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.

2. Installation and activation

To install the VEGA ZZ package, run the setup file (Vega_ZZ_X.X.X.X_Setup.exe) with administrator rights and follow the installation wizard. If you installed a firewall software, you must configure it, granting the network access to VegaZZ.exe and  REBOL.exe.

Staring from 3.1.2 release, both 32 and 64 bit versions of VEGA ZZ are provided in the same package and during the setup procedure, the best version for your operating system is automatically installed. If you choose to install the Live CD creator tool, both versions are installed in order to grant the run of the live version of VEGA on all Windows versions.
After the setup, run VEGA ZZ to begin the activation procedure needed to unlock the software: the activation is totally FREE.

Follow the procedure shown in this window:

• Connect to DDL registration server pushing the Click here ! button. The Internet Explorer window will be shown at the http://www.ddl.unimi.it/licman URL.
• Put in the form the product key reported at the step two and your e-mail address. It couldn't be needed to type the product key if it's already present in the form field. Please use a valid e-mail address, because it's required to send you the activation key file. If you want to activate more than one PC, use the same e-mail address in order to skip the user registration procedure.
• If you aren't already registered, complete the registration form.
• At the end of registration, two e-mails are sent automatically: the former is the registration confirm (if you aren't already registered) and the latter contains the activation key.
• Save the activation key attached to the license e-mail. The activation key is a small  binary encrypted file named vegazz.lic.
• Open it to install or alternatively copy the vegazz.lic file to the C:\ProgramData\VEGA ZZ\Data directory. Click the Open button of the activation window: an explorer window is opened, showing the right directory.
• Click the Ok button. If a problem is found, an error message is shown and the activation can be repeated until the Cancel button is clicked.
• If you find problems during the activation procedure, please see the FAQ section.

Please remember that the activation key is generated starting from the product key. The product and the activation keys are personal and they work with a specific PC/workstation only. You can't activate more than one PCs with the same activation key because each PC has a different and unique product key. The activation expires after 1 year for non-profit academic users and after 30 days for business companies. After this time it's possible to request another activation key. The two activation types can be selected during the registration procedure. The Authors can change the licensing method in any time on their own decision. The business companies can't access to the collaborative support without purchasing the Support Pack (available requesting it to the Authors): help or new feature requests will be trashed if they are submitted by companies without Support Pack. The Authors spent a lot of time to develop a software that, in some cases, includes better features and performances than several commercial packages. We request a little contribution to companies in order to continue the VEGA ZZ project otherwise destined to end in the near future.

2.1 Installation of optional components

The optional components require to pre-install VEGA ZZ on your PC. Some components aren't included because they may be not useful for all users and/or require a separate license agreement.

2.1.1 OpenCL acceleration

The HyperDrive library, that is the calculation core of VEGA, can take full advantages of the OpenCL enabled devices (GPU and accelerators). Although your PC has OpenCL device, it may be necessary to enable its support, installing suitable drivers. For more information about the OpenCL installation, click here. The performance boost could be amazing as reported in the following test:

System configuration:

AMD Phenom II X4 955 quad core 3.2 GHz,  4 Gb DDR3 Ram, Sapphire/ATI HD5770 1 Gb DDR5 PCIe card

Software for the test:

Windows 7 Professional x64, VEGA ZZ 2.4.0, HyperDrive 2.0 for K8 and more CPUs.

Type of test:

MEP surface calculation (Type: MEP, Dots, Probe Rad: 0, Density: 10) of the inositol monophosphate dehydrogenase (8598 atoms) which file name is impdh.pdb.bz2 and it's placed in the ...\VEGA ZZ\DemoZZ directory.

Test results:

The results are approximated and indicative for the performance boost.

2.1.2 VEGA ZZ Live CD Creator

VEGA ZZ Live CD Creator is a software developed to create live distributions starting from the VEGA ZZ files installed in your PC. A live distribution is an auto-starting CD or pen drive  that allows to use VEGA ZZ without installation and activation. In this way, you are able to use VEGA ZZ everywhere. To install it, you must choose the Live CD Creator component during the software setup.

2.1.3 MOPAC 2016 installation

The VEGA ZZ package includes MOPAC 7.01-4 for semi-empirical calculations, but it's possible to use the latest MOPAC 2016 that, if correctly installed, is automatically detected by VEGA ZZ. For copyright reasons, Mopac 2016 isn't included in the package but it can be obtained at http://openmopac.net.
Please follow these steps for a correct installation:

• Connect to http://openmopac.net/MOPAC2012.html and choose the Downloads page.
• Download 32 or 64 bit Mopac 2016 stand-alone for Windows depending on your operating system. Take care to select the right file to download: the non-stand-alone versions can't be used by VEGA ZZ.
• Unzip the archive and put Mopac2016.exe and libiomp5md.dll files in ...\VEGA ZZ\Bin\Win32 or ...\VEGA ZZ\Bin\Win64 directory.
• The Mopac 2016 installation is now completed.

2.1.4 NAMD installation

NAMD 2 is a parallel molecular dynamics software designed for high-performance simulation of large biomolecular systems. VEGA ZZ includes a user-friendly graphic interface making easier the use of this powerful package. To install NAMD, follow this procedure:

• Download the latest NAMD 2 package for windows from http://www.ks.uiuc.edu/Research/namd/. You can find it in the download page as Win32-i686 (Windows NT, 2000, XP, etc).
• Put your user name and password to login. If you are a new user, please proceed to the registration.
• Agree the license terms clicking the big button and download the zip file containing the package. The file name should be NAMD_X.X_Win32-i686.zip.
• Unzip all files in the ...\VEGA ZZ\NAMD directory.
• The installation is complete and now you can use NAMD selecting Calculate NAMD in the main menu (for more information, click here).

2.2.6 PLANTS installation

PLANTS docking software is not included in VEGA ZZ package and to install it, you must follow these steps:

• Complete the registration form in download page at http://www.tcd.uni-konstanz.de/
• Download the PLANTS Win32 (minGW).
• Rename the file name to Plants.exe and copy it to ...\VEGA ZZ\Bin\Win32 directory, where ...\VEGA ZZ is the VEGA installation directory.
• Download mingwm10.dll and copy it to ...\VEGA ZZ\Bin\Win32 directory.

Now PLANTS is ready to run in VEGA ZZ environment.

WARNING:

If you installed the 1.1 version built by Mingw32, it's strongly recommended to patch it by running Patch bin 1.1 script. To do it, select File Run script in the main menu (for more information click here), expand the script tree at Docking, thus at PLANTS level and finally double click Patch bin 1.1.c.

2.2.5 X-Score installation

X-Score 1.2 or 1.3 for Windows is not included in VEGA ZZ package, but is required to run some scripts such as X-Score.c and Rescore+.c. To intall X-Score, follow these steps:

• Open the following Web site: http://www.sioc-ccbg.ac.cn/?p=42&software=xscore
• Complete the on-line registration form.
• Log-in with your credential and download X-Score package for Windows platform.
• Open the tar file by WinRAR or other software able to unpack tar gizipped files.
• Extract xscore_win32.exe from xscore_win32\bin to ...\VEGA ZZ\Bin\Win32, where ...\VEGA ZZ is the VEGA ZZ installation path (usually C:\Program Files\VEGA ZZ).
• Rename xscore_win32.exe to xscore.exe.
• Extract parameter directory from xscore_win32 to ...\VEGA ZZ\Data directory. This last directory is hard to identify, because every Windows version creates it in a different place. To find it, open VEGA console from Start menu, type OpenDataDir and press enter.
• Rename parameter to Xscore.
• If you want to use xscore.exe from command prompt, open VEGA console and use xs command, that is a shell script that fixes the environment variable required by X-Score.

2.2 VEGA ZZ installation on Asus Eee PC

2.2.1 Introduction
2.2.2 What's you need
2.2.3 Preparing the Windows XP CD
2.2.4 Windows XP installation
2.2.5 Using a SD card to increase the storage
2.2.6 VEGA ZZ installation
2.2.7 Optimizing the VEGA ZZ configuration
2.2.8 Increasing the Eee PC computational power
2.2.9 More power ...

2.2.1 Introduction

With the Eee PC product line, Asus introduced a new notebook concept in which weight and dimensions are minimized to use the PC anywhere. This small PC is perfect to create an ultra-mobile workstation to explain the molecular modelling concepts in the classroom, to realize a new idea anywhere, to control your HPC system trough the wireless connection, etc.
At this time, Eee PC is available only with the powerful Xandros operating system that is unable to run VEGA ZZ. Fortunately, Asus included all drivers to install Windows XP, making possible to run VEGA ZZ. Due to the small SSD (Solid State Disk) storage system, the installation procedure requires attention to reduce the waste of disk space.

2.2.2 What's you need

• Asus Eee PC 4G or 8G (Surf).
• Microsoft Windows XP Professional (the Home edition seems to have problems with the Eee PC).
• Asus support DVD included in the Eee PC box.
• External USB DVD-Rom drive. It could be enough a CD-Rom drive, but a 2 Gb USB Pen Drive is required to install the drivers.
• 4-16 Gb SDHC card (optional if the operating system is enough shrink).
• A desktop Windows PC with CD/DVD writer.
• nLite software (available for free at http://www.nliteos.com).
• Windows XP Service Pack 2 or 3 (click here to download the SP2).
• XP Remove Hotfix Backup (click here to download the Zip file).
• EeeClock utility to change the Eee PC FSB from 70 to 100 MHz (click here to download it).
• Latest VEGA ZZ setup package (available for free at http://www.ddl.unimi.it/vega).

2.2.3 Preparing the Windows XP CD

Not all components installed by the standard Windows setup are really required (e.g. the driver database, some services, etc) and thanks to nLite is possible to exclude some of them to reduce the disk space occupied by the operating system.
A complete tutorial to create a slimmed installation CD is available at: http://wiki.eeeuser.com:80/howto:nlitexp

2.2.4 Windows XP installation

Before proceeding the Windows setup, backup your data because they will be overwritten.

• Plug the USB cord of the external CD/DVD-Rom drive into a free USB port of your Eee PC.
• Turn on your laptop and press F2 to go to the BIOS setup.
• In the Advanced settings page, switch the OS Installation field to Start.
• Go into Onboard Devices Configuration submenu and enable all peripherals.
• In the Boot page, go in the Boot Device Priority and put the USB CD/DVD-Rom drive as 1st Boot Device.
• Put the slimmed Windows XP CD in the drive.
• In the Exit page, choose Exit & Save Changes and press Enter.

After the reset, the Windows XP Setup procedure will start.

WARNING:
the following step deletes all data previously saved in the SSD and they will lost definitively.

• When the setup shows the disk where install the operating system, remove all four Xandros partitions and select all unpartitioned space using the NTFS file system.
• At the setup end, go to the BIOS settings (press F2 when the system boots) and in the Advanced settings page, switch the OS Installation field to Finish.
• In the Exit page, choose Exit & Save Changes and press Enter.

To reserve more disk space, you could disable the Automated System Recovery (ASR):

• Start Windows, go to the Control Panel (Start -> Settings -> Control Panel), click Switch to Classic View and double click the System icon.
• Select the System restore tab and uncheck Turn off System Restore on all drives.
• Click the OK button.

The system restore service is no more needed and so it can be disabled:

• Go to the Control Panel, double click Administrators Tools, double click Services.
• Double click System Restore Service and in the General tab push the Stop button.
• In the Startup type field, select Disabled.

Optionally, to speed-up the boot and increase the amount of free physical memory, the remote assistance and the desktop sharing van be disabled:

• Go to the Control Panel, double click System and select the Remote tab.
• Uncheck both Remote assistance and Desktop sharing.
• Press the OK button.

Driver installation:

• Put the Asus support DVD in the DVD-Rom drive. If your drive reads CDs only, use the DVD-Rom reader of your desktop PC to copy all files from the ASUS DVD to a pen drive (2 Gb are enough).
• The DVD should start automatically if the autorun is enabled, but if it's not enabled, run Setup.exe in the root directory.
• Use the automated procedure to install all drivers.

Update the operating system:

• Use Windows update to download the latest operating system hotfixes.
• Install DirectX 9 APIs using the Web setup (http://www.microsoft.com/directx)

These steps reduce the amount of disk space, removing the backup files:

• Open the command prompt and type:

sfc /purgecache

and press return to clear the system backup files.

• Download XP Remove Hotfix Backup, unzip and run it.
• Click the Continue button.
• Click Remove Backup Files and Add/Remove entries. In this way, the updates can't be uninstalled, but a large amount of disk space is freed.

Some other files can be deleted:

• Delete all directories in C:\WINDOWS\$hf_mig$ and not $hf_mig$. This is the hotfix setup directory.
• Delete all files and directories in C:\WINDOWS\Help and not Help. This directory contains the Windows XP help files: removing them, the help will be unavailable.

To increase the available disk space, it's possible to reduce the Internet Explorer file cache to 8 Mb and the size of the swap file used as virtual memory.

• Go to the Control Panel and double click the Internet Options icon.
• In the General tab, Browsing history section, click the Settings button.
• In the Temporary Internet Files box, put 8 as disk space.
• Click the Ok button.

Change the size of the swap file:

• In the Control Panel, double click the System icon.
• Choose the Advanced tab and in the Performance area, click the Settings button.
• In the dialog that opens up, choose the Advanced tab and select Change in the Virtual memory box.
• In the Paging file size for selected drive, put 256 in both Initial size and Maximum size fields.
• Click the OK button two times.

If you expanded the memory of your Eee PC from 512 Mb to 2 Gb, installing a 2 Gb SoDIMM DDR2 667 MHz module, you could consider to disable the virtual memory, selecting No paging file.

2.2.5 Using a SD card to increase the storage

A 4-16 Gb SDHC (Secure Digital High Capacity) card is a good choice to increase the storage size, moving some directories on it.

• Insert the card in the slot on the right side of your Eee PC. It will be automatically recognized by Windows XP.

A new SDHC card is pre-formatted with the FAT32 file system that is not very efficient to manage the disk space due to the too big cluster size. For this reason, some disk space is lost writing small files on the SD. To avoid the problem, you could format the card with NTFS file system that generates smaller clusters. Unluckily, Windows XP doesn't allow to format the removable devices with NTFS, but the convert.exe included in the standard Windows distribution can convert any disk from FAT16/32 to NTFS.

• Open the command prompt and type:

convert e: /fs:ntfs

• and press return. After few seconds, the old FAT32 disk is converted to NTFS.
• In the E: disk, create My Documents, Program Files and Temp directories.
• Change the pre-defined My Documents directory to E:\My Documents, clicking with the right mouse button on My Documents on the desktop, selecting Properties and changing the destination to E:\My Documents. In this way, all files putted in the My Documents folder will be automatically saved in the SD card.

Use the E:\Program Files directory to install the new software, reserving the internal SSD for the system files.
Another good idea to is to move the Outlook Express data files from the user profile directory in C: to E:

• Create the E:\My Documents\Outlook Express directory.
• Start Outlook Express and create your e-mail profile if you didn't create one.
• In the menu bar, select Tools -> Options ... and in the Maintenance tab click on the Store Folder button.
• In the dialog window, click the Change button and browse E:\My Documents\Outlook Express.
• Click OK. The changes will be made after you exit and restart Outlook Express copying automatically all files from the old to the new directory.

2.2.6 VEGA ZZ installation

In this section will be explained how to install VEGA ZZ on the Eee PC.

• Download the latest VEGA ZZ package and start the setup.
• Choose the setup language and press OK.
• Click Next, choose I accept the agreement and click Next.
• As installation directory, put E:\Program Files\VEGA ZZ and click Next.

The Eee PC has a Celeron M CPU and the components for the other CPU models can be omitted:

• Uncheck:
  - Optimized components for P4 CPUs (Intel Pentium IV)
  - Optimized components for K7 CPUs (AMD Duron, Athlon, Sempron)
  - Optimized components for K8 CPUs (Intel Opteron, Athlon 64/FX, Sempron 64)
• Uncheck other components also:
  - WinDD data de/compressor
  - VEGA SE (Screen Saver Edition)
• Click Next.
• Specify where to put the VEGA ZZ item in the Start menu and click Next.
• Look the file extension associations and press Next.
• Finally, click the Install button.
• Install the REBOL script engine in the E:\Program Files\REBOL directory.

At this step, you need to activate VEGA ZZ, following the procedure explained in the Installation and activation chapter.

2.2.7 Optimizing the VEGA ZZ configuration

VEGA ZZ 2.2.0 can detect the Eee PC and automatically enables some window optimizations, but if you are running a previous version, it may be possible that you need to switch from 800x480 to 800x600 screen resolution to manage the large windows.
The Intel GMA 900 graphic card is full working but has a limited OpenGL support:

• Multi-sample anti-aliasing not supported.
• Offline hardware rendering not fully supported (pbuffer).
• Vsync not available in window mode.
• Buggy implementation of the vertex buffer.

Intel claims OpenGL 1.4 features, but bugs and missing extensions makes this graphic adapter OpenGL 1.2 compliant only.

For the best view experience:

• Enable the vector anti-aliasing (click here).
• Disable the vertex buffer in surface rendering (click here).

2.2.8 Increasing the Eee PC computational power

The Eee PC is factory downclocked to increase the battery life, but if the stock computational power is not enough for you, it's possible to change the Front Side Bus (FSB) from 70 to 100 MHz. In this way, the CPU goes from 630 to 900 MHz with a 30 % increment of the computational power. This is not a real overclock because the Celeron M was designed by Intel to run with a 100 MHz FSB.

• Download the EeeClock software, unzip and run it.
• In the tray bar, click on the 70 icon and choose Full (100 MHz) in the menu. Your Eee PC is now running at 900 MHz.

You can change FSB in any time, but I found problems suspending the system when the FSB differs from 70 MHz (system lock).

WARNING:
The Author of this guide accepts no responsibility for hardware/software damages.

2.2.9 More power ...

If the Celeron M @ 900 MHz is not enough for your MM calculations, VEGA ZZ can help you to break this barrier thanks to the possibility to run remote jobs (see Configuration of remote hosts).

2.2.9.1 What's you need

• A fully configured Eee PC with VEGA ZZ (see above).
• Desktop PC or a HPC system running Windows or Linux.
• Network connection for both PCs.
• Latest VEGA ZZ setup package (available for free at http://www.ddl.unimi.it/vega).
• AMMP VEGA Edition package (for Linux host only, available for free at http://www.ddl.unimi.it/vega/download.htm).
• WarpGate package (for Linux host only, available for free at http://www.ddl.unimi.it/vega/download.htm).

2.2.9.2 Configuration of the Windows host

In this section will be explained how to configure a remote host in order to perform MM calculations submitted by the Eee PC (or any other remote PC).

• Install VEGA ZZ, checking Warp utilities for secure Internet connection in the Select Components page of the setup wizard.
• Activate VEGA ZZ if you want use it in interactive mode (see the Installation and activation chapter).

Now you need to configure the WarpTel service that is an encrypted telnet daemon (for more information, click here).

• Start the service in interactive mode (Start -> VEGA ZZ -> WarpProject -> WarpTel -> WarpTel).
• If you are running on Windows XP, unlock the software because the firewall has detected its TCP/IP port.
• Click on the green square icon on the tray bar and select Settings. The configuration dialog will be shown.
• Change the User name, the Password and annotate the WarpKey (copy & paste in an empty text file). The WarpKey is used to encrypt the connection and it's randomly generated when WarpTel starts at first time.
• Finally, click the Ok button.
• If your host has a DNS entry, annotate its name, otherwise open the command prompt and type

ipconfig /all

and press return.

• Annotate the IP address of the Ethernet card connected to the LAN.

It's possible to run WarpTel as Windows service and the procedure to do it is explained in the WarpTel manual.

2.2.9.3 Configuration of the Linux host

The configuration of a Linux host is a little bit hard and it's reserved to power users:

• Create an user account and annotate the user name and the password (both are required for the client configuration).

AMMP is the calculation module and must be installed:

• Download the AMMP full package, unpack it, choose the more appropriate executable for your system (Linux 32 or 64 bit) and copy ammp to the home directory of the user created previously.
• Change the file permissions, typing in the command shell:

chmod 755 ammp

• Enable the telnet daemon, because in some Linux distribution is disabled by default.
• In the firewall settings, close the TCI/IP port 23 and open the 7000. Both these operations are depending on the specific Linux distribution and so I'm unable to explain them step by step.

Now, you must install the WarpGate daemon that creates the encrypted tunnel between the host and the client. To do it, you must be logged as root.

• Download the WarpGate package for Linux, unpack it.
• Run WarpKeyGen to generate the 256 bit encryption key and annotate it.
• In the warpdata/cfg directory edit the warpgate.ini file, remove the default entry and put:

; Local port  Local conn.  Remote host                 Remote port  Type  Key
; ========================================================================================================================================
  7000            N        localhost                   23            TCP   <Put here the key generated by WarpKeyGen>

• Copy the warpgated executable in a system accessible directory (e.g. /usr/local/bin).
• Copy the waprgate.ini file in the /etc directory.
• Check the current runlevel, opening the /etc/inittab file and looking the id:X:initdefault line. X indicates the default runlevel (usually 5).
• Change the current directory to /etc/rc.d/rcX.d, where X is the runlevel.
• Create a soft link to warpgated:

ln -s /usr/local/bin/warpgated S98warpgated

• To start the service reboot the system or type /usr/local/bin/warpgated

2.2.9.4 Configuration of the client (Eee PC)

• Starts VEGA ZZ.
• In the menu bar, select Tools -> Host configuration: the Host configuration window will appear.
• Press the Add button.
• Put the host Name (e.g. My host), the Type (Linux for Linux 32 and 64 bit, Windows 9x for Windows 95/98/ME or Windows NT for Windows NT4/2000/XP/XP x64/Server 2003/Vista).
• Set the number of thread that the remote host is capable to run at the same time (it's the number of CPUs/cores, including the virtual CPUs).
• In the Address field, put the DNS host name or the IP address and type 7000 in the Port field.
• Put the User name, the Password and the WarpKey as in the WarpTel configuration.
• Check Encryption to enable the secure encrypted connection.
• Optionally type the host Description.
• Press the Save button.

The client configuration is finish and now a test is required.

2.2.9.4 Running a remote calculation

To do this step, the Eee PC must be connected to the LAN or to Internet if the host is connected to it. This is the best scenario because in this way you can use anywhere the computational power of the remote host. The Eee PC connection can be done indifferently by Ethernet or wireless adapters.

• Open the VEGA ZZ console (View -> Console). It's closed by default when the Eee PC is detected by VEGA ZZ 2.2.0.
• Open the molecule a3.mol2 in the ...\VEGA ZZ\Molecules directory (File -> Open).
• Select Calculate -> Ammp -> Minimization and in the Minimization tab, put 3000 Minimization steps, 0.01 as Toler and 0 Steepest steps.
• Choose Conjugate gradients as minimization algorithm.
• In the Hosts tab, click on one My host item. There are more than one hosts with My host name if the remote system can manage more than one thread at the same time.
• Click the Run button. If all settings are right, the calculation starts and the console shows the progress.

We successfully tested the Eee PC with a dual AMD Operton 250 @ 2.4 GHz workstation running Windows XP and a eight dual core AMD Opteron 875 @ 2.2 GHz (16 cores) HPC system running 64 bit Linux (CentOS distribution): imagine the amazing power of this last system inside your small Eee PC ...

3. Running VEGA ZZ

VEGA ZZ can be started in several ways:

• selecting VEGA ZZ item in the Windows Start Menu;

• double-clicking the VEGA ZZ icon on the Desktop;

• double-clicking the molecule/trajectory files associated to VEGA ZZ;

• using the Context Menu Send To item shown by clicking a file with the right mouse button;

• typing VEGAZZ without arguments in VEGA Console;

• typing in the command prompt:
  
  VEGAZZ <FILE_NAME>
  
  with this syntax,  VEGA ZZ starts loading and showing the specified molecule.

If you need to operate in command line mode without graphical output, you must type VEGA instead of VEGA ZZ in the command prmpt. For the complete command command syntax, click here.

Menu bar Tool bar 2

Window title     Tool bar 1 Graphic view Workspace controls Console Status bar

In the Window title bar are shown the  version, the communication port number, the active workspace number and the name of the workspace that corresponds to the molecule name. The communication port number is important to identify the VEGA ZZ session to witch send the script commands. You can start more than one VEGA ZZ.
The Menu bar allows the access to the main functions. For more information about the Main menu, click here.
Tool bar 1 and Tool bar 2 are classic tool bars that replicate some main menu commands for a fast-easy access. They can be closed and to reopen them, you must use View Tool bars item in Main menu.
The Workspace controls are useful to manage the multiple workspaces. A workspace is a separated area that can contains molecules, surfaces and trajectories without interferences between the other workspaces.
To add a new workspace, you must open the context menu clicking the Workspace controls box by the right mouse button and selecting New. To change the current workspace, you can click its name in the list or use the Q (previous) and W (next) keys.
To remove a single workspace, you must click it and select Remove in the context menu. If you want remove all workspaces, you must choose Remove all. Remember that the first (0)  workspace can't be removed.
The Graphic view shows the 3D representations of molecules, surfaces, etc and the Console displays text information only (calculation progress, results, etc). In this window you can type directly commands of the menu and extended commands in order to control VEGA ZZ without the GUI. To explore the command history, you can use the cursor arrows and Pg. Up and Pg. Down keys . The Console can be moved from its docking position and can be closed also clicking the button placed at the top-left corner. You can use View Console menu item to show or hide it.
The Status bar shows the current mouse mode (Rotate, Translate and Scale), the object that are subjected to the mouse 3D transformations (All, Molecule, Segment and Residue) and the mouse measurement mode (Atom, Rotation center, Distance,  Angle, Torsion and Angle between two planes). For more information about the mouse controls, click here.

4. Mouse, keyboard and joystick

4.1 Mouse

The mouse can be used to manage the 3D objects trough rotation, translation and scale operations, changing the mouse mode with the context menu and/or the M hotkey (see hotkeys section). To change a 3D property, you must drag the mouse from left to right and vice versa pressing the left mouse button. To apply a Z transformation (rotation or translation), you must drag the mouse holding the middle button or the left button and the shift key at the same time. The mouse wheel, if present, has some functions on the basis of the current mouse mode: it can rotate around Y axis, translate along the Z axis and zoom. To change the mouse settings, see the configuration of the human interface devices (HID).
In the main window, you can select some functions with the context menu, pressing the right mouse button:

Please note that the CmdName column contains the command name, that must be used with SendVegaCmd program to activate the menu functions in batch files (click here for more information).

There are other menu items that are sensible to the context and are shown if you click an atom or a bond by the right mouse button, as shown in the following table:

The following table includes the specific options to change a bond.

4.2 Keyboard

When the main window is active, some commands can be executed directly from the keyboard, like shown in the following table:

4.3 Joystick

To enable the joystick operation, you must check the Joystick enabled menu item present in the the context menu. The keyboard and the mouse are kept full operative. To change the joystick settings, see the configuration of the human interface devices (HID).

4.4 Interactive controls

Another way to control the VEGA 3D visualization, is the use of the 3D control window. It can be shown clicking View 3D controls.

The window contains seven dynamic buttons to control rotation, translation and scale factor. The bottom slider sets the sensitivity of the dynamic buttons. As an example, when you click X Translation button, the direction is due by the clicking point: if you click the left part of the button, the molecule is translated to left and clicking the right part, the it's translated to right. The translation speed is higher clicking the button extremities, but it's lower clicking the button center. The controls are connected to the selected object (world,  molecule, segment, residue). To transfer temporally the controls to the world, you can hold down the keyboard Control button (Ctrl). In this way, you can switch easily from word to molecule and vice versa.

5. The main menu

By VEGA ZZ main menu, you can access to main functions. The item layout is organized in menu bar and sub-menu as shown in the following tables. The CmdName column contains the command names usable in the scripts to activate directly the menu functions (for more information see the SendVegaCmd program and the extended command section).

5.1 File menu

5.2 Edit menu

5.3 View menu

5.4 Calculate menu

5.5 Tools menu

5.6 Bioinformatics

5.7 Help menu

5.8 The console context menu

The menu items shown below are accessible through the context menu of the console window.

6.1 Atoms

VEGA ZZ can add, remove and change atoms.

6.1.1 Add atom

Selecting Edit Add Atom it's possible to add one or more new atoms:

To add a new atom, choose the Element, the Hybridization and the Bond type, thus click the atom to which to connect it. You can specify where to place the new atom in the atom list choosing After the selected atom, At the residue end, At the molecule end. If you want to select an element not included in the Element box, click Other and put the element name in the Selected field.

WARNING:
If the bond type isn't shown in the main window, open the View settings and make it sure that the Multivector item in the Wireframe tab is checked.

6.1.2 Remove atom

If you want to remove one or more atoms, you can select the Edit Remove Atoms item in the main menu or click the Remove button of Add/remove atom dialog box.

Click the atom and it will be removed automatically.

6.1.3 Change atom

To change the atom properties, you can select Edit Change Atom/residue/chain menu item.

6.2 Atom/residue/chain properties

This dialog is shown clicking Edit Change Atom/residue/chain and allows to change some atom, residue and chain properties of the selected atom/molecule. For example, consider the following molecule fragment:

and imagine to click the C6 atom.

6.2.1 Edit atom By Atom tab, you can change atom name, element, residue name, residue number, chain indicator, atom type and partial charge of the picked atom. When you change a field, button is enabled and you can click it in order to apply the modifications. Alternatively, you can press the return key to apply the changes.

6.2.2 Edit residue Residue tab allows to change the properties (name and number) of the selected residue and the changes can be applied to all atoms or to the visible atoms only.

		6.2.3 Edit chain Chain tab allows to change the chain indicator of the selected molecule and it can be applied to all atoms or to visible atoms only.

6.3 Atom constraints

VEGA ZZ allows to specify constraint constants for each atom in order to fix/constraint them in molecular dynamics simulations (e.g. NAMD). The dialog box is accessible by Edit Coordinates Constraints menu item:

You can choose Fix/Free mode to fix/free atoms or Value mode for harmonic constraints (see the manual of the molecular dynamics software). In Value field of Parameters box, you can put the harmonic constant that can be from 0 (full free) to 1 (full fix). In Selection box, you can select the atoms to apply the constraints. Visible atoms options should be used with  Atom selection dialog box for complex constraints. Checking Color atoms, the atoms are colored by constraint value (blue = fix, green = free) as shown in the Colors box.

Examples:

	Fixed backbone
Freed a sphere around an atom

WARNING:
Remember that two file formats only can store the atom constraints and they are IFF and PDB. VEGA ZZ can read the constraints only from IFF files and it can write them to both formats. In PDB files, the constraints are placed in B column.

6.4 Centroids

VEGA ZZ can manage pseudo-atoms whose coordinates are calculated in real time as symmetry center and are named centroids. A centroid can be used to measure distance, angle, torsion, angle between two planes as a normal atom. In molecular dynamics analyses, the centroid position is automatically recalculated for each frame.
To define a new centroid, you must select Edit Add Centroid in main menu:

Picking the molecule atoms, whose maximum number is six (6), you can add a new centroid. The. Clicking New button,  a new centroid is added and clicking Reset button, the atom selection restarts from the beginning:

Clicking Keep fixed checkbox, it's possible to fix the centroid coordinates, disabling the automatic update when the coordinates of the other atoms are changed (e.g. during trajectory analysis or torsion edit).
To close the dialog box, click Close and to remove all centroids, select Edit Remove Centroids. The centroids can be removed as normal atoms also. A typical application example could be the measure of the distance between two rings, as shown in the following picture:

6.5 Bonds

VEGA ZZ can add, change, remove bonds and rebuild the connectivity by a dialog box.

6.5.1 Add bond

Selecting Edit Add Bonds in the main menu, it's possible to add one or more new bonds:

In Bond type box, you can choose the type of bond to add. Clicking the two atoms to bond you can connect them. A transparent cylinder indicates the selected bond:

Selecting Connectivity of all atoms or Connectivity of selected atoms in the What ? box and clicking Apply button, it's possible rebuild the connectivity of all atoms or of the selected atoms only. The Bond tolerance field allows to change the overlap of the covalent radii. This may be increased if the molecule has stretched bonds or decreased if the atoms are too close and the normal computed connectivity is wrong due to multiple bonds exceeding the atom valence.  Click here to change the default bond tolerance value.

6.5.2 Remove bond

If you want remove one or more bonds, you must select Edit Remove Bond in the main menu.

To remove one bond, you must click the two connected atoms and so it will be deleted. It's possible to remove also the Connectivity of all atoms or the Connectivity of selected atoms only, checking the specific items in the What ? box.

6.5.3 Change bond

To change a single bond or to detect the bond types of all atom pairs, you can select Edit Change Bond type menu item:

To change one bond, you must click One bond, select it picking the two atoms, choose the Bond type and than click Apply. To change the bond type to more than one bonds, you must follow the above steps checking  All atoms or Selected atoms only (visible atoms) in the What ? box.

Choosing Fix aromatic rings or Fix aromatic rings (sel. atoms), it's possible to fix the bond order of all/selected aromatic rings from alternate single - double bonds to partial double bonds.
Using the Find the bond types and Find the bond types (sel. atoms), it's possible assign the types of all/selected bonds. Please remember that the bond type information isn't used by VEGA to assign the force field or the atomic charges.

WARNING:
If these two functions don't appear to work (e.g. the visualization doesn't change), open the View settings and make it sure that the Multivector item in the Wireframe tab is checked. The default condition is unchecked.

To assign the bond types, VEGA uses a special ATDL template (BOND.tem) in which is reported the capability of each atom to bond it with a specific bond type. The supported bond types are:

If two atoms are connected and they have got the same atom type, the resulting bond type is the same indicated by the atom type:

A special check is done to detect the planarity of the resulting torsion in order to avoid the wrong assignment in 1,4 conjugated systems and in biphenilic systems:

\    |  /
 C=C-C=C    - Bond to detect
/  |    \
 2 2 2 2    Atom types

\    |  /                         \    |  /
 C=C=C=C      Planarity check      C=C-C=C
/  |    \                         /  |    \
  Wrong                              Correct

If two atoms are connected and they haven't the same atom type, the resulting bond type is single.

6.5.5 Swap bonds

To swap two bonds, for an example to invert the chirality, you can select Edit Change Swap bonds menu item:

This function doesn't require to define both bonds clicking on four atoms because the bonds to swap have a common atom (atom C in the window scheme) and so you must click only two atoms (A and B). To repeat the operation, you can click the Swap button.

6.6 Bonds, Angles and torsions

VEGA ZZ can change interactively bonds, angles and torsions defined by Selection Tool. To open the dialog, select the Edit Change Bond/Angle/Torsion item in the main menu.

To select new bonds, angles and torsions, you can open the Selection Tool by clicking Edit button. Alternatively, you can open the selections by drag & drop of a file or by the context menu (Open item). You can also save the selection by Save as... menu item of the context menu. The Bond/Angle/Torsion box shows the selected angles and torsions that can be changed selecting one and pushing the Change button. This is a dynamic button as explained for the 3D Controls dialog box. In Angle value or Torsion value field, it's possible to type the angle or the torsion value.

When you change the bond length, the Default length button and the Move all checkbox are active. Clicking the former, the bond length is automatically set to default value (e.g.  C-H bond is set to 1.14 Å) and checking the latter, when you change the bond length, the whole substructure connected trough the bond is moved instead of the single atom. To revert to the initial value, use the undo function.

6.7 Change the secondary structure of a peptide

VEGA ZZ is able to change the secondary structure of a peptide moving the Phi, Psi and Omega torsions. To show the dialog window, you must select Edit Change Secondary struct. in main menu.

The Structure type box allows to specify the secondary structure type: several pre-defined structure types are already defiend (Alpha helix, Left handed helix, 3.10 helix, Pi helix, Beta strand, Antiparallel beta strand and Parallel beta strand) but you can create custom structures selecting Custom and changing the Phi, Psi and Omega torsion values:

The checkboxes at the left of each torsion name allow to enable/disable which angles are changed to the characteristic secondary structure value, eventually preserving the original torsions. Checking Fix bond angles, the bond angles distorted by the rotation of the torsions are reverted to the canonical value and checking Consider selected atoms only, the torsion modification is applied to the selected/visible atoms only, keeping the other atoms unchanged.
Add the side chains and Add the hydrogens checkboxes are intentionally disabled and are operative when you build a peptide from its primary structure (for more information, see how to build a peptide). Clicking Apply button, the secondary structure of the peptide in the current workspace is changed.

WARNING:
the routine changing the torsion angles is working outside the rings. In other words, it's unable to change the secondary structure of cyclic peptides, including peptides with disulfide bridges. To avoid this problem, you could temporally open the ring breaking one bond (e.g. a disulfide bridge or a backbone bond), change the secondary structure and, if it's possible, rebuild the broken bond.

The following table shows Phi, Psi and Omega values of the most common secondary structures:

6.8 Add fragments

VEGA ZZ can edit and build molecules adding new fragments.  This feature is based on the integrated database engine that allows the use of standard fragment libraries and the creation of personalized too.
Selecting the Edit Add Fragments menu item, the following wizard is shown:

As first step, you must select the Group library and the Fragment. The library is automatically opened clicking on the group name. If Inherit residue name option is checked, the added fragment inherits the residue name, the residue number and the chain ID from the main molecule. Checking Inc. residue number, the residue number is automatically incremented starting from the specified number every time that a new fragment is added. That's useful to build a biopolymer.

When you click on the fragment name, its 3D structure is shown in the main window. Select Where to place the fragment in the atom list (After the selected atom, At the residue end and At the molecule end).  Press Next button to continue.

Now you must click the fragment hydrogen in the main window that will be merged with another one of the molecule to make the bond. Press Next to continue.

Selecting the molecule hydrogen and clicking Next button, the bond will be completed.

At the end, you can adjust the torsion angle between the molecule and the fragment clicking the torsion buttons. Click Finish to place definitively the fragment. Now the tool is ready to bind another fragment to the molecule.
Please remember that when the workspace is empty (no molecule loaded), only the first wizard step is operative and Previous button, when active, allows to go to the previous wizard step.

The fragment libraries are zip files placed in the Data/Fragments folder and they are created by Database Explorer. You can use this tool to change/expand the standard database. The preferred file format to use in these libraries is IFF, because it can contain the largest number of information.

6.9 Add hydrogens

In order to add hydrogens to a molecule or to change the ionization state, you can use the following dialog box that can be shown by Edit Add Hydrogens menu item:

6.9.1 Dialog options

In Actions box, you can choose to add the hydrogens and/or to ionize the molecule in the current workspace. You must remember that if you want to ionize, the molecule must have the hydrogens and the algorithm add/remove the hydrogens according to the predicted pKa values and the specified pH.

In Molecule type box, you can select the molecule type (Generic organic, Protein, Nucleic acid), in Position of hydrogens, you can select where the hydrogens will be placed in the molecule file (After each heavy atom or at Residue end) and in Options, you can also choose the nomenclature type used for the hydrogen atoms (normal progressive number or IUPAC nomenclature), the possibility to process the selected atoms only (Consider selected atoms only) and algorithm used to add the hydrogens. More in detail, if you check Use the bond order to assign the atom types, instead of the bond geometry, the bond order is not used to detect the atom hybridization. This feature is useful when the molecule has uncertain geometry (e.g. 2D instead of 3D structure) and the bond order is correctly assigned. When you enable the ionization feature by checking Ionize the molecule, you can also specify the pH of the solution (Ionization pH) in which the molecule is virtually present as solute and the tolerance (Ionization tol., in pH units) used to establish which protonation state is largely present. To this end, the Henderson-Hasselbalch equation is used: if you specify 1 as ionization tolerance, it means that, at the specified pH value, the concentration of the ionized form must be at least 10 times higher than the non-ionized one to consider the molecule as ionized.
Finally, you must click Add to add the hydrogens and/or to ionize the molecule.

6.9.2 About the method to add the hydrogens

To add the hydrogens, the recognition of atom types and valences is needed. The powerful ATDL geometry-independent engine can't be used because the atom valences are incomplete due to the missing hydrogens and so the implemented method is based on the original code included in Babel 1.6 (© 1992-96, W. Patrick Walters, Matthew T. Stahl) that detects the atom valences considering the atomic distances and the bond angles. Unluckily, this is the method limit, because some structures don't have a canonical geometry and so the valence detection can be wrong. VEGA introduces an algorithm that fixes the atom type and the valence detection when the user specify the type of the molecule. You must remember that this check is disabled selecting Generic organic molecule type.
The method can be summarized in the following steps:

• All hydrogens are removed in order to allow the correct atom type detection.

• Atom type and valence attribution: the atom types are detected using the Meng convention (E. Meng and R. Lewis, J. Comp. Chem., 12, pp 891-898, 1991) updating it with Nim atom type to detect the nitrogens in five member rings.

• Optionally, to fix the incorrect atom types, VEGA ZZ uses two templates (NA.hyb for nucleic acids and PROTEIN.hyb for proteins) placed in the Data directory. They are text files witch format is explained in the header.

• The required hydrogens are placed and bonded.

6.9.3 About the method to ionize the molecule

To predict the ionization state of a molecule, the knowledge of the pKa values of each moiety included in its structure is needed. At this time, it was implemented a fast method based on the recognition of acid and basic groups whose pKa values are known. The Handerson-Hasselbach equation is used to evaluate the ratio between the acid/base pairs at the specified pH value and the group is considered ionized only if the this ratio is grater than the ionization tolerance defined by the user. The algorithms is so summarized:

• Recognition of the acid hydrogens by using PKA.tem ATDL template.
• Attribution of the pKa values (see PK.par file in Data directory).
• Deletion of the hydrogens if the ratio between non-protonated (negatively charged) and protonated (neutral) state overcomes the ionization tolerance.
• Recognition of the basic groups by using PKB.tem ATDL template.
• Attribution of the pKa values.
• Addition of the hydrogens if the ratio between protonated (positively charged) and protonated (neutral) state overcomes the ionization tolerance.

All these steps are repeated until there are no hydrogens to add/remove.

6.10 Add a solvent cluster

Choosing Edit Add Cluster in the main menu, you can solvate a molecule with any type of solvent. The list of solvent is dynamically created, reading the ...\VEGA ZZ\Data\Clusters directory and can be refreshed closing and reopening the dialog window. Click here for more information about  the cluster file format.

You can select the type of solvent by the combo-box, but it's also possible to specify an external cluster file clicking the button.  The shape type (Box, Sphere and Layer) influences the meaning of Sides fields. If Type is Box, you can put the solvent box dimensions in Ångström. If Same is checked, the box will be cubic. If Type is Sphere, you can put the Radius of the cluster sphere in Ångström. If Type is Layer, you can specify the thickness of the solvent in Ångström. Overlap parameter indicates the maximum overlapping of the solvent-solute Van der Waals spheres. In Cluster position you can choose where the cluster is placed at the center of the box including the solute (Box center) or at the barycentre of the solute (Geometry center ). When you select Custom, you can specify the coordinates of the cluster centre. This feature is useful when you have to solvate with an asymmetric cluster (e.g. phospholipidic bilayer) and you want to place the solute in the middle. Checking Show the shape, a preview of the solvent shape is shown making easier the cluster setup. Clicking button, the cluster dimensions are automatically calculated on the basis of the solute size. This function isn't available if the shape type is set to Layer.
Click Ok to calculate the cluster.

		Water box (side = 20 Å)
Water sphere (radius = 10 Å)
		Water layer (thickness = 4 Å)

6.11 Add ions

The capability to add the ions is based on the source code (SODIUM by Alexander Balaeff), developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

6.11.1 Usage

Selecting Edit Add Ions in the main menu, you can add one or more counter ions to the active molecule:

You can indicate the number of ions (Ions to add), the Ion element, the Box thickness surrounding the macromolecule,  the Grid step to build the grid used to place the ions, the Atom-ion closest  distance and the Ion/ion closest distance in order to reduce the electrostatic repulsion. More in details, the Box thickness parameter is the thickness of the grid margin, surrounding the macromolecule (in Ångstroms): as an example, imagine a molecule with a cubic shape of 20x20x20 Å. A 10 Å Box thickness means that the ions will be placed in a theoretical box of 40x40x40 Å defining a 10 Å margin around the molecule. If you select Custom as ion type, you can specify other non-predefined ions typing the Element and the Charge in the two fields placed at top right corner of the window. If the molecule charge is a multiple of the ion charge, you can press the Neutralize button to calculate the number of ions needed to neutralize the system.
Click Add button to calculate the position of all ions: be patient, because the calculation is time expensive. The calculation progress is shown by a graphic bar.

WARNING:
If the molecule doesn't have atomic charges, you can't add the ions because isn't possible calculate the electrostatic interactions. In this case, VEGA shows a requester to add the atomic charges.

6.11.2 About the method

This program places the required number of ions around a system of electric charges, e.g., the atoms of a molecule. The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula  is used for the energy:

Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|

All the constants are dropped out from this formula, resulting in some weird energy units; that doesn't matter for the purpose of energy comparison.

To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations. The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function.

6.12 Remove dialogs

VEGA ZZ can remove groups of atoms considering molecule, segment, residue hierarchy.  To remove other groups of atoms,  you can combine the custom selection (View Select Custom) and Edit Remove Invisible atoms menu item.

6.12.1 Remove molecule(s)

The Remove molecule/s dialog is accessible trough the Edit Remove Molecule menu item:

You can delete one or more molecule by multiple selections in the list and clicking Remove button. The selection is highlighted in the main window coloring in red the selected and in white the unselected atoms. You can also select the molecule clicking it in the main window. By checking Center & zoom, when you remove a molecule, the view is automatically centred and zoomed on the remaining atoms.

This window allows also to Select/Unselect and to Move molecules.

6.12.2 Remove segment(s)

This dialog can be shown choosing Edit Remove Segment menu item:

It works in the same manner of the previous one and allows you also to Select/Unselect and to Move molecules. 

6.12.3 Remove residue(s)

To remove one or more residues, one can select Edit Remove Residue main menu item:

This dialog works in a little bit different mode: when you pick a residue atom in the main window,  the residue is removed immediately.

6.13 Build DNA/RNA

By this tool, you can build a nucleic acid (DNA/RNA) from its primary structure in single or double strand form. To show the dialog window, you must select Edit Build DNA/RNA in the main menu.

In the big editing box, you can type the nucleotide sequence or copy & paste it from another application (the characters not corresponding to a nucleotideare automatically removed), using the single character codes. Alternatively, the input can be performed by the four buttons (one for each nucleotide) at the window bottom. In the Type box, you can specify the type of helix you want to build:

• Right handed A-DNA (Arnott)
• Right handed B-DNA (Arnott)
• Right handed B-DNA (Langridge)
• Left handed B-DNA (Sasisekharan)
• Right handed A-RNA (Arnott)
• Right handed A-PRIME RNA (Arnott)

In the Strand box, you can indicate if to build a single (5'  3' or 3'  5') or double (Both) strand, while checking Add hydrogens, the hydrogens are automatically added to the model.

The Build button starts the building of the DNA/RNA.

6.13.1 Copyright

The code implemented in VEGA ZZ is based on Fd_helix program, which is copyrighted by David A. Case. The References for the fiber-diffraction data are:

• Arnott S., Hukins D.W.L., Dover S.D., Fuller W., Hodgson, A.R. "Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations. X-ray diffraction analyses of the molecule conformations of polyadenylic acid, polyinosinic acid, polycytidylic acid", J. Mol. Biol.. Vol. 81-2, 107-122, 1973.
• Arnott S., Chandrasekaran R.,  Birdsall D.L., Leslie A.G.W., Ratliff R.L. "Left-handed DNA helices", Nature, Vol. 283, 743-745, 1980.
• Lakshimanarayanan A.V., Sasisekharan V. "Stereochemistry of nucleic acids and polynucleotides. II. Allowed conformations of the monomer unit for different ribose puckerings",  Biochim. Biophys. Acta, Vol. 204, 49-53, 1970.
• Fuller W., Wilkins M.H.F., Wilson H.R., Hamilton L.D., Arnott, S. "The molecular configuration of deoxyribonucleic acid: IV. X-ray diffraction study of the A form",  J. Mol. Biol., Vol. 12-1, 60-76, 1965.
• Arnott S., Campbell Smith P.J., Chandraseharan R. in "Handbook of Biochemistry and Molecular Biology", 3rd Edition. Nucleic Acids Volume II ,
  Fasman, G.P., ed. (Cleveland: CRC Press, 1976), 411-422.

6.14 Build a peptide

This tool allows to build a peptide from its primary structure, defining the secondary structure type. To show it, you must select Edit Build Peptide in the main menu. The build procedure consists in two phases: 1) construction of the linear peptide; 2) change of the secondary structure.

In the big editing box, it's possible to type the aminoacid sequence or copy & paste it from another application, using the single character codes. Alternatively, the input can be performed by the twenty buttons (one for each aminoacid) at the window bottom. The Structure type box allows to specify the secondary structure type: several pre-defined structure types are already present (Alpha helix, Left handed helix, 3.10 helix, Pi helix, Beta strand, Antiparallel beta strand and Parallel beta strand), but the user can create custom structures selecting Custom and changing the Phi, Psi and Omega torsion values:

The checkboxes at the left of each torsion name allow to enable/disable which angles are changed to the typical secondary structure value, eventually keeping the values of the linear peptide generated in the first building phase.
By default, the tool builds the backbone without hydrogens only, but checking Add the side chains and Add the hydrogens, the user can complete the peptide structure. Clicking Build, the structure is generated in the current workspace if it's empty or in a new one if it contains a molecule.
Fix bond angles and the Consider selected atoms only checkboxes are intentionally inactive and they are operative changing the secondary structure of a 3D peptide.

6.15 Build a solvent cluster

By this dialog box, that can be shown selecting  Edit Build Cluster menu item, it 's possible to build a solvent cluster useful for the solute solvation (for more information, click here). In order to create a new solvent cluster usable by VEGA ZZ, you should follow these steps:

1. Generate the cluster with this tool.
2. Optimize it by MM/MD software (e.g. NAMD, Gromacs, etc).
3. Convert the optimized structure in PDB Fat format enabling bzip2 compression.
4. Rename the file, removing the file extension and capitalizing the name.
5. Copy the file to Data\Cluster directory.

6.15.1 The graphic interface

The following dialog box allows to build a cubic solvent cluster, specifying the dimensions of the box containing a single solvent  molecule (Cell size) and the number of cell copies in X, Y, and Z directions (Cell copies).

Clicking Auto, the cell size is assigned automatically by the monomer dimensions, considering the covalent radii of each atom. Clicking Build, the cluster is generated. The parameters shown above allow to create an ordered cluster.
If you want to obtain a disordered system, you must check Enable in Random rot. group-box, specifying the X, Y and Z  ranges used to generate the random rotation of each monomer placed in the cluster.

This is an application example: a chloroform cluster is built using random rotation with 360º rotation ranges (the same value for all three axis).

If the cell size is too small, the bumping probability between close monomers is high. It's possible to reduce this problem, checking Minimize bumps in the Optimization group-box. The position and the rotation of each monomer placed in the cluster is minimized using the fast Hooke-Jeeves algorithm. You can indicate number of minimization Steps and the RMS. The Overlap field contains the value of the maximum atom overlapping between two near molecules. Enabling Remove molecules, the bumping molecules that can't be optimized, are automatically removed from the cluster.

Clicking View 3D cell, a transparent box is shown in order to highlight the cell dimension. The magenta cross indicates the molecule symmetry center. You can change the molecule orientation in the cell using the move molecule function that can be enabled selecting Move Molecule item in the popup menu.

6.16 Build a molecule with SMILES

6.16.1 SMILES builder

VEGA ZZ can build molecules from their SMILES strings, selecting Edit Build SMILES in the main menu. The 1D structure of the SMILES string is converted to 3D clicking the Build button. You can select Current workspace or New workspace as Destination of the 3D structure.

When you edit the SMILES string, the 2D preview is automatically updated showing the changes.

If the current workspace is not empty, the Get button allows you to convert the 3D structure to a SMILES string. The same operation is possible by selecting Edit Copy special in the main menu and by choosing SMILES, but the resulting string is copied to the clipboard instead of the SMILES window.

6.16.2 Combinatorial SMILES builder

If you need to build a large number of molecules sharing the same scaffold, you can use the combinatorial SMILES builder, whose dialog window can be opened by selecting Edit Build Combi SMILES in the main menu. As in the standard SMILES builder, you can put directly the scaffold structure in the SMILES scaffold field or you can obtain it from the current workspace by clicking Get button. For example, imagine to build a set of derivatives of the benzoic acid:

To insert the variable positions in which the residues will be added, you must move the cursor in the SMILES string and click R button as shown below:

The next step is to add one or more SMILES databases to each variable position (R1 and R2 in this case). You can use a custom fragment database built by you (for more information about the SMILES database format, click here) by double clicking on each position row, by the context menu (Open item) and by drag & drop of the files over the position in the table. Alternatively, you can add the built-in databases by using the context menu. To each position, you can add more than one database and if a position doesn't have any database, it is simply ignored.

You can change the preview by moving the horizontal slider, by typing the compound number or by clicking the up and down buttons. The context menu of the table allows you to remove the fragments of a single position (Remove) or of all positions (Remove all). By the context menu of Scaffold and Preview boxes, you can copy the SMILES strings to the clipboard and print  the structures.

In the bottom right box, you can change the name prefix that will be used for each compound (Compound name field) and some parameters as the type of build. If you check Systematic build, all possible fragment combination are considered, otherwise each fragment is considered only one time. In the case shown above, unchecking Systematic build, only 9 molecules are built that is the smallest number of fragment for a specific position. When you build a large number of derivatives, it may be possible to obtain non-unique molecules for symmetry reasons or due to duplicated fragments in different databases. To avoid this problem, you can check Remove redundant molecules.

The resulting compounds are saved in a SMILES database when you click Build button and if you want canonical SMILES strings, you can check Canonical SMILES.

Notes:

When you obtained the molecules by this tool, it may be needed to convert the resulting SMILES database to another format or to convert the molecules to 3D. You can do these operations in easy way by opening the SMILES database in the database explorer and copying the molecules to an empty database in the format that you need activating the 3D conversion in the Options tab.

6.17 Build a molecule from its IUPAC name

VEGA ZZ can build molecules from their IUPAC name thanks to OPSIN software included in the package, selecting Edit Build IUPAC in the main menu. The  structure is built and converted to 3D by clicking the Build button. You can select Current workspace or New workspace as Destination of the 3D structure.

6.18 Save the molecule

VEGA ZZ uses customized file requesters, allowing to select some options:

To show this dialog box, you must select File Save main menu item or click the disk picture of the Tool bar 1. You can choose the File name and the file format (Save as), but you can also select the Compression mode (None, BZip2, GZip and Z Compress) and the possibility to save the Connectivity and the atom Constraints for the molecular dynamics. Two file formats only are able to store constraint data and they are PDB (in the B column for NAMD) and IFF/RIFF. The Big endian and 64 bit checkboxes are specific for IFF/RIFF format. The former allows to write in big endian format (it's the real IFF written by old VEGA releases) and the latter switches the saver in 64 bit mode in order to write files larger than 4 Gb.
Selecting AMMP and X-Plor PSF  file formats, it's possible to enable the force field parameter check (Force field parm. combo box), in order to fix the missing parameters if they aren't included in the parameter files. If one or more parameters aren't included, the missing parameter table is shown.
The supported file formats are: PDB 2.2 (*.pdb), PDB (*.pdb), PDB non std (*.pdb), PDB Atdl (*.pdb;*.pdba), PDB Fat (*.pdb;*.pdbf), PDBQ (*.pdb), PQR, (*.pqr), PQR XML (*.xml), Insight (*.car), Old Insight (*.car), Alchemy (*.alc;*.mol), AMMP (*.amp), AutoDock 4 PDBQT (*.pdbqt), AutoDock Vina PDBQT (*.pdbqt), ChemSol (*.cs), CIF (*.cif), mmCIF (*.cif), CML 2.0 (*.cml), CML (*.cml), CPMD XYZ (*.xyz), CRD (*.crd), CRT (*.crt), Cssr (*.cssr;*.csr), Fasta (*.fas), Gamess (*.inp), Gaussian cartesian (*.gjf), Gromacs/Gromos (*.gro), Gromacs/Gromos nm (*.gro), IFF/RIFF (*.iff), InChI (*.inchi; *.inc), InChI + Aux (*.inchi; *.inc), InChIKey (*.ikey), Indigo layered code (*.indigo), Info XML (*.xml),  MDL Mol (*.mol), Mol2 (*.ml2;*.mol;*.mol2), Mopac (*.dat;*.arc), Mopac cartesian (*.dat;*.arc), Quanta MSF (*.msf), QMC (*.qmc), SMILES (*.smi), X-Plor PSF (*.psf), XYZ (*.xyz).

Notes:
IFF files are compatible with old VEGA releases (pre-2.0.6 and pre-1.5.6) saving them in 32 bit big endian format (Big endian checked and 64 bit unchecked).

6.19 Merge with another file

VEGA ZZ can merge the molecule in the current workspace with one or more parts of another molecule. Choosing File Merge menu item, you can select the file to merge (source) with the molecule already in memory (target). In the dialog box, you can choose the fields included in the source molecule that will be read to be merged with the target:

The source and the target molecules must be compatible, otherwise an error message is shown (they must have the same number of atoms). It's possible to merge source and target molecules with a different number of atoms, selecting an atom subset of the target and checking Consider selected atom only. Obviously, the subset target must have the same number of atom of the source.
All and None buttons are useful to check/uncheck all fields at once. Merge button performs the merge.
Not all merge fields could be enabled, because not all file formats contains all information. The following table shows the fields that can be merged for each source file format:

Format

Elements

Atom names

Atom types

Atom charges

Residue names

Residue numbers

Chain IDs

Segments

Molecule IDs

Coordinates

Connectivity

Constraints

Alchemy

AMMP

AutoDock 4 PDBQT

CAR (old/new)

Chem3D

ChemDraw CDX

ChemSol

CIF/mmCIF

*

CML 1.0/2.0

CPMD XYZ

CRD

CRT

CSSR

Fasta

EMPIRE

GAMESS

Guassian input

Gaussian output

Gromos/Gromacs

HyperChem

IFF/RIFF 32/64 bit

LiGen binary/text pocket

MDL Molfile

MDL Extended Molfile

Mol2

Mopac cartesian

Mopac internal

Mopac Gaussian Z-matrix

MSF (Quanta)

NAMD binary

PDB

*

PDB 2.2

*

PDBA

*

PDBF

*

PDBL

PDBQ / Vina

*

PQR

*

PQR XML

QMC

Spillo RBS

TINKER XYZ

X-Plor PSF

XYZ

* The connectivity can be merged only if it's present in the file.

WARNING:

1. Isn't possible to merge molecules with a different number of atoms. If you want force the merge and the target atoms are more than source atoms, you can select a target atom subset and check Consider selected atom only.

2. If source and target have the same number of atoms, but differences in the element position are detected, a warning message is shown, allowing to choose to continue or to abort the merge.

6.20 Save the trajectory

VEGA ZZ allows to save/merge a MD trajectory file selecting the frames and changing the output format (trajectory or video stream). It supports both trajectory and video file formats. To show the following dialog window, you must select File Save Trajectory in the main menu:

By this file requester, you can choose the file name, the output format, the starting (Start) and the ending (End) trajectory frames and the number of skipped frames (Skip). The Active only option allows to save the active/visible atoms only (see the atom selection). You must remember that if you activate this option, the resulting trajectory isn't compatible with the molecule file used to open the starting one. By this way, you must remove the invisible atoms (Edit Remove Invisible atoms) and save the reference molecule file with the number of atoms compatible with the new trajectory (File Save as ...).
The Swap endian option is available for the CHARMM/NAMD DCD and IFF/RIFF formats only and it changes the byte order (big or little endian) in the resulting binary file, because this format is machine-dependent and it requires a conversion to be readable by specific CPU architectures. VEGA and VEGA ZZ don't require this conversion because they are able to detect the endian of the DCD and IFF/RIFF files and to check the hardware numeric format, applying the endian change if it's required. IFF/RIFF files are written in 64 bit mode in order to avoid the 4 Gb size limit.
The FP precision slider is active only if the Gromacs XTC file format is selected and it can be used to change the floating point precision to store the numbers in the output file (XDRF comtression). The floating point precision is expressed in decimal numbers after the point: e.g. a FP precision of 3 means that the coordinates expressed in Ångström (and not in nanometres) are stored with a precision of 0.001. Remember that higher precisions induce lower compression ratios and consequently larger files.

When you select a file name of an existing trajectory and click the Save button, a window is shown in order to choose the preferred operation:

Clicking Overwrite button, the pre-existent file will be overwritten, clicking Append button, the trajectory will be added to the end to the pre-existent file and clicking Cancel the save process will be aborted. The Append option isn't available when you select a video format.

The following table reports the file trajectory formats written by VEGA ZZ: the first column is the format name, the second one is the file extension, the third one is the type (T = trajectory, V = video),  the fourth indicates if the file is compressed:

When you select a video file format, another window is shown  to choose the suitable video encoding options (for more information, click here).

6.21 The clipboard

By Windows clipboard, it's possible to perform cut, copy and paste operations between different VEGA ZZ sessions and/or VEGA ZZ and other applications. VEGA ZZ has an enhanced implementation of the clipboard that allows manage some object types:

6.21.1 Files

You can copy files directly from Explorer into VEGA ZZ without the use of the File Open menu item.

Paste

6.21.2 Text

You can copy raw text from any application into VEGA and from VEGA to another application.

Copy text from VEGA:

Copy

Paste

Copy text and paste to VEGA:

Paste

You can also copy text including an URL or a .url file and paste to VEGA ZZ that download automatically the molecule for you.

6.21.3 Bitmap

You can copy bitmap graphic from VEGA ZZ to your preferred paint software.

Copy

Paste

6.21.4 Molecule objects

You can cut, copy and paste molecule objects between two or more VEGA sessions. Only the visible atoms are cut or copied to the clipboard, preserving all attributes.

Paste

7.1 Atom selection

You can hide and/or show atoms using the menu items in View Select in order to change the properties of the visible atoms only (e.g. color, measure, etc). If the predefined selections are insufficient, it's possible to create a custom selection, that can be made by atom specification, by range, by proximity and slice. This dialog box can be opened selecting the View Select  Custom item in the main menu.
All four operating modes share some input fields. You can create a totally new selection or you can update a pre-existing selection, clicking the Normal or Additive item in the Selection box. The box placed at right window corner contains the control buttons: All selects all atoms, None deselects all atoms, Invert inverts the selection, and adds/removes the atoms using the selected criteria. The Hydrognens, Backbone and Water buttons are for fast selections: the first one selects all hydrogens, the second one selects the backbone atoms and the third one selects the water molecules. Checking Invert, the meaning of the above buttons is inverted (e.g. clicking Hydrogens, all hydrogen atoms are unselected). The Display box contains controls useful to change the visualization in selective way: you can change the visualization mode (Don't change, Wireframe, CPK dotted, CPK wireframe, CPK solid, Ball & stick wireframe, Ball & stick solid, Stick wireframe, Stick solid, Tube and Trace) and the color of groups of atoms. This last option is enabled only if Change color is checked. For more information, see the Display modes section.

7.1.1 Selection by atom(s)

Examples:

The Reset button cleans the Selection field.

7.1.2 Selection by range

7.1.3 Using the proximity tool

7.1.4 Slice selection

7.2 Display modes

You can change the display mode of the active/visible atoms by View Display item of the main menu or Display item of the context menu or the atom selection dialog box. You can switch between wireframe, CPK dotted, CPK wireframe, CPK solid, ball & stick wireframe, ball & stick solid, stick wireframe, stick solid, trace and tube visualizations.

		Wireframe
CPK dotted
		CPK wireframe
CPK solid
		Ball & stick wireframe
Ball & stick solid
		Stick wireframe
Stick solid
		Tube
Trace

You can change some visualization parameters with the View Settings dialog. Click here for more information.

7.3 View settings

You can open the display settings dialog by View Display Settings item of the main menu or the Display Settings item of the context menu. Press the Done button to close the dialog.

7.3.1 General settings

The general settings are accessible in the bottom panel of the window. There are five tabs: Main, Axis, Fonts, Stereo and Refresh.

7.3.1.1 Main settings The Antialiasing combo box controls the hardware multisample anti-aliasing, if it's supported by the graphic card. The selectable values are in the 2 to 16x range (usually 2 to 6x) depending on the card features. Higher values allow to obtain better graphic quality. The Vector Antialiasing checkbox enables the hardware aliasing reduction for the lines only. Not all graphic accelerators have a full implementation of this function.   Anti-aliasing disabled Anti-aliasing enabled The Depth cueing checkbox enable the OpenGL fogging function in order to simulate the color variation of the objects more distant from the view point.

Depth cueing disabled	Depth cueing enabled

The Z clip slider allows to change the clipping value along the Z axis.

Z clip = 170	Z clip = 64

The Smart move checkbox allows to improve the 3D graphic feedback of big molecules switching the visualization in wire frame mode (the fastest available) when the user rotate/translate the molecule. This operation is done automatically if the molecule exceeds the specified number of atoms (Atoms field).
Default button reverts all parameters to the original (default) state/value.

7.3.1.2 Axis settings By Axis tab, it's possible to manage the Cartesian axis. They can be customized in several ways: you can change the Position (top left, top center, top right, center left, centered, center right, bottom left, bottom center and bottom right), the Style (solid and vector), the Scale %, the Width, the Resolution (available with the solid style only) and the colors of the axis and the labels.

7.3.1.3 Font settings In this tab, you can change font parameters  used in the 3D visualization.  The font Type could be Bitmap (standard quality), True Type  (best quality) and Stroke (fastest visualization). Bitmap and True Type fonts can be changed in the Font field but Stroke font can't be modified. Bitmap fonts have fixed sizes (see Size field), while True Type and Stroke fonts have variable sizes (see Scale slider). The Resolution slider is active for True type fonts only: it allows to change the detail level (from 0 to 100%), but you must remember that high details reduce the rendering speed. When the WireGL rendering is enabled, the Stroke font type is the only available.

7.3.1.4 Stereo settings A very interesting feature implemented in VEGA ZZ is the stereoscopic view. Different stereo modes are available: Active glasses This method offers a good experience of view but requires special hardware: a graphic card operating in stereo mode (cheap cards don't support it), a monitor supporting refresh rates greater than 100 Hz and shutter glasses (e.g. CrystalEyes by RealD Inc., NVIDIA 3D Vision). Anaglyph It is the cheapest way to have a stereoscopic view because requires inexpensive anaglyph glasses (they are glasses with polarized lens). The stereo experience is poor because this visualization method shows the scene only in gray scale or with a reduced set of color. The Anaglyph filter option allows to change the lens color in order to make VEGA ZZ compatible with a specific type of glasses. Side-by-side (SBS) It gives the best stereoscopic experience in particular if you are using head sets such as Oculus Rift and HTC vive. It is also named full side-by-side and can used with the modern 3D TV. Cross-eye The rendering method is the same of SBS, but the left and right frames are swapped. Half side-by-side (HSBS) The rendering method is the same of SBS, but a single frame is intended for both eyes at the same time with two halves on the left and right, and the entire frame for the left eye and right eye respectively scaled down horizontally to fit the left-half and right-half of the frame. In other words, the horizontal resolution is divided by two and the pixel aspect ratio is set to 1:2. Top and bottom (TAB) This method is similar to SBS, but instead to store left- and right-eye views a whole horizontally, the two frames are assembled vertically (top and bottom). Half top and bottom (HTAB) It is similar to TAB, but the vertical resolution is halved and the pixel aspect ratio is set to 2:1.    When you switch to this stereo mode, you can adjust the Eye offset and the Shift adjust to optimize the stereo effect.   Red-cyan stereo picture (Eye offset 0,1). WARNING: The Matrox FSAA 16x (implemented in the P-Series graphic cards) introduces artefacts in anaglyph stereo mode. For best results, disable it in the PowerDesk HF control panel. To save the pictures, use the offline software rendering enabling the 4 or 16x anti-aliasing for best results.   Checking 10 bit pixel format, 10 bits for each color channel are used instead of 8, obtaining a smoother view (230 = 1.073.741.824 vs. 224 = 16.777.216 colors). When you enable this feature, a requester is shown asking you to restart VEGA ZZ. If after the restart, 10 bit pixel format is unchecked, it means that your graphic card doesn't support the 10 bit color mode. A limited number of professional graphic cards supports this pixel format (e.g. AMD/ATI FireGL and NVIDIA Quadro) and, in some cases, must be enabled in the control panel. Moreover, a specific monitor is also required (e.g. HP DreamColor, Eizo ColorEdge series).

7.3.1.5 Refresh settings This tab allows to set refresh parameters useful to obtain smooth animations and fast graphic interface feedbacks. Checking Fast refresh, the main window refresh is done in a very fast mode: a copy of the scene is kept in the back buffer and when a repaint is requested, the scene is copied from the back to the front buffer without redrawing it. This procedure noticeably improve the main window refresh, but not all graphic cards support it. If you enable it and you have main window corruptions and artefacts when you translate the windows, your graphic card isn't compatible with the fast refresh mode. It's well know that this refresh mode is compatible with Matrox Graphics cards and with Microsoft and MESA 3D generic OpenGL drivers. The Animation frame rate (fps) field allows to change the maximum frame rate used during the animations: higher values correspond to smoother animations. Please remember that you can't override the graphic card refresh rate because VEGA ZZ is synchronized to it. As an example, if the graphic card refresh rate is set to 85 Hz, you can't obtain an animation frame rate greater than 85 frame per second. Animation timing sets the base speed used in the animations.

7.3.2 Wireframe settings The Smooth mode beautifies the vector visualization: Disabled Enabled The Multivector mode allows to view the molecule bond types (single, partial double, double and  triple): Disabled Enabled The Thickness slider changes the line thickness (from 1 to 5).

7.3.3 CPK settings You can adjust the sphere resolution (high best view more rendering time) and the dot size for dotted Van der Waals visualization.

7.3.4 Ball & stick settings You can adjust the sphere and the cylinder resolution. You can change also the sphere scale and the cylinder radius.

7.3.5 Stick settings For this display mode, you can change the resolution and the cylinder radius.

7.3.6 Tube settings For the tube visualization, you can change the interpolation type (cubic or biquadratic), the spline resolution, the cylinder resolution and the cylinder radius.

7.3.7 Trace settings For the trace visualization, you can change the cylinder resolution and the cylinder radius.

7.4 Molecule colors

The color of visualized atoms can be changed selecting the items in View Color menu (click here for more information). The coloring methods are:

	Color by atom (white = hydrogen, green = carbon, red = oxygen, blue = nitrogen, yellow = sulfur, cyan = fluorine, magenta = chlorine or unknown atom, orange = bromine, violet = iodine).

Color by residue

	Color by chain

Color by segment A different color is selected for each segment (e.g. protein, water, ligand) in the molecule or assembly.

Color by molecule

Color by H-Bond It colors the H-bond acceptor (blue) and donor (magenta) atoms.

Color by charge The color ramp indicates the more negative (blue) and the more positive (red).

Color by constraint  It colors the molecule by constraint: blue fixed, green freed.

If you want to change the color schemes, you must use Color settings dialog. Using the View Color Selection menu item, it's possible to choose the color of the visible atoms from the color table, as shown below:

To apply the color changes, you must click Ok button or double click the color box.

7.5 Color settings

Thanks to this dialog box that can be visualized selecting View Color Settings, it's possible to change some interesting color parameters for a nice view.

7.5.1 Background settings

7.5.2 Atom settings

7.5.3 Residue settings

7.5.4 Monitor settings

7.5.5 Other settings

In this tab, you can change the color of the H-bond acceptors, H-bond donors and non H-bond involved atoms. Moreover, you can change the color of flexible and rigid bonds.

7.6 Light settings

This dialog box can be shown by selecting View Light in the main menu and allows the light source management.

VEGA ZZ light engine supports up to four directional light sources and one ambient light. The number of the directional light could be reduced to one if the graphic card OpenGL driver doesn't support more than one light source. Each light source, selectable by Sources box, can be independently enabled or disabled (see Enabled checkmark in Position box) and moved in the scene clicking the small buttons in the corners of the blue box. To move inside the blue box position layers, you must click the layer outside the small buttons and to show all layers, you must click button. For each light source, in the Light colors box, you can change the diffusion and the specularity colors. You can also switch on/off the ambient light and change its color (see Ambient light box).
In Lighting window, you can change Material properties as the specularity (from 0 to 100), the shininess (from 0 to 100) and the vector reflection (enabled/disabled).
To revert to pre-defined lighting parameters, you can click Default button.
The lighting engine could be disabled unchecking the Lighting enabled item at top-left window position.

7.7 Molecule information

VEGA ZZ can calculate many information about the molecule in the current workspace: total number of atoms, number of heavy atoms, number of residues, number of contained molecules, number of water molecules, molecular weight, coordinates of geometric center, coordinates of mass center, approximate dimensions, total charge (calculated using the atomic charges), dipole, surface area, surface diameter, volume, volume diameter, ovality, Crippen's logP (A.K. Ghose, A. Pritchett , G.M. Crippen, "Atomic Physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: Modelling Hydrophobic Interactions", J. Comput. Chem., Vol. 9, 80-90 (1988)) and lipole, Broto's logP (P. Broto, G. Moreau, C. Vandycke , "Molecular Structure: perception, autocorrelation descriptor and SAR studies", Eur. J. Med. Chem.,  Vol. 19, 71-78 (1984)) and lipole, Virtual logP, polypeptidic charge, amino acidic or nucleotidic composition.

Selecting View Information from the main menu, the VEGA ZZ shows a dialog box in which it's possible to set the probe radius for surface calculations and the maximum number of allowed atoms for time-expensive calculations (e.g. volume, surfaces, Virtual logP, etc). To perform all calculations, you must click Calculate button or select Calculate item from File menu.

7.7.1 The menu bar

The menu bar functions are summarized in the following table:

WARNING:

Any change to the probe radius field has effects on surface calculations only and not on the volume.

7.8 Hydrogen bonds

VEGA ZZ can evaluate the hydrogen bond energy by CHARMM force field implemented in HyperDrive library. The hydrogen bonds are highlighted in the main window in order to analyze them. The hydrogen bonds dialog is shown selecting Measure Hydrogen bonds in the context menu (press right button on the 3D visualization area):

In the Donors/Acceptors boxes, you can select which atoms will be considered in the evaluation of the H-bonds. The Parameters box includes the force field parameters: Cutoff, Threshold, Attractive exponent, Repulsive exponent, HA angle cosine exponent and AA angle cosine exponent. For more information about these parameters, see the CHARMM force field documentation. Checking the Selected atom only field, the active/visible atom will be considered only and checking Save the results, all H-bond are stored in a CSV or DIF file. Label box allows to choose which labels are shown for each h-bond detected by the algorithm. Default button resets all parameters to the default condition, and Show button starts the evaluation of H-bonds.

7.9 Save the image

VEGA ZZ allows to save the current molecule as 2D, 3D, 360° panorama and cubic panorama sketches to bitmap and vector-based files. This function is useful to insert images in documents (e.g. Microsoft Word, HTML pages, etc). To show the following dialog window, you must select File Save image in main menu or click the camera picture of the Tool bar 1:

The following table shows the file formats supported by VEGA ZZ: the first column is the format name, the second one is the file extension, the third one is the type (V2 = vector-based 2D, V3 = vector-based 3D and B = bitmap) the fourth one is the image type (2D = 2D sketch, 3D = 3D view, 360° = 360° equirectangular and cube panorama) and the last one indicates if the effects are applicable:

The Rendering modes and the Effects are available for the 3D bitmap formats only. The Snapshot mode does an exact copy of the current view with the same resolution. If you want to obtain an image differing from the size of the current view, you must use Hardware or the Software modes. In both cases, you can choose a pre-defined  or a custom resolution. The Hardware rendering is performed directly by the GPU (Graphic Processing Unit)  installed in the graphic card and uses its memory. The resulting rendering is better than the software-based, because it applies the enhanced hardware anti-aliasing and the texture filtering (if they are available). You must remember that the this feature is available in high-performance graphic cards with a strong OpenGL support (e.g. ATI, NVIDIA and Matrox). If your display adapter doesn't support this rendering mode, an error message is shown.  Another problem afflicting this mode, is the memory installed on the graphic card that influences the maximum rendering resolution. For this reason, if you try to render a bitmap larger than the graphic memory, an error message is shown. Graphic cards with at least 128 Mb of RAM are recommended for this operating mode. The Software rendering mode works with all graphic cards, because it uses the system memory instead of the hardware features. In this way, it's possible to render very large images, but the quality isn't so good, even if often it's comparable to that of a cheap graphic card. The real limit of the Software rendering is inside the Microsoft OpenGL driver: it supports one light source only and so it's impossible to render all four light sources that VEGA ZZ can manage. To improve the Software rendering, you could activate the AntiAlias option reducing the jagged edges. The algorithm oversamples the image (4x or 16x) increasing its size to 2x or 4x, performing a more precise rendering. Finally, it resizes the image to the user-defined dimension applying  a smoothing pixel algorithm. The 16x AntiAlias generates better images but it requires a lot of memory.
 

If the output format is a true-color bitmap file, it's possible to apply some Effects:

		Picture without effects
Gaussian blur
		Emboss
Gray scale
		Gray scale + emboss

Notes about the vector file formats:
The conversion of an OpenGL scene to a 2D vector scene is very complex and requires some computational time. Not all OpenGL objects can be rendered and so is possible that some details are missing in the rendered file (e.g. transparencies, smooth vectors). Please remember that VEGA ZZ doesn't require the expensive Adobe Acrobat to create the PDF file. Click here to see an example of a PDF file.
The conversion to the VRML format is provided by the Gl2Vrml library that reconstructs the three-dimensional scene decoding the OpenGL feedback buffer and this operation is very fast thanks to the code optimization (SSE, 3DNow! and parallel code). To show the VRML world, a VRML viewer is required (e.g. ParallelGraphics Cortona VRML Client or Cosmo Player).

Download a VRML 2.0 plug-in to show the 3D object

VRML 2.0 output example

The POV-Ray output is provided in order to render the scene with the Persistence of Vision Ray Tracer. You must remember this implementation is experimental and the polygons outside the OpenGL view port are cut-out from the final scene creating uncompleted objects.

POV-Ray rendering example

7.10 Video encoding

VEGA ZZ can encode video streams that the user can include in PowerPoint presentations, HTML documents, Video CD/Super Video CD/DVD medias, on-line video streaming applications, etc. At this time, it's possible to convert MD trajectories to high quality videos choosing the Save trajectory item in the File menu. When the video format is selected, the codec option window is shown:

A codec is a software component with the capability to encode and decode audio/video streams. In the Codec list, you can select the codec that will be used to encode the video stream. Each codec has specific application fields and you should select the more suitable one. As an example, if you want to perform video editing, the best choice is a codec with low compression ratio for the best quality and full frame encoding (e.g. Huffyuv, DV, M-JPEG, Lagarith). In this specific application field, you can't use MPEG-1, MPEG-2, DivX, XviD (MPEG-4) because not all frames are full encoded but some of them are compressed by difference from the previous one. The  video editing requires "single frame" precision cut,  that isn't possible when you use MPEG encoding methods.
In the Video codec information box, the properties of the selected codec are shown: the FOURCC code is a four character string used by  Windows Multimedia System to recognize and manage the codec and it's the same used in the AVI file header, Driver name is the DLL file name encapsulating the codec, Delta frame indicates if the codec supports delta frames and Format restrictions reports limits and warnings about  the codec.
The Quality slider allows to change the compression quality (high quality = low compression ratio) or the bitrate for MPEG-1 and MPEG-2 (VOB) compression. The bitrate must be correctly selected if you want obtain standard medias: e.g. if you want to create a Video CD (VCD), you must select MPEG-1 compression and 1150 as bitrate to obtain a full compliant media.
About button shows the codec copyright message and Configure button opens the codec control panel, if it's available. To configure the codec, you must consult its documentation.
In Rendering mode box, you can select the rendering method (for more information, see the Save image section).
In Resolution box, you can select the frame size only if the Hardware or the Software rendering modes are selected. It's also possible to enter custom resolutions. In the following table, the standard frame sizes are shown: