bodil

Last updated: 19 February 2009.

Known issues

• Driver issue: Linux Fedora Core 3 i386 kernel-2.6.11 with nvidia-7664 works but side-by-side stereo may be very slow if hardware stereo support is enabled.
• Driver issue: Linux Fedora Core 3 i386 kernel-2.6.11 (or 2.6.10) with nvidia-7174 crashes graphics.
• Bug: Windows version may crash with large number of drawn 3D objects.
• Bug: Exit from Bodil can crash on Windows.
• Feature: No global save option.

Change log

2005-04-22 version 0.8.1beta (mainly bugfix)

• Build on Windows XP with Qt 3.3.4, (MinGW-3.2.0-rc-3, gcc 3.4.2)
• Build on Linux Fedora Core 3 i386 with Qt 3.3.4, (gcc 3.4.3, glibc 2.3.5)
• Build on Linux Fedora Core 3 x86_64 with Qt 3.3.4, (gcc 3.4.3, glibc 2.3.5)
• Build on Linux Fedora Core 1 with Qt 3.3.4, (gcc 3.3.2, glibc 2.3.2)
• Build on IRIX 6.5.22m with Qt 3.3.4, MIPSpro 7.4.1m
• Added a very simple license management: without proper license key the program will quit in 30 minutes.
• Implemented read for GridKont binary files.
• Added 'Parse_Delphi' to read and write binary potential map from DelPhi/GRASP.
• Bugfix: Can now call './Bodil' from the BODILDIR/bin directory.
• Bugfix: Misindexing of CONECT records that refered to ATOM records (PDB write).
• Bugfix: IUPAC hydrogen names in PDB format caused a crash.
• Bugfix: Removal of entirely empty row from Alignment.
• Bugfix: IRIX build now correctly includes object files.
• Bugfix: Ca-trace color is smooth again.
• Bugfix: Renamed hydrogen atoms within Rotamer library. The original version is retained too.
• Bugfix: Smoother SSE graphics crashed on 2-residue-long strand. Now draws those as a simple tube.

2004-05-08 version 0.8.0beta bugfix

• Build on RedHat Linux 7.3 with Qt 3.3.1, (gcc 3.3.3, glibc 2.2.5)
• The included HOMODGE binary was replaced to fix missing Proline CD atoms.

2004-04-21 version 0.8.0beta

• Build on Windows with Qt 3.3.1, MinGW 3.1.0 (gcc 3.2.3)
• Build on Linux Fedora Core 1 with Qt 3.3.1, (gcc 3.3.2, glibc 2.3.2)
• Build on IRIX 6.5.22m with Qt 3.3.1, MIPSpro 7.4.1m
• Bugfix: Alignment duplication should now work after removal of some columns.
• Bugfix: Alignment range was not validated after column deletion.
• Bugfix: Unrecognized characters now convert to gaps in PIR parser.
• A short tutorial was added.
• Consolidated main program libraries to one so/dll.
• Settings can be changed interactively, and will be saved on exit.
• Malign correctly handles empty sequences.
• Alignment has a defined range property.
• Alignment object behaviour redesigned.
• Better quality SSE graphics, with more tunable options.
• Added 'Parse_AVS' module for reading AVS field format.
• Dynamic memory allocation redesigned. Should help on Win32.
• Phylip interface 'Clustering' resurrected.
• Parse_Raster3D: Objects by rendering modes in main data structure.
• 3DView: Push rendering modes to main data structure.
• Main data structure re-designed.
• Superimposer: Iterative refinement of superimposition.
• Alignment editor: Can add SSE for first sequence.
• Added 'Parse_Malform' that prints all seqids for alignment.
• Added 'StreamEditor' for directly accessing "stream" interface.
• Some parsers support already "stream" interface.
• Parser format determination improved.
• Plugin API interface is more structured.
• 3DView: ShowTransform prints MolScript compatible Transform.
• 3DView: option UseLists enables storing lines in displaylist
• 3DView: option UseTexture can disable textured aromatic bond

2003-03-24 version 0.7.5beta

• Build on Windows with Qt 3.1.1, MSVC++6sp5
• win32Bug: Cannot read files from network-mounted drives
• Bug: Malign and empty sequence -> crash
• Bug: Electrostatic potential distributes oddly.
• 3DView options StrandThickness and StrandWidth
• Bugfix: Strand draws correctly and more smoothly
• Bugfix: Character widths in Alignment editor no work on win32
• Bugfix: GRO parser does not chrash on 2-letter group names
• BondSides and BallDepth changeable as LOD in GV.
• Atom selection query: Global/Current tree.
• Can select Hydrogens in Structure editor
• Alignments are drawn in 3D with lines connecting equivalent acids.
• Bugfix: Mol2-parser checks that bonds in file connect existing atoms.
• Malign: do not generate tree to file or datastructure.
• The starting script can now be referred to via soft link.
• Alignment editor: Font width is determined differently.
• Changed ResidueTypes interface to NOT pass std::map (crashed on Windows)
• Replaced QString with std::string on part of core data interface.
• Introduced Visitor Pattern to core data structure.
• Atom charge and type can be modified.
• Change 'Volume' to use Bloomenthal's triangulation algorithm.
• Build with Qt 3.1.1
• Fixed 'Parse_Grid' to correctly save first selected Grid.

2002-12-05 version 0.7.4beta

• Build with Qt 3.0.6, (gcc 3.2 / MIPSpro 7.3.1.3m)
• Malign touched Alignment even on 'Cancel'. Fixed.
• PDB parser allows saving all models.
• OpenDialog updates 'Recent Files' list more properly.
• Config-system reworked. Preferences.conf
• More 3DView options set in *.conf file
• Added 'Parse_Igrd' module for parsing InsightII ascii grid files.
• Added 'TreeViewer' module for showing an alignment-related tree. EXPERIMENTAL
• Malign has 'prealigned sequences' functionality.
• Compilation with MSVC 6 succeeds. Not stable.
• Disabled VertexArray-based rendering (for Radeon8500).
• Implemented platform specific OpenGL hardware stereo option.
• Implemented OpenGL 2D text for win32.
• Changed from tmake to qmake for Makefile configuration.

2002-06-14 version 0.7.2beta

• Mutate Residues with atoms (uses Rotamer-lib)
• Alignment editor: Renumber residues in selected range
• More than one Alignment Editor simultaneously.
• Alignment editor: MidButton on (row,col) moves a gap from end of (row) to pointed location. If necessary, a column of gaps is appended first.
• Residue properties stored by separate ResidueTypes class.
• Regular expressions in atom charge rule file.
• Config settings can be reloaded from files.
• pir-format has a comment line, always.
• Window frame widgets back in dialogs, more or less.
• 3DView: Options/Lights allows change of background colour.
• Alignment editor: Shft-left on columns marks a range; Range Select/Remove available
• Alignment editor: Secondary structure shown for first sequence
• Data tree reorganization: Molecule now has Composites: Groups, Helices, Strands, Turns
• Chain has a renumber method to change residue numbering
• Bugfix: Mol2-parser handles broken SUBSTRUCTURE entries
• Bugfix: Secondary structure is now computed for all selected chains
• Structure editor: interface changes, Delete All/Groups methods added
• Atom numbers from files are read in (but not written out)
• Plugins have Command( string, data ) as new interface-function.
• Superimposer: RMSD superimposes selected, matching atoms from alignment
• Superimposer clears selections on Delete Events to prevent dangling pointers.
• Surfaces
• Electrostatic potential
• Using Qt 3.0.3

2001-11-02 version 0.7beta

First public release