1. Introduction
VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements that make very easy your research jobs.
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Snapshot view highlighting the real time graphic quality of VEGA ZZ package. |
3D Graphic Features:
Extreme OpenGL implementation for an incredible real-time rendering quality: lighting (4 light customizable light sources + ambient light), alpha blending, hardware anti-aliasing (if supported by the graphic cards), material management, SkyVision (3D backgrounds).
Stereo view (shutter and anaglyphic glasses).
3D molecule view: wireframe with multivector bonds, CPK, ball & stick, stick, trace and tube. All representations can be mixed thanks to the new selection tool.
Atom labels (atom name, element, atom type, atom number, atomic charge, fixing value, residue, residue name, residue number).
Enhanced atom coloring methods: atom, residue, chain, segment, molecule, constraints and custom.
Atom selection & picking.
3D surface: dotted, mesh, solid, solid transparent. Thanks to the HyperDrive technology, the calculation is very fast. The surfaces can be colored by atom, residue, chain, segment, molecule, surface ID and property. The color gradient used in the property coloring mode can be customized by the user that can define the number and the type of colors.
Multiple surface management.
All 3D object can be managed with mouse, joystick and dials (rotation, translation, scale and animations.
3D interactive monitors calculated in real time (distance, angle, torsion and angle between two planes).
Simulation trajectory visualization and animation with full support for Accelrys archive file (.arc), BioDock output, CSR (Accelrys conformational search), DCD, ESCHER NG, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Tripos Mol2 multi-mode and PDB multi-model formats.
Snapshot, hardware and software image rendering with the capability to create images bigger than the monitor size. The software rendering includes an anti-aliasing algorithm with user-selectable 4x or 16x super sampling. The supported output formats are: BMP, GIF 256 colors, JPEG, PCX, PNG, PNM, RAW, SGI, TGA and TIFF.
Vector graphic rendering engine. It's possible to export the view in PostScript, Encapsulated PostScript, PDF, SVG, LaTex, POV-Ray and VRML 2.0 formats.
Native video compression for animations: the trajectory files can be converted in real animation files (AVI, MPEG-1 and MPEG-2) without external software. VEGA uses the Windows codecs for the standard AVI files and a built-in library to encode MPEG-1 & 2 streams. The MD animations can be converted in DVD, Super Video CD, Video CD and video streams for the Web in easy way.
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The powerful lighting engine implemented in VEGA ZZ allows realistic views. |
Graphic User Interface:
All VEGA ZZ functions are available trough menu and/or requesters.
Draggable toolbars.
Extended menu with accelerators.
Contextual menus.
Buttons, radio buttons, combo boxes, list boxes, check boxes and sliders.
Cut, Copy & Paste operations.
Multiple workspaces with easy access.
Command console integrated in the main window.
Customizable glass windows.
Html help.
Editing:
Undo and redo functions with multiple levels.
Add, change remove atom/s.
Add, change, remove bond/s.
Add, remove hydrogens.
Add solvent. Several solvent clusters are included: acetone, ammonia, CH2Cl2, CHCl3, formaldehyde, methane, methanol, octanol-water, POPC crystal, POPC liquid, water.
Add ions (any type without restrictions).
Add aminoacid side chains with chirality check.
Add fragments & 3D molecular editor. Several fragment libraries are included as building blocks.
Peptide builder with the capability to specify the secondary structure.
2D molecular editor (provided by ISIS/Draw).
Atom type an charges attribution.
Remove residue, segment and molecule.
Centroid management.
Connectivity builder and bond type finder.
Change bond length, angle and torsion values.
Protein secondary structure editing.
Solvent cluster builder.
Molecular dynamics constraints (atom fixing and harmonic constraints).
File merge: VEGA ZZ is able to merge files in different formats, in order to take selectively coordinates, parameters, fields and properties of each file.
Trajectory file manipulation: the MD flies can be converted in other formats removing/skipping frames. The supported output formats are: NAMD/CHARMM DCD, IFF/RIFF, Mol2 multi-model, Gromacs TRR, Gromacs XTC (the compression ratio is user-selectable) and PDB multimodel.
Print engine: VEGA ZZ sends the images to the printer at full resolution.
Calculation Tools:
Molecular mechanics & energy minimization provided by AMMP. The implemented minimization algorithms are: steepest descent, trust (modified steepest descent), conjugate gradients, quasi-Newton, truncated quasi-Newton, genetic algorithm, polytope simplex and rigid. Remote hosts can be used to increase the AMMP calculation performances.
Conformational search (grid scan, random and Boltzmann jump).
Analysis of molecular dynamics trajectory files (distances, angles, torsions, angles between two planes, dipole moment, gyration radius, ILM, MLP, lipole, PSA, RMSD, surface area, surface diameter, volume and volume diameter).
Molecular similarity (superimposition).
Protein-protein and protein-DNA docking system (ESCHER NG).
Graphic interface for Mopac 7.01 (included in the package).
Molecular properties.
Interaction analysis of ligand-receptor complexes.
Secondary structure prediction (Predator).
Interactive protein check (chirality, peptidic bond geometry, missing residues and ring intersection).
Ramachandran plot calculation.
Prediction of protein pKa values (PROPKA).
Extra Tools:
PDB interface to download the structures directly in VEGA (PowerNet plug-in).
Integrated Mini Text Editor.
Integrated Graph Editor.
Task manager.
External Tools:
File decompressor (WinDD).
REBOL Web server for on-line documentation.
OpenGL setup utility.
Diagnostic tool for bug report.
Scripting Languages:
REBOL scripting language for batch processing, multiple calculations and multiple host communication. The REBOL interpreter is included in the OpenGL package.
C script engine: you can create super-fast scripts in C language directly in the VEGA ZZ environment. They are built in real time by Tiny C compiler included in the package.
Support for standard batch files trough SendVegaCmd command.
Other languages can be used writing specific interface code.
The standard VEGA command line version is included.
Other Features:
Database engine (directory, sdd anz zip support).
Plug-in system to expand the VEGA capabilities.
Integration with mobile devices trough ActiveSync® and IrDA connection.
Full language localization.
HyperDrive technology. It allows to take full advantages of multiprocessor systems, Hyper Threading CPUs (e.g. Pentium 4) and multi-core CPUs (e.g. Athlon X2 and Pentium D)
Pentium optimized code and 586, 686, Pentium 4, K6, Athlon/Duron DLLs for maximum performances.
Demo.