relax SVN archive

Modified the descriptive paragraph for relax to reflect the broader focus of the program.

Changed the header for the relax webpages to reflect the expansion of scope of the 1.3 line.

relax is no longer simply for proteins or relaxation data. Therefore the old description:

"Protein dynamics by NMR relaxation data analysis"

has been replaced by:

"Molecular dynamics in the name of experimental NMR"

New argument for label of hetero nucleus in PDB file is added.

The idea is to create a settings entry, where users can specify the name of the heteronucleus. This is not important to select type of hetero nucleus (C, N...), but also to define the exact name of the heteronucleus (N, NH, HN, N1....).

Space characters around '=' were removed.

The ending of the output file has the ending '.out'.

relaxGUI adds current time to pipe name to allow multiple execution of same calculation.

relaxGUI adds current time to pipe name to allow multiple execution of same calculation.

Number of maximum iterations is included in executing dauvergne_protocol.py.

Merged revisions 11206-11210 via svnmerge from
svn+ssh://michaelbieri@.../svn/relax/1.3

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r11206 | bugman | 2010-05-19 18:49:53 +1000 (Wed, 19 May 2010) | 8 lines

Created the rdc.corr_plot() and pcs_corr_plot() user functions.

These are for creating correlation plots of measured vs. back-calculated RDCs and PCSs.

A couple of N-state model methods (return_grace_string() and return_units()) were added to allow the
user functions to work.
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r11207 | bugman | 2010-05-19 19:31:30 +1000 (Wed, 19 May 2010) | 6 lines

Added a maximum global iteration arg and check into the dauvergne_protocol.py module.

This was requested by Michael in the commit for r11194 at
https://mail.gna.org/public/relax-commits/2010-05/msg00022.html.
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r11208 | bugman | 2010-05-20 17:24:42 +1000 (Thu, 20 May 2010) | 16 lines

Bug fix for catching the looping around the universal solution in the dauvergne_protocol module.

This was first identified by Seb in the post at
https://mail.gna.org/public/relax-users/2007-09/msg00010.html (Message-id:
<46EEA6B2.90606@...>).

The problem was the automatic looping over optimisation cycles in the full_analysis.py script. This
code is now in the dauvergne_protocol auto_analyses module. The issue was a never-ending looping
around the universal solution (the optimisation minimum combined with Occam's razor or the model
selection minimum). This should now be caught and the protocol terminated at the end of the first
completed loop. The fix was to compare the chi2, selected models, diffusion tensor, and model-free
parameters to every iteration, starting from the first. This will not be optimal if the protocol is
interrupted in the middle of one such loop, but will just mean that a few extra iterations will be
required to complete the loop.
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r11209 | bugman | 2010-05-22 00:17:46 +1000 (Sat, 22 May 2010) | 3 lines

Modified the relax checklist to include minfx bundling.
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r11210 | bugman | 2010-05-22 00:59:46 +1000 (Sat, 22 May 2010) | 3 lines

More updates to the release checklist.
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relax version 1.3.5.

This is a long awaited major feature and bugfix release!