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| version = 4.0.3
| prev = 4.0.2
| next = 4.1.0
| keywords = Fast superimposition, Google Cloud deployment scripts, OpenMPI, per-atom RMSDs
| type = Minor feature and bugfix
<section begin=description/>
This is a minor feature and bugfix release. The [http://www.nmr-relax.com/manual/structure_rmsd.html 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 [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function] now correctly calculates the RMSD value, and the inversion recovery relaxation curve-fitting equations are now correct.
<section end=description/>
<section begin=metadata/>
Version 4.0.3 <br/>
(28 October 2016, from /trunk) <br/>
http://svn.gna.org/svn/relax/tags/4.0.3
<section end=metadata/>
<section begin=features/>
* Per-atom RMSD calculation by the [http://www.nmr-relax.com/manual/structure_rmsd.html 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.
<section end=features/>
<section begin=changes/>
* Addition of the atomic boolean argument to the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function] front end. This will be used to enable the calculation of per-atom RMSDs.
* Created the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_rmsd_spins Structure.test_rmsd_spins system test] for checking the per-atom RMSD calculation. This is for the new option in the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
* Implemented the per-atom RMSD calculation for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].
* Fixes for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_fit.Relax_fit-class.html#test_inversion_recovery Relax_fit.test_inversion_recovery system test]. The wrong equation was used in the <code>calc.py</code> Python script used to calculate the peak intensities in the <code>test_suite/shared_data/curve_fitting/inversion_recovery/*.list</code> 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 [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#validate_models internal structural object validate_models() method] was being called once for each structure via the [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#selection selection() method] prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object. This resulted in the [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#_translate _translate() internal structural object method], which converts all input data to formatted strings, being called hundreds of millions of times. Therefore [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#selection selection() method] no longer calls [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#validate_models 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 [https://gna.org/bugs/?25084 bug #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 printout for Windows versions of the <code>file</code> program. This enables the C modules to be identified as 32 or 64-bit, if the <code>file</code> program is installed.
<section end=changes/>
<section begin=bugfixes/>
* Fix for [https://gna.org/bugs/?24723 bug #24723]. This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean. The quadratic mean and quadratic standard deviation are now correctly calculated, and the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_rmsd structure.test_rmsd], [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_rmsd_molecules structure.test_rmsd_molecules], and [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_rmsd_ubi structure.test_rmsd_ubi] system tests have been updated for the fix.
* Bug fix for the inversion recovery equations [https://gna.org/support/?3345 sr #3345]. The inversion recovery experiment was incorrectly implemented as I(t) = {{:Iinf}} - {{:I0}}e<sup>-{{:R1}}t</sup> whereas it should be I(t) = {{:Iinf}} - ({{:Iinf}} - {{:I0}})e<sup>-{{:R1}}t</sup>.
<section end=bugfixes/>
* [http://wiki.nmr-relax.com/Relax_4.0.3 Official release notes on the relax wiki].
* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2540 |text=Gna! news item]}}.
* [https://www.mail-archive.com/relax-announce@gna.org/msg00061.html Mail Archive]
* [https://mail.gna.org/public/relax-announce/2016-10/msg00000.html Local archives].