Main features

Trp-Cage Miniprotein Construct TC5b

  3D graphic features
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Extreme OpenGL implementation for an incredible real-time rendering quality: lighting (4 customizable light sources + ambient light), alpha blending, hardware anti-aliasing, material management, 3D backgrounds.

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Stereo view (shutter or anaglyphic  glasses).

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

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3D molecule view: wireframe with multivector bonds, CPK, ball & stick, stick, trace and tube. All representations can be mixed thanks to the selection tool.

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Atom labels (atom name, element, atom type, atom number, atomic charge, chirality, fixing value, residue, residue name, residue number).

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

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Atom selection & picking.

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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 defining the number and the type of colors.

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Multiple surface management.

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All 3D object can be managed with mouse, joystick and dials (rotation, translation, scale and animation).

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3D interactive monitors calculated in real time (distance, angle, torsion and angle between two planes).

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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, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Tripos Mol2 multi-model, PDB multi-model and PDBQT multi-model formats.

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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.

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Vector graphic rendering engine. It's possible to export the view in LaTex, PostScript, Encapsulated PostScript, PDF, POV-Ray, SVG and VRML 2.0 formats.

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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.

     
     
  Graphic user interface
-   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 menus 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 and bonds.
-   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 editors: SketchEl (included in the package) and ISIS/Draw.
-   SMILES editor with automatic 3D conversion.
-   SMILES combinatorial builder.
-   Build molecules by IUPAC name (powered by Opsin).
-   Atom type 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.
-   Constraint management for MM/MD calculations.
-   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 provided by AMMP: energy minimization (single point, steepest descent, trust, conjugate gradients, quasi-Newton, truncated Newton, genetic algorithm, polytope simplex and rigid body), 0D to 3D and 2D to 3D conversion, interaction analysis, neural network to find the 3D space filling the curve corresponding to the structure, rigid docking.
-   Conformational search: grid scan, random search and Boltzmann jump. VEGA ZZ is able to find automatically the flexible torsions.
-   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, ILM, MLP, lipole, ovality, PSA, RMSD, surface area, surface diameter, volume and volume diameter).
-   Cluster analysis of the molecular dynamics and conformational search trajectory files (cluster by coordinates, by torsion and by torsion RMSD).
-   Structure based virtual screening (GriDock/AutoDock, AutoDock Vina and PLANTS).
-   Molecular similarity (superimposition).
-   Protein-protein and protein-DNA docking (ESCHER NG).
-   Graphic interface for Mopac 7, included in the package, and Mopac 2007/2012 (32 and 64 bit), not included but available at: http://openmopac.net/MOPAC2012.html
-   Protein cavity detection (fpocket).
-   Molecular properties calculation.
-   Interaction analysis of ligand-receptor complexes.
-   Secondary structure prediction (Predator).
-   Interactive protein check (bond length, chirality, peptidic bond geometry, missing residues and ring intersections).
-   Real time bump-check.
-   Ramachandran plot calculation.
-   Prediction of protein pKa values (PROPKA).
    Calculations of solvation free energy using the Langevin Dipoles solvation model (ChemSol 2).
-   Calculation of isotopic distribution (isotopic pattern).
-   Mass spectrometry tools.
      
     
  Supported file formats
-   Molecule (input): Alchemy, Accelrys Insight .car and .arc, Accelrys Quanta/CHARMm CRD, CSR, MSF and DCD, AMMP, BioDock output, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), Chem3D, ChemDraw CDX, ChemSol, CML 1.0 and 2.0, CPMD XYZ, ESCHER NG solutions, Fasta, GAMESS cartesian input and output, Gaussian cartesian input and output, Gromos/Gromacs .gro and .xtc, Gaussian input and output, HyperChem .hin, Interchange File Format (IFF/RIFF 32 and 64 bit), IIUCr Crystallographic Information Framework (CIF, mmCIF), IUMSC CRT, LiGen binary/text pocket, QMC, MDL Molfile, MDL Extended Molfile (V3000), Mopac internal coordinates, Protein Data Bank (PDB), Data Bank with ATDL atom types (PDBA), Protein Data Bank Fat (PDBF), Protein Data Bank MultiModel, PDBQT MultiModel (AutoDock Vina), SMILES, Spillo RBS, Tinker XYZ, Tripos Sybyl (Mol2), X-Plor PSF.
-   Molecule (output): Accelrys Insight .car (archive 1 and 3), Accelrys Quanta/CHARMm CRD and MSF, Alchemy, AMMP, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), ChemSol, CML 1.0 & 2.0, CPMD XYZ, Fasta, GAMESS cartesian, Gaussian cartesian input, Gromos/Gromacs .gro, Interchange File Format (IFF), IUCr Crystallographic Information Framework (CIF, mmCIF), IUMSC CRT, MDL Molfile, MDL Extended Molfile (V3000), Mopac cartesian coordinates, Mopac internal coordinates, Protein Data Bank (PDB), Protein Data Bank with ATDL atom types (PDBA), Protein Data Bank with atomic charges (PDBQ), Protein Data Bank Fat (PDBF), Protein Data Bank Large (> 99999 atoms, PDBL), Protein Data Bank simplified, PQR, SMILES, Spillo RBS, Tripos Sybyl (Mol2), X-Plor PSF.
-   Trajectory: Accelrys archive file (.arc), AutoDock 4 DLG output, BioDock output, Crystallographic Information Framework multi-model (CIF, mmCIF), CSR (Accelrys conformational search), DCD (CHARMM, NAMD), ESCHER NG, Gromacs TRR, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Mol2 multi-model and PDB multi-model file formats.
     
     
  Scripting language
-   The REBOL scripting language is included in the package for batch processing, multiple calculations and multiple host communication.
-   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.
-   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 in the package.
     
     
  Other features
-   Database engine (directory, IUPAC names, Merck MMD, Microsoft Access, Mol2, ODBC, Sdf, SMILES, SQLite, and zip support).
-   Plug-in system to expand the VEGA 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.