OpenStructure 1.3.3
Release Notes
Changes In Release 1.3.3
- fix context menu/main menu for newer Qt versions
- CreateEntityFromView remembers chemical type (BZDNG-430)
- fix gfx.PrimList.SetLineWidth
- Fix remote=true for MMCIF loader (BZDNG-449)
- made CreateViewFromAtoms more flexible (BZDNG-408)
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
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