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 | deletes all objects (molecules, surfaces, etc). A confirmation request is shown. |
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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 ...). |
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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). |
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Ctrl+P | mPrint | makes the hardcopy of the current 3D window rappresentation. |
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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. |
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Titles | - | mDemoTitles | if checked, shows the subtitles 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 | 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. | |
Copy Bmp | CopyBmp | copies the current 3D view into the clipboard using the bitmap format |
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. |
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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. |
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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. |
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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. |
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Animation | A | mAnimation | if checked, enables the animation mode. You can use the mouse and/or the keyboard to change the animation. |
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Light | L | mLight | if checked, enables the OpenGL light effects (shades, reflections, etc). | |
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). |
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). |
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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. |