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. Please remember that only the IFF format stores all atom information and this is useful to create sanpshots of the current work.
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 Image   - mSaveImg

saves the GL window into a bitmap file. The supported formats are: Windows Bitmap (.bmp), Compuserve GIF (.gif), JPEG (.jpg, .jpe, .jpeg), OpenIL (.oil), ZSoft PCX (.pcx), Portable Network Graphics (.png), PNM (.pnm, .pbm, pgm, ppm), Raw data (.raw), Silicon Graphics (.sgi), Targa (.tga) and Tiff (.tif).

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.

Last file(s)   - -

it's the list of the last four files opened. Using these items, you can re-open the files directly without the use of the file requester of the Open item.

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.
Cut   Ctrl+X mCut cuts the current 3D view and puts it into the clipboard.
Copy   Ctrl+C mCopy

copies the current 3D view into the clipboard using the custom VEGA format.

Copy Special   - mCopySpecial opens a requester in order to select the format used to put the data into the clipboard.
Paste   Ctrl+V mPaste pastes the data from the clipboard.

 

4.3 View menu

Item Subitem Accelerator CmdName Description
Select All - mSelectAll selects all atoms.
None - mSelectNone unselects all atoms.
Invert - mSelectInvert

inverts the current selection. In other hands, it swaps the invisible with the visible atoms.

Backbone - mSelectBackbone shows the backbone.
No hydrogens - mSelectNoHyd hides the hydrogens.
No water - mSelectNoWater hides the water molecules.
Custom - mSelectCustom

opens the dialog box for custom selection.

Display Wireframe V mShowWire

switches the current display mode in Wireframe, Van der Waals dotted, Van der Waals vectorized, Van der Waals solid, CPK with vectors, CPK solid and liquorice.

VdW Dotted mShowVdwDot
VdW mShowVdwWire
VdW Solid mShowVdw
CPK mShowCpkWire
CPK Solid mShowCpk
Liquorice mShowLiquorice
Settings - mShowSettings shows the display settings dialog box.
Color By atom - mColorByAtom sets the molecule color by atom.
By residue - mColorByRes color the molecule by residue.
By chain - mColorByChain color the molecule by chain identificator.
By molecule - mColorByMol sets the molecule color by molecue.
By charge - mColorByCharge

color the atoms on the basis of the partial charges.

Selection - mColorSel color all displayed atoms with the specified color.
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).
Console   - mConsole Show/hide the console window.
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).

Interactions   - mInteractions

opens the dialog for the evaluation of the interactions.

 

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   F1, Ctrl+H 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.
Last error   - mHlpLastErr shows the last error message.
VEGA on the Web   - mHlpWeb points your default Internet browser to VEGA main page.
About   - mHlpAbout shows the copyright message.