4. The main menu OpenGL

Main menu structure

From the VEGA main menu, you can select the most important functions. The item layout is organized in menu bar, menu and sub-menu. 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).

 

4.1 File menu

Item Subitem Accelerator CmdName Description
New   Ctrl+N mNew deletes all objects (molecules, surfaces, etc). A confirmation request is shown.
Open   Ctrl+O mOpen opens a new molecule. The multiselection is allowed
Save As...   Ctrl+S mSave saves the molecule/assembly.
Compression None - mCmpNone allows to select the compression mode (none, BZip2, GZip and Z Compress), that is used when the molecule is saved (see Save As...). If you select none, the saved file will be uncompressed.
  BZip2 - mCmpBz2
  GZip - mCmpGz
  Z-Compress - mCmpZ
Connectivity   - mConnect if checked, creates the connectivity when you save a molecule (see Save As ...).
Save Bmb   - mSaveBmp saves the GL window into a bitmap file.
Print   Ctrl+P mPrint makes the hardcopy of the current 3D window rappresentation.
Demo mode Run Ctrl+D mDemoStart stars the demo.
  Stop - mDemoStop stops the demo.
  Music - mDemoMusic if checked, plays the background music during the demo execution.
  Titles - mDemoTitles if checked, shows the subtitles during the demo execution.
Exit   ESC mExit closes VEGA. If a molecule is loaded, a requester is shown.

 

4.2 Edit menu

Item Subitem Accelerator CmdName Description
Remove Hydrogens - mRemoveHydrog removes all hydrogens from the molecule.
  Water - mRemoveWater removes water molecules from the assembly.
  Surface - mSurfRemove removes the calculated surface.
Ren. Residues   - mRenumberRes renumbers the residue sequence.
Normalize   - mNormalize normalizes the coordinates.
Copy Bmp     CopyBmp copies the current 3D view into the clipboard using the bitmap format

 

4.3 View menu

Item Subitem Accelerator CmdName Description
Display Wireframe V mShowWire switches the current display mode in Wireframe, Van Der Waals with vectors, Van der Waals solid, CPK with vectors and CPK solid.
  VdW mShowVdwWire
  VdW Solid mShowVdw
  CPK mShowCpkWire
  CPK Solid mShowCpk
Color By atom - mColorByAtom sets the molecule color by atom.
  By molecule - mColorByMol sets the molecule color by molecue.
Label atom Off - mLblOff no atom labels.
  Name - mLblAtmName shows the atom labels by name.
  Element - mLblAtmElement shows the atom labels by element.
  Number - mLblAtmNumber shows the atom labels by atom number.
  Type - mLblAtmType shows the atom labels by atom type (force field).
  Charge - mLblAtmCharge shows the atom labels by atom charge.
Reset                          - mResetView resets the current view, resetting the rotations, the translations and the scale factor.
Animation   A mAnimation if checked, enables the animation mode. You can use the mouse and/or the keyboard to change the animation.
Light   L mLight if checked, enables the OpenGL light effects (shades, reflections, etc).
Information   - mMoleculeInfo shows the informations about the molecule.

 

4.3 Calculate menu

Item Subitem Accelerator CmdName Description
Charge & Pot.   - mCalcCharge assigns the atomic charges and/or potentials.
MoPac   - mCalcMoPac opens the dialog window for MoPac calculations.
Surface Calculate - mSrfCalc calculate a surface.
  Save - mSrfSave saves the calculated surface.
  Color - mSrfColor opens the dialog window to change the color of the surface.
  Remove - mSrfRemove removes the surface (there is the same item in Edit -> Remove -> Surface)
Cluster   - mCalcCluster adds a solvent cluster.
Analysis   - mAnalysis opens the dialog box to analyze a molecular dynamic trajectory file.
BioDock   - mBioDock starts the graphic interface for BioDock (molecular docking package).

 

4.4 Tools menu

Item Subitem Accelerator CmdName Description
GraphED   - mGraphEd starts the graphic editor for data manipulation.
MiniED   - mMiniEd starts the mini text editor that is integrated in VEGA.
WinDD   - mWinDD executes WinDD to decompress the data files.
Task Manager   Ctrl+T mTaskMan opens the integrated task manager to manipulate the running tasks (e.g. MoPac, BioDock, ecc).
Edit Prefs   - mPreferences opens the MiniED with preferences file (Vega\Data\prefs).

 

4.5 Help menu

Item Subitem Accelerator CmdName Description
Contents   - mHlpContents opens this help.
MoPac manual   - mHlpMoPac opens the MoPac manual.
Keys   - mHlpKeys shows a window with the list of all key with the associated finctions.
VEGA on the Web   - mHlpWeb points your default Internet browser to VEGA main page.
About   - mHlpAbout shows the copyright message.