5. The main menu
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). |
|
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 |
mDbOpen |
Open or create a new database. |
||
mDbExplore |
Explore and manage the database contents. |
|||
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. |
||
- |
mSaveTraj |
Save the current active MD/docking trajectory converting it into the specified format. Cut/skip frame and remove atoms operations can be applied. |
||
- |
mSaveImg |
Save the OpenGL view into a bitmap or a vector file. |
||
Export to Excel |
- |
mExcel |
Export the current molecule data in Microsoft Excel. |
|
|
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 |
Undo | Ctrl+Z | mUndo |
Undo the last operation. The default number of undo/redo levels is 20 and can be changed in the Preferences dialog window. |
|
Redo | Ctrl+Y | mRedo | Redo the previous operation. | |
Add |
- |
mAddAtom |
Add one or more atom with specific hybridization and bond type. |
|
- |
mAddHydrogens |
Add the hydrogens. |
||
Side chains |
mAddChains |
Add the aminoacid side chains. No bumps detected. |
||
- |
mAddBonds |
Add one or more bonds. |
||
- |
mAddCentr |
Add one or more centroid (pseudo-atom). |
||
- |
mAddFragments |
Enable the access to the fragment libraries to build interactively the molecule. |
||
- |
mAddCluster |
Add a solvent cluster. |
||
- |
mAddIons |
Add ions to the molecule. |
||
Remove |
- |
mRemoveMol |
Remove one or more molecules. |
|
- |
mRemoveSeg |
Remove one or more segments. |
||
- |
mRemoveResidue |
Remove one or more residues. |
||
- |
mRemoveAtom |
Remove interactively one or more atoms. |
||
mRemoveCentr |
Remove all centroids. |
|||
Invisible atoms |
- |
mRemoveInvisAtm |
Remove all invisible atoms. |
|
Hydrogens |
- |
mRemoveHydrog |
Remove all hydrogens from the molecule. |
|
Apolar hydrog. |
- |
mRemoveHydrogApol |
Remove the apolar hydrogens from the molecule. |
|
Water |
- |
mRemoveWater |
Remove water molecules from the assembly. |
|
- |
mRemoveBonds |
Remove one or more bonds. |
||
All surfaces |
- |
mSurfRemove |
Remove all calculated surfaces. |
|
Graphic objects |
- |
mRemoveGraphObj |
Remove all VEGA GL graphic objects. |
|
Build |
- |
mBuildCluster |
Show the dialog to build a solvent cluster. |
|
Peptide | - | mBuildPeptide | Show the peptide builder. | |
Change |
- |
mEditAtm |
Change the atom, residue and chain properties. |
|
- |
mChangeBonds |
Change the bond type. |
||
- |
mSwapBonds |
Swap two bonds. |
||
- |
mChangeTorsion |
Change bond length, bond angle and torsion angle. |
||
Secondary struct. |
- |
mChangeSecStruct | Change the secondary structure of a protein. | |
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, translating the center of mass to the axis origin. |
|
- |
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. |
|
Ctrl+X |
mCut |
Cut the current 3D view and put it into the clipboard. |
||
Ctrl+C |
mCopy |
Copy the current 3D view into the clipboard using the VEGA custom format. |
||
- |
mCopySpecial |
Open a requester in order to select the format used to put the data into the clipboard. |
||
Ctrl+V |
mPaste |
Paste the data from the clipboard. |
5.3 View menu
Item |
Subitem |
Accelerator |
CmdName |
Description |
Molecule |
- |
mSelectMolecule |
Select/unselect one or more molecule. |
|
Segment |
- |
mSelectSegment |
Select/unselect one or more segments |
|
- |
mSelectAll |
Select all atoms. |
||
- |
mSelectNone |
Unselect all atoms. |
||
- |
mSelectInvert |
Invert the current selection. In other hands, it swaps the invisible with the visible atoms. |
||
- |
mSelectBackbone |
Show the backbone. |
||
- |
mSelectNoHyd |
Hide the hydrogens. |
||
No apolar hydrogens |
- |
mSelectNoApolHyd | Hide the apolar hydrogens. | |
- |
mSelectNoWater |
Hide the water molecules. |
||
Sup. atoms |
- |
mSelectSupAtm |
Selection of the superficial atoms that are accessible by the solvent. |
|
Unconstrained atoms |
- |
mSelectUnconstr | Show the unconstrained atoms. For more details, see the constraints section. | |
- |
mSelectCustom |
Open the dialog box for custom selection. |
||
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. |
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mShowCpkDot |
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mShowCpkWire |
||||
mShowCpk |
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mShowBallWire |
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mShowBall |
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mShowStickWire |
||||
mShowStick |
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mShowTrace |
||||
mShowTube |
||||
- |
mShowSettings |
Show the display settings dialog box. |
||
- |
mColorByAtom |
Set the molecule color by atom. |
||
- |
mColorByRes |
Color the molecule by residue. |
||
- |
mColorByChain |
Color the molecule by chain identificator. |
||
- |
mColorByMol |
Set the molecule color by molecule. |
||
- |
mColorBySeg |
Color the molecule by segment. |
||
- |
mColorByHBond |
Color the atoms by the property to accept or donate the H-bonds. |
||
- |
mColorByCharge |
Color the atoms on the basis of the partial charges. |
||
- |
mColorByConstr |
Color the atoms by constraint value (blue fixed, green free). |
||
- |
mColorSel |
Color all displayed atoms with the specified color. |
||
- |
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. |
|
Chirality |
- |
mLblAtmChiral | Show the R/S chirality of the asymmetric atoms. | |
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. |
|
|
- |
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. |
|
- |
mConsole |
Show/hide the console window. |
||
- |
m3dControls |
Show/hide the 3D control window. |
||
Standard |
- |
mTbStandard |
Show/hide the tool bar. |
|
Tools |
- |
mTbTools |
||
- |
mMoleculeInfo |
Show the information about the molecule. |
5.4 Calculate menu
Item |
Subitem |
Accelerator |
CmdName |
Description |
- |
mCalcCharge |
Assign the atomic charges and/or potentials. |
||
Ammp |
- |
mAmmpMin |
Open the Ammp dialog window to perform an energy minimization. |
|
Conformational search |
- |
mAmmpTsrc |
Open the Ammp dialog window to perform a conformational search. |
|
NAMD |
- |
mNAMD |
Open the NAMD dialog window to perform a molecular dynamics or an energy minimization |
|
- |
mCalcMoPac |
Open the dialog window for Mopac calculations. |
||
- |
mSurface |
Calculate, color and manage the surfaces. |
||
- |
mAnalysis |
Open the dialog box to analyze a molecular dynamic trajectory file. |
||
- |
mSimilarity |
Show the similarity toolbox. |
||
- |
mBioDock |
Start the graphic interface for BioDock (molecular docking package). |
||
- |
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 |
- |
mGraphEd |
Start the graphic editor for data manipulation. |
||
- |
mMiniEd |
Start the mini text editor integrated in VEGA. |
||
- |
mWinDD |
Execute WinDD data decompressor software. |
||
VEGA On-line |
- |
mVegaOnLine |
Open the Web browser accessing to the VEGA On-line service. |
|
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. | |
- |
mConfigHID |
Open the dialog window to configure the human interface devices (mouse and joystick). | ||
- |
mConfigHost |
Configure the hosts to run remote calculation jobs. | ||
- |
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 |
VEGA ZZ manual |
F1, Ctrl+H |
mHlpContents |
Open this help. |
|
Mopac manual |
- |
mHlpMopac |
Open the Mopac manual. |
|
Mopac 2007 manual |
- |
mHlpMopac2007 | Open the on-line Mopac 2007 manual. | |
NAMD user's guide |
- |
mHlpNAMD | Open the on-line NAMD user's guide. | |
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. |