relax version 1.3.0.

Item posted by Edward d Auvergne <bugman> on Mon 19 Feb 2007 12:47:37 PM UTC.

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 either http://nmr-relax.com/download.html or http://download.gna.org/relax/.

Full list of changes

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.