4. The main menu | ![]() |
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. |
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Open | Ctrl+O | mOpen |
Open a new molecule. The multiselection is allowed. |
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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). |
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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. |
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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. |
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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). |
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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). |
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Ctrl+P | mPrint | Perform the hardcopy of the current 3D window representation. |
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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. |
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Titles | - | mDemoTitles | If it's checked, the subtitles are showed during the demo execution. |
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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. |
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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). |
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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. |
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Atom | - | mRemoveAtom |
Remove interactively one or more atoms. |
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Centroids | mRemoveCentr |
Remove all centroids. |
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Invisible atoms | - | mRemoveInvisAtm |
Remove all invisible atoms. |
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Hydrogens | - | mRemoveHydrog |
Remove all hydrogens from the molecule. |
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Water | - | mRemoveWater |
Remove water molecules from the assembly. |
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Bonds | - | mRemoveBonds |
Remove one or more bonds. |
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Surface | - | mSurfRemove |
Remove the calculated surface. |
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Build | Solvent cluster | mBldClust |
Show the dialog to build a solvent cluster. |
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Change | Atom/residue/chain | - | mEditAtm |
Allow to change the atom, residue and chain properties. |
Bonds | - | mChangeBonds |
Change the bond type. |
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Torsion | - | mChangeTorsion | ||
Ren. Residues | - | mRenumberRes |
Renumber the residue sequence. |
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Coordinates | Apply transf. | - | mApplyTransf |
Apply the transformation matrix to the atomic coordinates. |
Normalize | - | mNormalize |
Normalize the coordinates. |
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Invert Z coordinates | - | mInvertZ |
Invert the Z coordinates in order to obtain the enantiomer. |
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Constraints | - | mConstraints |
Select atom constraints for molecular dynamics simulations. |
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Segments | Fix | - | mSegFix |
Find the segments in the active/visible atoms. |
Merge | - | mSegMerge |
Merge the active/visible segments. |
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Cut | Ctrl+X | mCut |
Cut the current 3D view and put it into the clipboard. |
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Copy | Ctrl+C | mCopy | Copy the current 3D view into the clipboard using the VEGA custom format. |
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Copy Special | - | mCopySpecial |
Open a requester in order to select the format used to put the data into the clipboard. |
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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. |
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None | - | mSelectNone |
Unselect all atoms. |
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Invert | - | mSelectInvert | Invert the current selection. In other hands, it swaps the invisible with the visible atoms. |
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Backbone | - | mSelectBackbone |
Show the backbone. |
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No hydrogens | - | mSelectNoHyd |
Hide the hydrogens. |
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No water | - | mSelectNoWater |
Hide the water molecules. |
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Custom | - | mSelectCustom | Open the dialog box for custom selection. |
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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. |
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Color | By atom | - | mColorByAtom |
Set the molecule color by atom. |
By residue | - | mColorByRes |
Color the molecule by residue. |
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By chain | - | mColorByChain |
Color the molecule by chain identificator. |
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By molecule | - | mColorByMol |
Set the molecule color by molecule. |
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By segment | - | mColorBySeg | Color the molecule by segment. | |
By charge | - | mColorByCharge | Color the atoms on the basis of the partial charges. |
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By constraint | - | mColorByConstr | Color the atoms by constraint value (blue fixed, green free). | |
Selection | - | mColorSel |
Color all displayed atoms with the specified color. |
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Label atom | Off | - | mLblOff |
No atom labels. |
Name | - | mLblAtmName |
Show the atom labels by name. |
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Element | - | mLblAtmElement |
Show the atom labels by element. |
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Number | - | mLblAtmNumber |
Show the atom labels by atom number. |
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Type | - | mLblAtmType |
Show the atom labels by atom type (force field). |
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Charge | - | mLblAtmCharge |
Show the atom labels by atom charge. |
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Fixing value | - | mLblAtmFixVal |
Show the atom labels by fixing value (constraint). |
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Residue | - | mLblResidue |
Show the residue labels with name, number and chain. |
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Residue name | - | mLblResName |
Show the residue name labels. |
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Residue number | - | mLblResNumber |
Show the residue number labels. |
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Reset | - | mResetView | Reset the current view, resetting the rotations, the translations and the scale factor. |
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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. |
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Light | L | mLight |
If it's checked, the OpenGL light effects are enabled (shades, reflections, etc). |
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Console | - | mConsole |
Show/hide the console window. |
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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. |
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MoPac | - | mCalcMoPac | Open the dialog window for Mopac calculations. |
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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. |
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Remove | - | mSrfRemove | Remove the surface (there is the same item in Edit -> Remove -> Surface) |
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Analysis | - | mAnalysis | Open the dialog box to analyze a molecular dynamic trajectory file. |
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Similarity | - | mSimilarity | Show the similarity toolbox. | |
BioDock | - | mBioDock | Start the graphic interface for BioDock (molecular docking package). |
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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. |
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MiniED | - | mMiniEd |
Start the mini text editor integrated in VEGA. |
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WinDD | - | mWinDD |
Execute WinDD data decompressor software. |
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Task Manager | Ctrl+T | mTaskMan | Open the integrated task manager to manipulate the running tasks (e.g. Mopac, BioDock, etc). |
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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. |
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MoPac manual | - | mHlpMoPac |
Open the Mopac manual. |
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Keys | - | mHlpKeys |
Show a list window of all key with the associated functions. |
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Last error | - | mHlpLastErr |
Show the last error message. |
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VEGA on the Web | - | mHlpWeb |
Open the VEGA main page on the Web. |
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About | - | mHlpAbout |
Show the copyright message. |