1. Introduction

VEGA ZZ is a complete molecular modelling suite that includes several features to make very easy your research jobs.

Snapshot view highlighting the real time graphic quality of VEGA ZZ package.

3D Graphic Features:

• OpenGL implementation for 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 (Side-by-side (SBS), half side-by-side, cross-eye, top and bottom, half top and bottom stereoscopic, shutter and anaglyphic modes).

• 10 bit output for each color channel for a smoother view (2³⁰ = 1.073.741.824 vs. 2²⁴ = 16.777.216 colors).

• 3D molecule view: wireframe with multi-vector 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, chirality, fixing value, residue, residue name, residue number).

• Enhanced atom coloring methods: atom, residue, chain, segment, molecule, constraints and custom.

• Atom and bond selection & picking.

• 3D surface: dotted, mesh, solid, solid transparent. Thanks to the HyperDrive technology, the calculation is very fast, using multiple CPUs or the OpenCL acceleration when available. 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 animation).

• 3D interactive monitors calculated in real time (distance, angle, torsion, angle between two planes, hydrogen bonds and E/Z geometry).

• Real time bump check.

• Simulation trajectory visualization and animation with full support for Accelrys archive file (.arc), AutoDock 4 DLG, BioDock output, CSR (Accelrys conformational search), DCD, ESCHER NG, GRAMM, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Tripos Mol2 multi-model, PDB multi-model and PDBQT 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. Moreover, it is possible to render 360° (equirectangular) and cube (cube faces) panoramas ready to be published by social networks.

• Vector graphic rendering engine. It's possible to export the view in PostScript, Encapsulated PostScript, PDF, STL (ASCII and binary), 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, mkv, MPEG-1, MPEG-2, MPEG-4 AVC, MPEG-H HEVC (h265) and QuckTime) without external software. VEGA ZZ uses the Windows codecs for the standard AVI files and a built-in library to encode the other streams. The MD animations can be converted in BluRay, DVD, Super Video CD, Video CD and video streams for the Web in easy way.

The powerful lighting engine implemented in VEGA ZZ allows realistic views.

Graphic User Interface:

• DPI aware application.

• All VEGA ZZ functions are available trough menu and/or requesters.

• Magnetic windows that can be assembled and managed as an whole large window.

• Possibility to load and save window layouts for specific operations.

• Extended menu with accelerators.

• Contextual menus.

• Buttons, radio buttons, combo boxes, list boxes, check boxes and sliders.

• Cut, copy & paste operations.

• Multiple workspaces.

• 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, CCl₄, DMSO, ethanol, formaldehyde, methane, methanol, octanol-water, POPC crystal, POPC liquid, water.

• Add ions (any type without restrictions).

• Change the ionization state according to the specified pH value.

• 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.

• Optical structure recognition.

• 2D molecular editors: Ketcher (included in the package) and ISIS/Draw.

• SMILES editor with automatic 3D conversion.

• Combinatorial SMILES builder based on fragment libraries.

• Build molecules by IUPAC name (powered by Opsin).

• Atom typing (ATDL and SMARTS) and charges attribution.

• Remove residues, segments and molecules.

• Centroid management.

• Connectivity builder and bond type finder.

• Change bond length, angle and torsion values.

• Protein secondary structure editing.

• Solvent cluster builder.

• Atom constraints for molecular dynamics (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), PDB multimodel and PDBQT 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).

• Molecular dynamics provided by NAMD (not included in the package, but available for free at http://www.ks.uiuc.edu/Research/namd/). The most common function are accessible trough the graphic interface and the simulation can be interactively launched in the VEGA ZZ environment.

• 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).

• Structure based virtual screening (provided by GriDock/AutoDock and AutoDock Vina).

• WarpEngine technology for collaborative computing (virtual screening and semi-empirical calculation).

• Molecular similarity (molecule superimposition).

• Protein-protein and protein-DNA docking (ESCHER NG).

• Graphic interface for MOPAC 7.01 (included in the package), and MOPAC 2007/2009/2012/2016 not included but available at http://openmopac.net/MOPAC2012.html.

• Complete system to collect and manage metabolic reactions (MetaQSAR).

• Protein cavity detection (fpocket).

• Molecular properties.

• Interaction analysis of ligand-receptor complexes.

• Secondary structure prediction (Predator).

• Interactive protein check (bond length, chirality, peptidic bond geometry, missing residues and ring intersection).

• Real time bump-check.

• Ramachandran plot calculation.

• Prediction of protein pK_a values (PROPKA).

• Calculations of solvation free energy using the Langevin Dipoles solvation model (ChemSol 2).

• Calculation of isotopic distribution (isotopic pattern).

Integrated Tools:

• PDB interface to download the structures directly in VEGA (PowerNet plug-in).

• Mini text editor.

• Graphic/plot viewer.

• Task manager.

External Tools:

• File decompressor (WinDD).

• OpenGL setup utility.

Scripting Languages:

• 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.

• PHP, Python, R and REBOL scripting languages for batch processing, multiple calculations and  multiple host communication. All three interpreters are included in VEGA ZZ package.

• Ajax technology to integrate Web-based applications in the VEGA ZZ graphic environment (e.g. Java applets to edit 2D structures).

• 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, IUPAC names, Merck MMD, Microsoft Access, Mol2 multimodel, ODBC, Sdf, SMILES, SQLite and zip support).

• Plug-in system to expand the VEGA ZZ capabilities.

• Full language localization.

• HyperDrive technology. It allows to take full advantages of multiprocessor systems, hyper threading and multi-core CPUs.

• Support for OpenCL technology.

• Demo.