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

Delete all objects (molecules, surfaces, etc). A confirmation request is shown.

Open   Ctrl+O mOpen

Open a new molecule. The multiselection is allowed.

Merge   Ctrl+M mMerge

Merge a file with the molecule already loaded. It's possible to select the sections to merge (e.g. coordinates, connectivity, residue names, etc).

Save As...   Ctrl+S mSave

Save the molecule/assembly. Please remember that only the IFF format stores all atom information and this is useful to create snapshots of the current work.

Compression None - mCmpNone

This submenu 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 it's checked, when you save a molecule (see Save As ...) the connectivity is created.

Constraints   - mConstrSav

If it's checked, the constraint data is saved. The file formats that can include this information are: IFF, PDB, PDBA, PDBF, PDBNOTSTD (according to NAMD convention). 

Save Image   - mSaveImg

Save 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

Perform the hardcopy of the current 3D window representation.

Demo mode Run Ctrl+D mDemoStart Start the demo.
Stop - mDemoStop Stop the demo.
Music - mDemoMusic

If it's checked, when the demo run, the background music is played.

Titles - mDemoTitles

If it's checked, the subtitles are showed 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

Close VEGA. If a molecule is loaded, a requester is shown.

 

4.2 Edit menu

Item Subitem Accelerator CmdName Description
Add Atom - mAddAtom

Add one or more atom with specific hybridization and bond type.

Bonds - mAddBonds Add one or more bonds.
Centroid - mAddCentr

Add one or more centroid (pseudoatom).

Cluster - mAddCluster Add a solvent cluster.
Ions - mAddIons Add ions to the molecule.
Remove Molecule - mRemoveMol

Remove one or more molecules.

Segment - mRemoveSeg

Remove one or more segments.

Atom - mRemoveAtom

Remove interactively one or more atoms.

Centroids   mRemoveCentr

Remove all centroids.

Invisible atoms - mRemoveInvisAtm

Remove all invisible atoms.

Hydrogens - mRemoveHydrog

Remove all hydrogens from the molecule.

Water - mRemoveWater

Remove water molecules from the assembly.

Bonds - mRemoveBonds

Remove one or more bonds.

Surface - mSurfRemove

Remove the calculated surface.

Build Solvent cluster   mBldClust

Show the dialog to build a solvent cluster.

Change Atom/residue/chain - mEditAtm

Allow to change the atom, residue and chain properties. 

Bonds - mChangeBonds

Change the bond type.

Torsion - mChangeTorsion  
Ren. Residues - mRenumberRes

Renumber the residue sequence.

Coordinates Apply transf. - mApplyTransf

Apply the transformation matrix to the atomic coordinates.

Normalize - mNormalize

Normalize the coordinates.

Invert Z coordinates - mInvertZ

Invert the Z coordinates in order to obtain the enantiomer.

Constraints - mConstraints

Select atom constraints for molecular dynamics simulations.

Segments Fix - mSegFix

Find the segments in the active/visible atoms.

Merge - mSegMerge

Merge the active/visible segments.

Cut   Ctrl+X mCut

Cut the current 3D view and put it into the clipboard.

Copy   Ctrl+C mCopy

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

Copy Special   - mCopySpecial

Open a requester in order to select the format used to put the data into the clipboard.

Paste   Ctrl+V mPaste

Paste the data from the clipboard.

 

4.3 View menu

Item Subitem Accelerator CmdName Description
Select Molecule - mSelectMolecule Select one or more molecule.
Segment - mSelectSegment Select one or more segments
All - mSelectAll

Select all atoms.

None - mSelectNone

Unselect all atoms.

Invert - mSelectInvert

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

Backbone - mSelectBackbone

Show the backbone.

No hydrogens - mSelectNoHyd

Hide the hydrogens.

No water - mSelectNoWater

Hide the water molecules.

Custom - mSelectCustom

Open the dialog box for custom selection.

Display Wireframe V mShowWire

Switch the current display mode to 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

Show the display settings dialog box.

Color By atom - mColorByAtom

Set 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

Set the molecule color by molecule.

By segment - mColorBySeg Color the molecule by segment.
By charge - mColorByCharge

Color the atoms on the basis of the partial charges.

By constraint - mColorByConstr Color the atoms by constraint value (blue fixed, green free).
Selection - mColorSel

Color all displayed atoms with the specified color.

Label atom Off - mLblOff

No atom labels.

Name - mLblAtmName

Show the atom labels by name.

Element - mLblAtmElement

Show the atom labels by element.

Number - mLblAtmNumber

Show the atom labels by atom number.

Type - mLblAtmType

Show the atom labels by atom type (force field).

Charge - mLblAtmCharge

Show the atom labels by atom charge.

Fixing value - mLblAtmFixVal

Show the atom labels by fixing value (constraint).

Residue - mLblResidue

Show the residue labels with name, number and chain.

Residue name - mLblResName

Show the residue name labels.

Residue number - mLblResNumber

Show the residue number labels.

Reset                          - mResetView

Reset the current view, resetting the rotations, the translations and the scale factor.

Animation   A mAnimation

If it's checked, the animation mode is enabled. You can use the mouse and/or the keyboard to change the animation.

Light   L mLight

If it's checked, the OpenGL light effects are enabled (shades, reflections, etc).

Console   - mConsole

Show/hide the console window.

3D controls   - m3dControls Show/hide the 3D control window.
Information   - mMoleculeInfo

Show the information about the molecule.

 

4.3 Calculate menu

Item Subitem Accelerator CmdName Description
Charge & Pot.   - mCalcCharge

Assign the atomic charges and/or potentials.

MoPac   - mCalcMoPac

Open the dialog window for Mopac calculations.

Surface Calculate - mSrfCalc Calculate a surface.
Save - mSrfSave Save the calculated surface.
Color - mSrfColor

Open the dialog window to change the color of the surface.

Remove - mSrfRemove

Remove the surface (there is the same item in Edit -> Remove -> Surface)

Analysis   - mAnalysis

Open the dialog box to analyze a molecular dynamic trajectory file.

Similarity   - mSimilarity Show the similarity toolbox.
BioDock   - mBioDock

Start the graphic interface for BioDock (molecular docking package).

Interactions   - mInteractions

Open the dialog for the evaluation of the interactions.

 

4.4 Tools menu

Item Subitem Accelerator CmdName Description
GraphED   - mGraphEd

Start the graphic editor for data manipulation.

MiniED   - mMiniEd

Start the mini text editor integrated in VEGA.

WinDD   - mWinDD

Execute WinDD data decompressor software.

Task Manager   Ctrl+T mTaskMan

Open the integrated task manager to manipulate the running tasks (e.g. Mopac, BioDock, etc).

Edit Prefs   - mPreferences

Open the  preferences file (Vega\Data\prefs) with MiniED .

 

4.5 Bioinformatics

Item Subitem Accelerator CmdName Description
Web resources   - mBioResources

Start the web browser to explore the bioinformatics resources on the Web. 

 

4.6 Help menu

Item Subitem Accelerator CmdName Description
Contents   F1, Ctrl+H mHlpContents

Open this help.

MoPac manual   - mHlpMoPac

Open the Mopac manual.

Keys   - mHlpKeys

Show a list window of all key with the associated functions.

Last error   - mHlpLastErr

Show the last error message.

VEGA on the Web   - mHlpWeb

Open the VEGA main page on the Web.

About   - mHlpAbout

Show the copyright message.