OpenStructure 1.3.2

Release Notes

Changes In Release 1.3.2

  • Fixed atom ordering in the GetFrameFromEntity() function in the structure_analysis.py module.
  • Fix atom indices generated by CoordGroup::Filter()
  • small tweaks to lDDT output
  • small tweaks to molck
  • Repaired bio unit parsing from mmCIF file/ PDBizing bio units, before chains with different transformations were ignored
  • use new remote loader written in Python to work around crash on Mountain Lion

Changes In Release 1.3.1

  • Export missing default argument for AligmentHandle.ToString
  • Automatically attach entity view in SequenceFromChain
  • Export GetMatchingBackboneViews to Python
  • Fix compilation with boost 1.33.1
  • Allow renumbering of single chain

Changes In Release 1.3.0

  • Scene background can now be set to a gradient or an image
  • Better Handling of HSV colors
  • Table: direct access to columns tab['x'] is also available as tab.x
  • Table: Export to ConTeXt and HTML tables
  • Table: Barplot interface
  • The BLAST binding supports newer versions of BLAST
  • Bindings for CAD score
  • Update directory layout of OST to be more conformant with the site-package system of Python: Instead of storing the modules in lib{64}/ost/ost, they are now in lib{64}/python{{VERSION}}/site-packages/ost
  • Added molck, the molecular checker. A small command-line tool to clean PDB files, e.g. remove atoms with zero occupancy, "virtual atoms", hydrogens etc.

Changes In Release 1.2.3

  • PDBWriter: Prevent writing of out-of-bounds atom coordinates.

Changes in Release 1.2.2

  • Fixed loop indentation in the PDBize function for bio units, leading to exponential running time/ memory consumption. This problem only affected a fraction of PDB entries.

Changes in Release 1.2.1

  • Use RPATH for linux bundles. No longer requires LD_LIBRARY_PATH to be set for chemdict_tool and lddt [BZDNG-385]
  • "install command line tools" also symlinks lddt, and chemdict_tool [BZDNG-386]
  • Fixed broken the_hammer.py example [BZDNG-387]
  • MacOS X: Make sure to use python2.6, not python as pyexec [BZDNG-388]
  • Fix example directory path for MacOS X bundle [BZDNG-389]
  • PDBWriter: Insert newline after END [BZDNG-391]
  • Added missing documentation for a few AlignmentHandle methods
  • Workaround for naccess which was failing when directory contains dots.
  • Fixed superposition dialog for unnamed chains
  • Fixed byte-swapping issue for DCD trajectories
  • Fixed FFT panel update after switching data in main viewer
  • Added missing pdbx_struct_assembly.id export
  • lDDT: Updated default angle and bond tolerance parameters from 8 stddev to 12 stddev.

Changes in Release 1.2 (since 1.1)

  • added mmCIF parser to enable loading of mmCIF files. The following categories are currently understood: atom_site, entity, entity_poly, citation, citation_author, exptl, refine, pdbx_struct_assembly, pdbx_struct_assembly_gen, pdbx_struct_oper_list, struct, struct_conf, struct_sheet_range, pdbx_database_PDB_obs_spr, struct_ref, struct_ref_seq, struct_ref_seq_dif
  • trajectory analysis support
  • better intergration with numpy
  • added Smith-Waterman local align and Needleman-Wunsch global align algorithms
  • static linking of C++ executables
  • support for building OST library with no gfx, gui, info libraries. This leads to a compact application bundle that can easily be deployed
  • work around compiler bugs in gcc-4.1 enabling compilation with CentOS 5.5's default compiler and libraries
  • introducing the new table class, supporting all kinds of analyses on tabular data, including plotting and statistical analyses.
  • added stereochemical plausibility checks and support for multiple references to lDDT
  • new superposition dialog in DNG

Project Funding

Swiss Institute of Bioinformatics

Biozentrum, University of Basel