10. History
- Release 1.5.1 (16/12/2003)
- Chem3D loader.
- Accelrys archive file (.arc) support in the trajectory analysis.
- Capability to add the hydrogens.
- RMSD calculation in the trajectory analysis.
- CHARMM lipid and GRID force field templates.
- POPC lipid bilayer cluster in crystal and solid phase.
- Fix: energy interaction evaluation.
- Fix: PSF X-Plor file saver. Now is full compatible with NAMD.
- Fix: NAMD 2.5b2 & 2.5 output format detection.
Windows/OpenGL updates:
- ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking
system.
- Database engine for directory, sdf and zip files.
- Complete 3D molecular editor with fragment libraries (Add fragment
function).
- Multiple workspaces.
- Remove residue/s dialog box.
- Molecule place dialog box.
- Added the capability to show the worst energy interacting residues
with biomacromolecule (Evaluation of the interaction).
- Fix/merge molecules.
- Multiple Mini Editor and Graph Editor windows.
- Now the centroids can be updated dynamically or kept fixed.
- The residue renumbering is now available for all atoms and for the
selected atoms only.
- Fixed single atom remove function.
- Changed the keys to control the mouse function (R = rotation, S = scale, T
= translation).
- New extended commands: AddIons, AddHydrog, DbClose, DbCreate, DbGet,
DbGetId, DbInfo, DbOpen, GraphSetCur, RemAtoms, WksChange, WksLock, WksNew,
WksNext, WksPrev, WksRem, WksRemAll, WksRemCur, WksSetName, WksUnLock.
- New system variables: GraphID, WksCurName, WksCurNum, WksTot.
- Updated Fmod DLL to 3.70.
- New demo music "Rainstorm Cloudburst Mix" by Chris
Hülsbeck.
- Release 1.5.0 (24/06/2003)
- PDB 2.2 loader and saver.
- Experimental PSF X-Plor topology saver.
- Improved GAMESS support. Now VEGA reads the minimized structures and the
atomic charges.
- Added the capability to read the connectivity and the bond types of Alchemy,
CSSR, MDL Mol, Mol2, PDB (including all subformats), QMC and IFF file formats.
- Ultra fast connectivity calculation routine.
- Now IFF and PDB file formats support the atom constraints.
- Read & write substructure record in Mol2 file format.
- New trajectory file formats: Quanta conformational search (CSR), ESCHER
Next Generation solutions.
- Added the lipole measure (Broto & Moreau, Ghoose & Crippen) in the
trajectory analysis.
- Support of multiple chains in IFF file format.
- Bond, CFF91, CHARMM 22 for nucleic acids, CHARMM 22 for proteins, H-bond, MM2, MM3, force field templates.
- The atom type length is expanded from 4 to 8 characters trough the 64 bit
technology (e.g. Tripos atom types).
- Added acetone, ammonia, chloroform, dicloromethane, formaldehyde, methane,
methanol octanol-water solvent clusters.
- New specifications for IFF (1.3), PDBA (1.1), PDB FAT (1.1) file formats.
- Fix: ATDL engine.
- Fix: IFF multi-segment saver.
- Fix: trajectory analysis water exclusion routines.
- Fix: angle between two planes in trajectory analysis.
- Win32: basic 3D molecular editor with add, remove, change atom capability
and bond manipulation (add, remove, change, connectivity rebuilder and
bond type finder).
- Win32: molecular similarity toolbox (molecular superimposition).
- Win32: change torsion dialog box.
- Win32: solvent cluster builder.
- Win32: add ions function (based on Sodium source code developed by
Alexander Balaeff).
- Win32: merge file function. You can merge two files specifying the parts
to keep or discard (e.g. coordinates, atom types, atomic charges,
etc).
- Win32: ClustalX plugin. It allows to integrate molecular biology
tools (ClustalX and NJPlot) in the VEGA environment.
- Win32: atom constraints dialog box for dynamics simulations (e.g. NAMD).
- Win32: 3D interactive monitors for distance, angle, torsion, angle between two planes.
- Win32: world relative translation and rotation of each molecule.
- Win32: open/save in selection tool (trajectory analysis).
- Win32: select molecules and select segments dialogs.
- Win32: remove molecules and remove segments dialogs.
- Win32: remove invisible atoms.
- Win32: fix/merge segments.
- Win32: color by fixing value.
- Win32: labels by fixing value, residue, residue name and residue number.
- Win32: show/hide atoms by molecule and improved atom selection.
- Win32: invert Z coordinates function in order to obtain the enantiomer.
- Win32: apply 3D transformation to coordinates.
- Win32: now it's possible apply the force field and the atomic charges to
all atoms, and to active (visible) atoms only.
- Win32: event logging in PowerNet plugin.
- Win32: changed extended commands: Charge, ForceField.
- Win32: new extended commands: Angle, Distance, Merge, PlaneAng, Torsion,
TrjGraphEne.
- Win32: new system variables: TotActAtm, TotMol.
- Win32: updated DevIL DLLs to 1.6.5.
- Win32: new demo music "Giana Sister (Machinae Supremacy Remix)" by Chris
Hülsbeck.
- Release 1.4.3 (11/12/2002)
- Alchemy loader & saver.
- MDL Molfile saver.
- CSV and Raw surface format.
- Gromacs .xtc support for the trajectory analysis.
- Multi-model PDB support for the trajectory analysis.
- ILM calculation in the trajectory analysis.
- The IFF file format was expanded in order to support the surface maps.
- Win32: new geometry transformation engine.
- Win32: added By segment coloring method.
- Win32: surface calculation for selected atoms.
- Win32: trajectory analysis for selected atoms.
- Win32: interactive selection of the conformations trough the graph editor.
- Win32: added the Data De/compressor Engine support in the graph editor.
- Win32: now the graph editor supports Gromacs log files.
- Win32: REBOL/View instead of REBOL/Core scripting language.
- Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose,
GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew,
GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower).
- Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion,
GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX,
GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir).
- Win32: WinDD 1.4.
- Win32: new demo music by Chris Hülsbeck.
- Release 1.4.2 (03/09/2002)
- Updated the Gasteiger-Marsili charge attribution.
- GAMESS output loader.
- Fix: mol2 sever (now the am bond order is correctly assigned).
- Win32: PowerNet plugin: TCP/IP protocol and PDB interface.
- Win32: the REBOL scripting language
is now included in the package.
- Win32: edit atom, residue and chain properties.
- Win32: console command history.
- Win32: smart move rendering option.
- Win32: new extended commands (ChDir, ColorIdDlg, ColorRgbDlg, ConClrHist,
ConCls, ConSave, ConSet, ConWin, DirDlg, ErrMsg, LogOff, MessageBox, MainWin,
MiniEd, Mopac, OpenDlg, SaveDlg, SaveImg, ShutDown, SrfCalc, SrfColor,
SrfColorBy, Text).
- Win32: new system variables (ConBufSize, ConHistSize, ConPosX, ConPosY,
ConSizeX, ConSizeY, ConVisible, CpuFeatures, CpuName, CpuType, CpuVendor,
CurDir, GlassWin, IsRunning, Os, OsFamily, ScreenDepth, ScreenX, ScreenY).
- Win32: TurboPack for AMD Athlon/Duron and for Intel Pentium 4.
- Win32: new demo song by Gianna Pica.
- Win32: updated Fmod DLL to 3.6.
- Release 1.4.1 (03/06/2002)
- GAMESS cartesian file loader and saver.
- Fix: HyperChem .hin loader.
- Fix: XYZ detection.
- Fix: Insight surface loader.
- Fix: generation of solvent cluster.
- Fix: Pentium III-M CPU detection.
- Win32: interaction energy evaluation for the analysis of the docking results.
- Win32: new console with direct command interface.
- Win32: advanced cut, copy & paste routines.
- Win32: Predator plugin interface.
- Win32: glass windows (Windows NT/2000/XP only).
- Win32: PLUGINGET command added.
- Win32: Dhrystone plugin 1.1.
- Win32: updated DevIL DLLs to 1.3.1.
- Release 1.4.0 (15/04/2002)
- MDL Mol file loader.
- Improved IFF file format (new chunks).
- Extended command line interface for language scripting.
- Return code handler.
- Fix: Biosym archive 3 (.car) loader now reads the element column.
- Fix: mol2 hack for Insight generated mol2 files.
- Fix: mol2 saver.
- Manual: added Frequently Asked Question (FAQ) page.
- Win32: atom picking and interactive measures/selection (atom, distance, angle, torsion
and angle betwee two planes).
- Win32: plugin system to expand the VEGA capabilities.
- Win32: Dhrystone Test plugin (tstdhry.dll) to test the CPU performance.
- Win32: joystick control.
- Win32: color requester.
- Win32: customizable atom selection.
- Win32: some new commands can be send trough the standard window port, in order to
interpret complex command sequences.
- Win32: now the trajectory animation is compatible with the new refresh mode.
- Win32: the selection tool for trajectory analysis supports the atom picking.
- Win32: the trajectory files can be opened directly with File -> Open menu
item.
- Win32: dynamic loading for devil.dll, fmod.dll, ilu.dll, ilut.dll, libbz2.dll, z32.dll
and zlib32.dll.
- Win32: VEGA selects the DLLs with the optimizations for the installed CPU.
- Win32: new menu items: Help -> Last error and Display -> Select ->
None.
- Win32: new demo music by Chris Hülsbeck.
- Release 1.3.2 (6/11/2001)
- Now VEGA can read the DCD files in little or big endian format without conversion.
- Added the PDB ATDL (PDBA) file support (read and write).
- Fix: Fasta saver.
- Win32: more mouse controls trough the middle button and the wheel.
- Win32: added Select menu item to show/hide a part of a molecule.
- Win32: added Color -> By residue, Color -> By chain and Color
-> By charge menu item.
- Win32: new Save Image output formats (Gif, Jpeg, OpenIL, PCX, PNG, PNM, Raw,
SGI, Targa and Tiff).
- Win32: added the View Settings dialog box.
- Release 1.3.1 (02/10/2001)
- Win32: improved CPK visualization.
- Win32: added VdW Dotted and Liquorice visualization modes.
- Win32: some configuration parameters (window size and position, menu checkmarks, etc)
are stored when the program is closed.
- Win32: menu history of the opened files.
- Win32: added window popup menu to resize the main.
- Win32: more than one VEGA session can be opened at the same time.
- Win32: drag & drop function to open the molecules.
- SendVegaCmd can control more than one VEGA session.
- SendVegaCmd asyncronous mode.
- Release 1.3.0 (13/09/2001)
- Data De/Compressor Engine updated: now you can pack the output in BZip2,
GZip,
PowerPacker (Amiga only) and Z-Compress.
- ILM (Molecular Hydropathicity Index) surface calculation.
- Polar surface area calculation (PSA).
- HyperChem HIN loader.
- Added charge and force field check in CVFF energy evaluation.
- Connectivity routine rewritten and more fast.
- Surface routines totally rewritten for load/save operations.
- DCD analyzer can load both CRD or MSF packet files.
- Water remove option (-w) in trajectory analysis.
- Fix: gromos loader/saver.
- Fix: multiple PDBF loading.
- Fix: routine for ring search.
- Fix: CHARMm force field template.
- Fix: a little bug in msf loader.
- Fix: Mopac loader more compatible.
- Fix: solvent layer calculation.
- Linux: first official release.
- Unix: fixed water detection routine.
- Win32: Graphic interface with 3D OpenGL output.
- Win32: fixed program path detection.
- Win32: fixed CTRL+C execution halting.
- Win32: setup program for easy insallation.
- Win32: WinDD Data Decompressor software included
in the package.
- Release 1.2
- Data Decompressor Engine with BZip2, GZip, PowerPacker and Z-Compress compatibility.
- Language localization trough the IFF catalog system and localization package.
- Loader for Sybyl .rgn files.
- The environment variable VEGADIR is not more needed for Amiga and Win32 versions.
- COMFA field calculation: lypophilic.
- CHARMm force field template fixed.
- Biosym surface atom label fixed.
- Amiga: fixed some endian problems.
- Sources: multiple test script
- Sources: Z32, Z and Bzip2 libraries and DLLs.
- Sources: StripCR utility with patter matching
- Win32: added pattern matching.
- Win32: fixed msf saver.
- Win32: fixed remove hydrogens (-r) and remove waters (-w) functions.
- Release 1.1a
- Fixed an heavy bug in PDB loader and saver.
- Mol2 filter more compatible.
- Release 1.1
First public release.
- Release 1.0
Only for internal use.