relax 1.3.0

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Description

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.


Download

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).


CHANGES file

Version 1.3.0
(19 February 2007, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.0


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)
  • Splitting of the pdb user function into pdb.read and pdb.vectors (these have been subsequently renamed). (see 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.


Links

For reference, the following links are also part of the announcement for this release:


Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.


See also