Version History

BALL and BALLView 1.2: 14.11.2007

BALLView:

• Integrated molecule editor
• Volume rendering for electrostaticsm, projection onto planes, field lines
• Improved cartoon and ribbon models, non-photorealistic shading (toon shader)
• Off-screen rendering
• Toolbars for quick access to important functionality
• Numerous improvements to the interface
• Merck Molecular Force Field (MMFF 94)
• Automated download of structures from PDB and PubChem

BALL:

• Protein-protein docking code based on Fourier correlation (requires FFTW library)
• MMFF94 force field
• Small molecule database interface (FORMAT/DBInterface) allows the storage and retrieval of small molecules and their conformations in a relational database
• A SMARTS matcher
• Kekulizer algorithm for aromatic structures
• Support for Dunbrack's backbone-dependent rotamer libraries

General things:

• Autobuild script allows much simpler installation of BALL
• Support for PowerPC architecture (Linux)

BALL 1.1.1: 22.12.2005

Added:

• Support for Python under Windows
• Python support for further classes
• Support for creating animations and movies from Python scripts
• Further Python example scripts
• Some useful hotkeys for Python Scripts in BALLView
• Support for SD files in BALLView
• Context sensitive HTML documentation in BALLView
• BALLView again has a fourth drawing precision "ultra" for real fast graphics accelerator cards
• Amber charges and radii for nucleotides
• Picking support for bonds
• Coloring by molecule

Changed:

• BALL and BALLView libraries are now built as DLLs under Windows
• Both libraries are now compiled with optimization under Windows
• Improved useability of the DisplayProperties Dialog
• Visual improvements for the cartoon model, e.g. for DNA and Strands
• Renamed Mesh::colorList to Mesh::colors
• Exception::InvalidRange now has a float value
• Bond::TooManyBonds moved to Exception namespace
• A standard BALLView Python startup script will be executed in any case. It can be found in BALL/data/startup.py. Users can choose an additional startup script, that will be run afterwards.
• PyInterpreter and PyWidget report the reason if the Python module cannot be loaded
• Removed Notification and changed the way to register for Log access
• Removed GLQuadricObject. This functionality is available through GLRenderer
• Improved PreferenceEntry class and reading/storing code for preferences
• Coloring of surfaces by grid: the way autoscale works and the default colors
• Renamed ColorTable to ColorMap
• Cleanup of the Scene code for move, rotate, zoom: Now cleaner, smaller and faster code.
• Adapted DownloadPDBDialog to new rcsb.org website

Fixed:

• Crash while reading PDB files with too many bonds
• Crash while wrongly using malformed boolean expression "residueID(...)"
• Crash in CalculateSecondaryStructureProcessor, when one SS is part of another
• Crash while running an MDS with trajectory if the DCD file could not be written
• Crash with representations for two different systems
• Crash with mouse movements while animation is running
• Memory issues with Python objects (e.g. inserting GeometricObjects into Representations)
• FragmentDB entries for H-atoms in nucleotides
• NMRViewer und underlying widgets did not compile
• Problems in persistence with g++ 4.x series
• Hangup in socket interface with g++ 4.x series
• Problems with POSIX compliance of socket classes
• Mouse sensitivity changed in Rotate mode when focusing on small structures
• Lighting, especialy for directional lights
• Saving and loading of BALLView project files
• Accelerators for menu entries didnt always work
• Splitting of surfaces for given distance: computed incorrect surfaces
• POVRay export: degenerated objects (with a length of 0) and meshes with only one color
• Browse button didnt work in Molecular Dynamics Simulation dialog
• Incorrect bond orders and GLN amide group planarity in fragment database
• PeptideBuilder: Naming of peptides; enabled support for paste in Dialog
• Opening of files in current directory per command line with BALLView
• Update of Representations after changing Selection color
• Problems with rendering Labels on Windows and MacOS
• Problems with Directory and Sysinfo on Windows
• Problems with ATI graphics cards: Line Models and Polygon Smoothing
• Minor problems with the clipping planes
• Minor problems with dashed bonds in the Ball-and-Stick model
• Missing assignment operator in RotamerLibrary

BALL 1.0pre1: 23.12.2002

Additional platform:

• Windows (Microsoft Visual Studio .NET)

Bugs fixed:

• several bugs in the kernel
• PDB reader
• visualization

Added + improved:

• faster AMBER force field implementation
• faster kernel data structures
• molecular surface computation (really fast now)
• support for QT 3.X
• surface computations (including transparent surfaces) in MolView
• export of MolView scenes to PovRay
• coloring of surfaces w.r.t. grid data (e.g. electrostatic potential)

BALL 1.0b: 17.01.2002

Bugs fixed:

• Lots of stuff in Expression, HINFile, PDBFile
• some bugs in molview
• FragmentDB::AddHydrogensProcessor was basically reimplemented
• clean up of the NMR classes
• AutoDeletable did not work correctly due to a strange problem with multiple inheritance
• too many to count everywhere else...

Added + improved:

• first official support for the Python bindings (still experimental, though)
• QSAR: a trivial framework for the implementation of molecular descriptors
• File: allows the expansion of filenames to URLs (again)
• MDL MOL files and SD files
• SMILES parser (experimental)
• several chapters in the tutorial
• Solvent excluded surface should be much faster
• AMBER force field got some speedup for partially selected structures

Known, but not yet fixed:

• File and TCPTransfer occasionally show strange baehavior when retrieving files via the network
• XDR support does not work under Tru64/cxx -- call configure with "--without-xdr"
• String_test is really huge -- some compilers choke on it (internal stack overflow, virtual memory exhausted) -- we can't do much about that...

BALL 1.0a BF1: 30.07.2001

Bugs fixed:

• genericPDBFile: assigned incorrect element if the element columns did not contain a valid element symbol

• FileSystem: canonizePath expanded ../../ to .., thus leading to problems with relative paths for in File and derived classes (PDBFile, HINFile, etc.)
• APPLICATIONS/PB: Makefile used incorrect linker options correctly on Tru64
• configure: did not abort if neither gethostname, nor sysinfo were found (see unfixed bug below)
• FragmentDB::AddHydrogensProcessor caused a core dump for residues where only one reference atom was available (e.g. water)

Known, but not fixed:

• Expression does not evaluate all bracketed expressions correctly
• configure causes some problems on Tru64 (fails to find gethostname). Workaround: in BALL/source type "touch config/configure.in;make configure" and proceed as usual. The problem is probably somehow caused by some incompatibility between certain autoconf versions and some Tru64 header header files, but I couldn't nail it down yet...

Added, changed:

• ResidueChecker: checks for overlapping atoms and duplicate atom names in a residue
• Test for FileSystem
• Python support functional (though still experimental, requires a patched version of SIP-2.5pre4, available from the BALL website). Recommended for seasoned Python veterans only.
• BALL exceptions are know derived from std::exception
• added fragment for Zinc (ZN.db)
• The interface of GeneralException was slightly modified to achieve compatibility with the Python wrapper classes
• The interface of RegularData2D::getMinValue/getMaxValue has changed
• The interface of Object has changed (ever so slightly)
• Changed the GridIndex typed of RegularData2D and RegularData3D (towards a more consistent IF)
• The structure of ResidueChecker was modified to make way for a more modular design in the future

Additional bugs:

• no unknown bugs have been found

BALL 1.0a: 19.07.2001

Way to many changes to enumerate here....

BALL 0.95a: 05.05.2000

New: - tutorial (at least a beginning)

• support for Tru64 Unix with Compaq C++ 6.2, Solaris 8
• complete rewrite of the energy minimization part
• switching functions added for CHARMM and AMBER
• reaction field energy implemented (Poisson-Boltzmann code)
• new architecture with better modularity for MolVIEW
• new example application: PB - Finite Difference Poisson-Boltzmann Solver
• new website
• license terms

Simplified Handling of torsion angles

Nearly complete tests and documentation for all mathematical classes

Better testing.

Hundreds of pages of documentation added for the Reference Manual.

Minor improvements here and there.

BALL 0.9a: 18.01.2000

First public alpha release