-07 09:29:57 +0200 (Fri, 07 Sep 2012) | 5 lines
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).
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r17477 | bugman | 2012-09-07 10:21:46 +0200 (Fri, 07 Sep 2012) | 5 lines
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).
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r17478 | bugman | 2012-09-07 10:46:18 +0200 (Fri, 07 Sep 2012) | 6 lines
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!
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r17479 | bugman | 2012-09-07 10:48:15 +0200 (Fri, 07 Sep 2012) | 9 lines
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.
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r17480 | bugman | 2012-09-07 11:03:10 +0200 (Fri, 07 Sep 2012) | 5 lines
Modified the test_bug_20152_read_dc_file() GUI test to catch the RelaxError!
This error is because of the old PDC format.
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r17481 | bugman | 2012-09-17 10:51:37 +0200 (Mon, 17 Sep 2012) | 3 lines
Comment spelling fix.
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r17482 | bugman | 2012-09-17 13:35:40 +0200 (Mon, 17 Sep 2012) | 3 lines
Changed the RelaxError for missing relaxation times in the relaxation curve-fitting analyses.
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r17483 | bugman | 2012-09-17 13:58:27 +0200 (Mon, 17 Sep 2012) | 6 lines
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.
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r17484 | bugman | 2012-09-17 16:44:01 +0200 (Mon, 17 Sep 2012) | 6 lines
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).
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r17485 | bugman | 2012-09-17 18:05:56 +0200 (Mon, 17 Sep 2012) | 6 lines
Expanded the spin ID list for the structure.load_spins user function.
This now includes the spins "@N", "@NE1", "@C", "@H", "@O", "@P", ":A@...", ":A@...", ":G@...",
":G@...", ":C@...", ":C@...", ":U@...", ":U@...", ":U@...".
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r17486 | bugman | 2012-09-18 10:51:49 +0200 (Tue, 18 Sep 2012) | 3 lines
MS Windows fix - the NOE system and GUI tests are now less strict in checking the errors.
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r17487 | bugman | 2012-09-18 12:11:17 +0200 (Tue, 18 Sep 2012) | 6 lines
Updated the scripting section of the intro chapter of the user manual for non-technical users.
See http://www.mail-archive.com/relax-users@.../msg01253.html and bug #20174
(http://gna.org/bugs/?20174).
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r17488 | bugman | 2012-09-18 15:19:03 +0200 (Tue, 18 Sep 2012) | 6 lines
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.
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r17489 | bugman | 2012-09-18 16:15:01 +0200 (Tue, 18 Sep 2012) | 6 lines
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.
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r17490 | bugman | 2012-09-18 18:15:51 +0200 (Tue, 18 Sep 2012) | 6 lines
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.
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r17491 | bugman | 2012-09-18 19:23:14 +0200 (Tue, 18 Sep 2012) | 5 lines
Added @HE1 to the spin ID list of the structure.load_spins user function.
This is only seen in the GUI.
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r17492 | bugman | 2012-09-18 19:44:54 +0200 (Tue, 18 Sep 2012) | 6 lines
Updated the model-free GUI auto-analysis buttons for multiple spin name types.
The @H and @N names in the wizards behind the 'Dipolar relaxation', 'X isotope', and 'H isotope'
buttons have been changed to @H* and @N* to support Trp NE1-HE1 atom pairs.
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r17493 | bugman | 2012-09-19 09:19:54 +0200 (Wed, 19 Sep 2012) | 5 lines
Fix for bug #20181 - the GUI sequence editor window TypeError problem.
This is the fix for the bug reported at https://gna.org/bugs/?20181.
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r17494 | bugman | 2012-09-19 09:35:49 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the descriptions of the structure.read_pdb user function arguments.
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r17495 | bugman | 2012-09-19 09:37:07 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the descriptions of the structure.read_xyz user function arguments.
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r17496 | bugman | 2012-09-19 09:43:30 +0200 (Wed, 19 Sep 2012) | 7 lines
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.
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r17497 | bugman | 2012-09-19 10:02:13 +0200 (Wed, 19 Sep 2012) | 6 lines
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.
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r17498 | bugman | 2012-09-19 10:53:11 +0200 (Wed, 19 Sep 2012) | 5 lines
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.
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r17499 | bugman | 2012-09-19 10:55:30 +0200 (Wed, 19 Sep 2012) | 7 lines
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.
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r17500 | bugman | 2012-09-19 11:22:35 +0200 (Wed, 19 Sep 2012) | 3 lines
Fixes for the User_functions.test_structure_pdb_read() GUI test.
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r17501 | bugman | 2012-09-19 11:24:21 +0200 (Wed, 19 Sep 2012) | 7 lines
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.
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r17502 | bugman | 2012-09-19 11:27:52 +0200 (Wed, 19 Sep 2012) | 5 lines
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.
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r17503 | bugman | 2012-09-19 11:38:56 +0200 (Wed, 19 Sep 2012) | 3 lines
Small fix for the User_functions.test_structure_pdb_read() GUI test.
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r17504 | bugman | 2012-09-19 11:40:28 +0200 (Wed, 19 Sep 2012) | 6 lines
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.
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r17505 | bugman | 2012-09-19 14:16:04 +0200 (Wed, 19 Sep 2012) | 6 lines
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.
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r17506 | bugman | 2012-09-19 14:55:33 +0200 (Wed, 19 Sep 2012) | 5 lines
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.
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r17507 | bugman | 2012-09-19 14:57:03 +0200 (Wed, 19 Sep 2012) | 6 lines
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.
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r17508 | bugman | 2012-09-19 15:42:33 +0200 (Wed, 19 Sep 2012) | 6 lines
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.
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r17509 | bugman | 2012-09-19 15:43:04 +0200 (Wed, 19 Sep 2012) | 3 lines
Added some labelling to the infrastructure chapter of the user manual for referencing.
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r17510 | bugman | 2012-09-19 15:49:35 +0200 (Wed, 19 Sep 2012) | 3 lines
A small edit to the intro chapter for the multi-processor operation and logging.
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r17511 | bugman | 2012-09-19 16:19:47 +0200 (Wed, 19 Sep 2012) | 3 lines
Additions to the scripting section of the relaxation curve-fitting chapter of the user manual.
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r17512 | bugman | 2012-09-19 16:57:35 +0200 (Wed, 19 Sep 2012) | 7 lines
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!
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r17513 | bugman | 2012-09-19 17:03:20 +0200 (Wed, 19 Sep 2012) | 3 lines
Improvements to the duplicate user manual title finding script.
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r17514 | bugman | 2012-09-19 17:22:47 +0200 (Wed, 19 Sep 2012) | 3 lines
Fix for the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed up.
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r17515 | bugman | 2012-09-19 17:25:16 +0200 (Wed, 19 Sep 2012) | 3 lines
The HTML files for the user manual now have longer names - this is needed for removing the duplicates.
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r17516 | bugman | 2012-09-19 17:33:55 +0200 (Wed, 19 Sep 2012) | 5 lines
Elimination of all duplicated chapter, section and subsection titles in the user manual.
This fixes bug #20185 (https://gna.org/bugs/?20185).
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r17517 | bugman | 2012-09-19 18:41:08 +0200 (Wed, 19 Sep 2012) | 5 lines
The graphics.fetch_icon() function argument 'format' can now be set to None.
This will return the file path without the extension.
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r17518 | bugman | 2012-09-19 19:03:48 +0200 (Wed, 19 Sep 2012) | 3 lines
Fix for the graphics.fetch_icon() function for when no file format is specified.
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r17519 | bugman | 2012-09-19 21:49:04 +0200 (Wed, 19 Sep 2012) | 6 lines
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).
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r17520 | bugman | 2012-09-19 22:29:43 +0200 (Wed, 19 Sep 2012) | 5 lines
Fixes for the user function icons in the HTML version of the user manual.
These icons are now placed on the correct HTML page.
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r17521 | bugman | 2012-09-19 22:30:27 +0200 (Wed, 19 Sep 2012) | 3 lines
Fixed a section titled 'Introduction' clashing with the intro chapter of the user manual.
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r17522 | bugman | 2012-09-19 22:46:36 +0200 (Wed, 19 Sep 2012) | 5 lines
The latex2html compilation of the user manual now ignores the \bibitem{} commands.
This is needed for the HTML version of the user manual.
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r17523 | bugman | 2012-09-19 22:47:29 +0200 (Wed, 19 Sep 2012) | 5 lines
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.
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r17524 | bugman | 2012-09-20 11:41:19 +0200 (Thu, 20 Sep 2012) | 3 lines
Modified the dauvergne_protocol sample script to handle tryptophan indole NE1 data.
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r17525 | bugman | 2012-09-20 12:08:11 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a section label to the intro chapter of the user manual.
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r17526 | bugman | 2012-09-20 12:09:59 +0200 (Thu, 20 Sep 2012) | 5 lines
Removed \verb from the \newcommand definitions as that is forbidden in LaTeX.
Now Python code is formatted using a small TT font.
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r17527 | bugman | 2012-09-20 12:11:11 +0200 (Thu, 20 Sep 2012) | 6 lines
Removed the \pycodestar{} references in the development chapter.
This command has been deleted as \newcommand cannot have \verb inside it! The \pycodestar{x}
references have been changed to \verb*!x!.
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r17528 | bugman | 2012-09-20 12:14:31 +0200 (Thu, 20 Sep 2012) | 3 lines
Spacing fix.
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r17529 | bugman | 2012-09-20 12:21:46 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a subsubsection label to the data model chapter of the user manual.
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r17530 | bugman | 2012-09-20 16:34:18 +0200 (Thu, 20 Sep 2012) | 3 lines
Created the User_functions.test_value_set GUI test demonstrating the failure of the value.set user function.
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r17531 | bugman | 2012-09-20 17:21:44 +0200 (Thu, 20 Sep 2012) | 5 lines
Fix for bug #20189 (https://gna.org/bugs/?20189).
The Sequence GUI element can no handle values of None.
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r17532 | bugman | 2012-09-20 17:39:30 +0200 (Thu, 20 Sep 2012) | 6 lines
The GUI model-free auto-analysis dipole_pair.define field values have been changed again.
These now default to @N and @H, as @N* and @H* will connect @N spins to @HE1 spins and @H spins to
@NE1 spins!
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r17533 | bugman | 2012-09-20 17:46:26 +0200 (Thu, 20 Sep 2012) | 5 lines
Fixed the dipole_pair.define user function calls in the dauvergne_protocol.py sample script.
This is a recently introduced problem only present in the trunk.
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r17534 | bugman | 2012-09-20 20:32:32 +0200 (Thu, 20 Sep 2012) | 7 lines
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.
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r17535 | bugman | 2012-09-20 20:47:09 +0200 (Thu, 20 Sep 2012) | 3 lines
Added a BMRB section to the end of the model-free chapter of the user manual.
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r17536 | bugman | 2012-09-20 20:49:02 +0200 (Thu, 20 Sep 2012) | 3 lines
Removed the out of date and useless README file for the HTML version of the user manual.
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r17537 | bugman | 2012-09-21 10:22:46 +0200 (Fri, 21 Sep 2012) | 3 lines
Added the use of the program 'nice' to the model-free GUI tutorial in the user manual.
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r17538 | bugman | 2012-09-21 11:09:52 +0200 (Fri, 21 Sep 2012) | 6 lines
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.
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