February 13, 2008
Molekel 5.3 is available for download.
Bugs have been fixed and new features added; new features include display of radiation spectra and enhanced rendered quality through anti-aliasing and depth-peeling (to properly render overlapping transparent surfaces).
Some of the new rendering techniques might not work properly on some OS/Graphics Card combination. So far we have seen issues with transparency on SuSE 10.3 / NVIDIA 8800 Ultra systems. On Windows XP with NVIDIA cards make sure the image settings are set to "Let the 3D application decide" in the NVIDIA Control Panel.
Changelog
- Added support for depth peeling for correct rendering of transparent objects; requires an OpenGL 2.0 card and might not work properly on some systems. Depth peeling parameters affecting rendering speed/quality of transparent objects can be set through the Display->View Properties dialog.
- Added plot of infrared and Raman spectra with PostScript and PDF output
- Integrated with VTK 5.1 (cvs version since there is no official release yet)
- Added support for anti-aliasing, disabled by default; can be enabled through the Display->View Properties dialog.
- It is now possible to change transparency and colors of orbital surfaces.
- Added support for persistent settings in Electron Density Surface dialog.
- Added new x-ray shaders that work properly with VTK 5.1.
- Fixed bugs:
- 392 - Add support for multi-molecule Gamess input
- 401 - Cannot delete Connolly surface
- 403 - Command line support
- 404 - Error reading Molden molecular orbital data
- 405 - Transparency not consistent for both orbital colors (dependent on specific card/driver)
- 406 - Animation runs after deleting the molecule
- 408 - Feature request: start orbital index from zero
- 420 - Settings not saved when closing window
- 421 - Surface from Grid Data: Elapsed time report wrong
- 422 - Cannot save animations with transparent SES
January 22, 2008
Downloading of tarballs of code repository snapshots is again available through the new WebSVN interface here.
January 15, 2008
Status update:
Molekel 5.3 will be released in the next couple of weeks, several bugs have been fixed (check individual open bugs in the bug tracking system for updates) and some new features introduced; some of them are:
- Support for VTK 5.0.3 and the new VTK 5.1.x snapshots (through conditional compilation)
- Full control over color and transparency of some molecular surfaces
- Better Molden support
- Raman and Infrared spectra with export to PDF and PostScript
- Antialiasing and depth peeling (allows for correct rendering of depth-order independent transparent surfaces)
- 64 bit linux builds
- Persistent storage of many GUI parameters
- Documentation:
- new flash tutorials on shaders and latest features
- updated online documentation
- Build system: updated shell scripts and documentation to better guide developers through the compilation process
The main tasks we are working on at the moment are:
- licensing issues that prevent Molekel to be distributed as a Debian package and may create problem in the future
- Q5COST support: new hdf5 based file format for quantum chemistry
- offscreen rendering issues
- Molekel file format (won't be added to the 5.3 release)
- New molecular rendering engine that will allow real-time high-quality display on modern hardware (NVIDIA 7000 series or better) of big (>100k atoms) molecules; this will allow us to get rid of Molecular Inventor & OpenMOIV and fix the licensing issues mentioned above as well.
- Code distribution: it is not possible anymore to get a tar archive of the source code through the SVN interface, we therefore need to provide source download in some other way (access through svn is available though)
- Updating scripts for automated testing
Also note that the mailing lists cannot be used anymore due to spam, no spam message should have reached any subscriber though.
July 19, 2007
Molekel 5.2 has been released.
Several bugs have been fixed and some major features have been introduced; please check out the change-log below. We delayed the release to accommodate some last minute feature requests and to investigate some issues with the Molden reader which are not completely solved, so chances are a bug fix release will be out pretty soon.
Changelog
Moved to OpenBabel 2.1, this allowed to fix some problems when reading big PDBs (>64k atoms).
Added support for GLSL shaders: after a molecule has been selected it is possible to assign vertex and pixel shader to the molecule and any generated surface. Shader parameters can be saved/loaded to/from text files. The following data types are currently supported for uniform parameters:
- float
- vec2
- vec3
- vec4
- bool
- int
If a parameter name contains the string 'color' or 'colour' (case insensitive) it is possible to set the value through a color dialog.
In case shaders are not supported (OpenGL 2.0 required) the shaders menu item is disabled.
Added support for multiple vibrational modes: any number of vibrational modes can now be combined to animate atoms.
Added option in Display menu to hide selection bounding boxes.
Added support for record/playback of GUI events, this is mainly used for automated GUI testing and demo purposes.
Animation export can now be interrupted by clicking on the 'stop' button.
Added optional command line parameters:
- -load <file type> <file path>
- -size <window width> <window height>
- -position <window upper left corner x> <window upper left corner y>
- -settings [<key1 value1> <key2 value2> ...] if not arguments are provided current settings info is printed to console
- -events <file path> <initial delay (s)> <time scaling>
Added support for PNG output.
Fixed bugs:
- 382 - Electron density surfaces are not animated
- 383 - Animation of SES is not reset
- 384 - Grid data surface dialog's 'Generate' button not disabled
- 388 - Cannot load GAMESS file with Hessian runs
- 389 - Cannot load basis set from GAMESS output
- 390 - Cannot specify file format when saving
- 393 - Bounding box not updated when animating.
- 394 - Program may crash when changing animation mode.
June 8, 2007
Added new Feature Requests section listing all the received feature requests. This should make it easy to verify the status of each new feature.
Added new dialog to select the size of the 3D view into trunk source tree.
Added new Event Record/Playback framework into trunk source tree; it is now possible to record and playback interaction events; useful for recording macros and performing automated testing. The Record/Playback system is independent of widget size and location and has been implemented as a separate module (utility/events source directory) which can be reused in any Qt application. Should work fine with any Qt Widget (i.e. no native dialogs or non-qt windows/menus) on Windows, Mac and Linux. On Mac OS some tricks have been implemented to record actions triggered by menu events since the no QEvent is received by Qt when interacting with the top menu bar.
May 11, 2007
Molekel 5.1.1 has been released.
Changelog
- Added support for ADF Tape41 files, look into the data dir for a sample file; logging information is currently printed to standard output
- Fixed bugs:
- 361 - Cannot change selection box color
- 362 - Cannot unpick atom/bond
- 363 - Wrong bonds computed
- 375 - Wrong atom size
- 376 - MEP scalar bar doesn't change when selecting molecule
We were actually hoping to release a version with GLSL shader support as requested by several users; however due to the issues we are experiencing with different graphic card/driver/OS combinations we definitely need more time for testing and we won't be able to release a GLSL-enabled version before the end of June.
February 9, 2007
Molekel 5.1 has been released together with some Flash presentations and demo videos, on-line documentation has been updated and a new Gallery section has been added to the website.
All the files can be downloaded from the file download section.
Changelog
- Removed local documentation: the documentation menu item now opens the on-line documentation
- Enhanced visual quality by patching the OpenMOIV library
- Added option to change atom and bond size
- Added option to change the material color for SoCylinder/SoSphere
- Added option to load the atom color table from file (sample color file in data dir)
- Added animation of molecules read from multi-frame PDB and XYZ
- Added option to use cube data as Molecular Electrostatic Potential when computing SAS or SES
- Added Z-matrix format (to build molecule from one z-matrix, see .zmatrix example in data dir)
- Added option to change animation step
- Added option to save one image per molecular orbital (only one molecular orbital per-image is displayed in the saved images)
- Added option to smooth with Laplacian smoothing iso-surfaces generated from Gaussian cube files
- Molekel now asks for confirmation before deleting a molecule
- Fixed bugs:
- 333 - Molecule is scaled when window resized, surface is not
- 334 - Cannot open file specified on command line.
- 335 - PDF and PostScript files are not replaced
- 337 - Loading of PDBs with multiple molecules is slow, adding support for multi-frame pdbs has fixed this bug
- 340 - Molden input issues: Bohr units were not supported
- 341 - Program may crash when selecting a molecule loaded from pdb: issues with OpenBabel::ReadFormula(); see OpenBabel bug 1632403
- 356 - Cannot load files on Mac OS X: an OpenBabel patch for version 5.0 has been made available, the new version doesn't need this patch.
January 2, 2007
Linux x86 patch released: the glibc-2.3 patch makes Molekel 5.0 work on SuSE Linux 10.0 and other glibc-2.3 systems.
If you get an error similar to the following:
.../lib/tls/libc.so.6: version 'GLIBC_2.4' not found (required by ./lib/libQtCore.so.4)
download this patch and replace <molekel root>/lib/libQtCore.so.4 with the version found in this archive.
Download Molekel glibc-2.3 patch
December 30, 2006
Molekel 5.0 for PowerPC Mac has been released.
December 21, 2006
Molekel 5.0 released
Latest changes:
- Animation of molecular surfaces during animation export
- PostScript and PDF export
- Support for Molden input
- Documentation
December 19, 2006
Final builds of Molekel 5 for Linux, Mac OS X Intel and Windows XP/2000 have been deployed on test machines.
Website is being updated.