5. The main menu

Main menu structure

With the VEGA ZZ main menu, you can access to main functions. The item layout is organized in menu bar, menu and sub-menu. Please note that 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

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 one or more (multiselection) molecules, surfaces and trajectories. If a molecule is already present in the workspace, a dialog is shown in order to select the placing mode (append, replace and new workspace).

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).

Database

Open

 

mDbOpen

Open or create a new database.

Explore

 

mDbExplore

Explore and manage the database contents.

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.

Save trajectory

 

-

mSaveTraj

Save the current active MD/docking trajectory converting it into the specified format. Cut/skip frame and remove atoms operations can be applied.

Save image

 

-

mSaveImg

Save the OpenGL view into a bitmap or a vector file.

Export to Excel

 

-

mExcel

Export the current molecule data in Microsoft Excel.

Print

 

Ctrl+P

mPrint

Perform the hardcopy of the current 3D window representation. VEGA ZZ print with the maximum resolution allowed by the printer for the best quality.

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 shown 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

 

-

mExit

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

 

5.2 Edit menu

Item

Subitem

Accelerator

CmdName

Description

Add

Atom

-

mAddAtom

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

Hydrogens

-

mAddHydrogens

Add the hydrogens.

Side chains

 

mAddChains

Add the aminoacid side chains. No bums are detected.

Bonds

-

mAddBonds

Add one or more bonds.

Centroid

-

mAddCentr

Add one or more centroid (pseudo-atom).

Fragments

-

mAddFragments

Enable the access to the fragment libraries to build interactively the molecule.

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.

Residue

-

mRemoveResidue

Remove one or more residues.

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.

All surfaces

-

mSurfRemove

Remove all calculated surfaces.

Graphic objects

-

mRemoveGraphObj

Remove all VEGA GL graphic objects.

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.

Swap bonds

-

mSwapBonds

Swap two bonds.

Angle/torsion

-

mChangeTorsion

Change one or more angles or torsions.

Renumber residues

-

mRenumberRes

Renumber the residue sequence. It's possible renumber all atoms or the selected only.

Coordinates

Apply transf.

-

mApplyTransf

Apply the transformation matrix to the atomic coordinates.

Invert Z coordinates

-

mInvertZ

Invert the Z coordinates in order to obtain the enantiomer.

Normalize

-

mNormalize

Normalize the coordinates.

Constraints

-

mConstraints

Select atom constraints for molecular dynamics simulations.

Molecules

Fix

-

mMolFix

Find the molecules in the active/visible atoms.

Merge

-

mMolMerge

Merge the active/visible molecules.

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.

 

5.3 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.

Sup. atoms

-

mSelectSupAtm

Selection of the superficial atoms that are accessible by the solvent.

Custom

-

mSelectCustom

Open the dialog box for custom selection.

Display

Wireframe

V

mShowWire

Switch the current display mode to wireframe, CPK dotted, CPK wireframe,CPK solid, ball & stick wireframe, ball & stick solid, stick wireframe, stick solid, trace and tube.

CPK dotted

mShowCpkDot

CPK wire

mShowCpkWire

CPK solid

mShowCpk

Ball & stick wire

mShowBallWire

Ball & stick Solid

mShowBall

Stick wire

mShowStickWire

Stick solid

mShowStick

Trace

mShowTrace

Tube

mShowTube

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 H-bond

-

mColorByHBond

Color the atoms by the property to accept or donate the H-bonds.

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.

Settings

-

mColorSet

Show the Color settings dialog box.

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.

Light

 

-

mLight

Open the light control window.

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.

Console

 

-

mConsole

Show/hide the console window.

3D controls

 

-

m3dControls

Show/hide the 3D control window.

Tool bars

Standard

-

mTbStandard

Show/hide the tool bar.

Tools

-

mTbTools

Information

 

-

mMoleculeInfo

Show the information about the molecule.

 

5.4 Calculate menu

Item

Subitem

Accelerator

CmdName

Description

Charge & Pot.

 

-

mCalcCharge

Assign the atomic charges and/or potentials.

Ammp

Minimization

-

mAmmpMin

Open the Ammp's dialog window to perform an energy minimization.

Conformational search

-

mAmmpTsrc

Open the Ammp's dialog window to perform a conformational search.

MoPac

 

-

mCalcMoPac

Open the dialog window for Mopac calculations.

Surface

 

-

mSurface

Calculate, color and manage the surfaces.

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.

Protein Check

AA chirality

-

mChkAaChirality

Check the alpha carbon chirality. It reports warnings and shows the aminoacids if they are D or pseudo D. Pseudo D are aminoacids with distorted geometry that can be converted in L by energy minimization.

Peptidic bonds

-

mChkPeptBond

Check the geometry of the peptidic bonds. If cis bonds are detected, they are show in the main window.

Missing res.

-

mChkMisRes

Search the missing residues in the aminoacid sequence checking the residue numbers.

Ring inter.

-

mChkRingInter

Search the intersections between bonds and rings. It works with non-peptidic molecules also.

AA contacts

-

mChkAaContacts

Show the contacts between aminoacids. For each residue is shown a label of two numbers: the first one is the number of contacts, the second is the average distance between the residues.

 

5.5 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.

VEGA On-line  

-

mVegaOnLine

Open the Web browser accessing to the VEGA On-line service.

Task Manager

 

Ctrl+T

mTaskMan

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

Plug-in configuration

 

-

-

Sub-menu for the plug-in configuration. It could be customized by the plug-ins.

HID configuration

 

-

mConfigHID

Open the dialog window to configure the human interface devices (mouse and joystick).

Host configuration

 

-

mConfigHost

Configure the hosts to run remote calculation jobs.

 Preferences

 

-

mPreferences

Edit the preferences.

 

5.6 Bioinformatics

Item

Subitem

Accelerator

CmdName

Description

Web resources

 

-

mBioResources

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

 

5.7 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.

Check for updates

   

mHlpChkUpdates

Check if new updates are available.

About

 

-

mHlpAbout

Show the copyright message.