14.4 VEGA ZZ commands

These commands are for VEGA ZZ only.

 

 

ACTIVATE
Activate the main window, giving the input focus to it.

 

Parameters:
None

 

Return values:
Error code if it fails.

 

Example:
ACTIVATE

 

See also:
None


AMMPSEND   (CHAR)Commands
Send a command string to AMMP, locking the current workspace. To unlock it, use WKSUNLOCK command. Please remember that AMMP executes commands in asynchronous mode: it means that AMMPSEND doesn't wait the end of the commands execution.

Parameters:
Commands    Command string. It may contain more then one command and each command must  terminated by the semicolon character (;).

Return values:
Error code if it fails.

 

Example:
AMMPSEND    "Monitor;"

 

See also:
AMMPSENDMOL, AMMPSTARTCALC, WKSUNLOCK.


AMMPSENDMOL   (MCHAR)Fix
Send the molecule in the current workspace to AMMP, setting the parameters to default and locking the current workspace. To unlock the workspace, use WKSUNLOCK command.

Parameters:
Fix    Atom fixing. It could be: NONE, FIX and TETHER.

Return values:
Error code if it fails.

 

Example:
AMMPSENDMOL    None

 

See also:
AMMPSEND, WKSUNLOCK.


AMMPSETFF   (CHAR)ForceField
Set the AMMP force field used to save the molecule in AMMP format or to send the data to AMMP host. The corresponding .tem and .inp files must be present in the VEGA ZZ\Data directory, otherwise an error message is shown.

Parameters:
ForceField    Force field name.

Return values:
Error code if it fails.

 

Example:
AMMPSETFF    CHARMM

 

See also:
AMMPSENDMOL, SAVE.


AMMPSTARTCALC
This command notifies to VEGA ZZ that a new AMMP calculation being to start. VEGA ZZ locks the workspace, disables the menus and enables the context menu to stop the calculation. Use the AMMP's CONFIRMEND command before the last calculation command, in order to enable AMMP notification when the calculation is finished. To check if the calculation is running, read ISRUNNING variable.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
AMMPSTARCALC
AMMSEND   "calcend; cngdel  1000   0   0.01;"

 

See also:
AMMPSEND.


AMMPUPDATEFREQ   (MCHAR)Type   (UINT)Frequency
Set the AMMP update frequency of output files.

Parameters:
Type    Frequency type. It can be: MIN (Minimization), TSRC (conformational search).
Frequency Update frequancy (it must be greater than zero).

Return values:
Error code if it fails.

 

Example:
AMMPUPDATEFREQ    MIN   10

 

See also:
AMMPSEND, AMMPSENDMOL.


ANGLE   (CHAR)Atom1   (CHAR)Atom2   (CHAR)Atom3   (INT)Flags
Measure the bond angle between three atoms.

Parameters:
Atom1    Atoms defining the bond angle. See SELECT command for the correct syntax.
Atom2
Atom3
Flags Control flags that can be combined by OR logical operator or sum:
  
Flag Value Description
MEAS_3DOBJ 1 Show the measure indicator in the main window.
MEAS_3DTXT 2 Show the measure value in the main window.
MEAS_CONTXT 4 Show the measure value in the console window.

Return values:
The command returns the angle value in degrees and if it fails, the error code is shown.

 

Example:
ANGLE    C1   C2   C3   7

 

See also:
DISTANCE, PLANEANG, SELECT, TORSION.


ANTIALIAS   (BOOL)Mode
Enable/disable the anti-aliased visualization.

Parameters:
Mode    1 (true) enables the anti-aliasing and 0 (false) disables it.

Return values:
Error code if it fails.

 

Example:
ANTIALIAS    1

 

See also:
DEPTHCUE, SMARTMOVE, mLight, mShowSettings.


BACKCOLOR   (UINT)Color
This command changes the background color. Please remember that if no molecule are loaded, the background remains black and it changes even if one molecule is open.

Parameters:
Color    Color in RGB format (0 <= Color <= 16777215).

Return values:
None.

 

Example:
BACKCOLOR    1111111

 

See also:

COLORRGBDLG.


BALLSTICKPROP   (UINT)ShpereRes   (UINT)SphereScale  (UINT)CylinderRes  (FLOAT)CylinderRad
Change the ball & stick visualization properties.

Parameters:
ShpereRes    Sphere resolution (12 <= SphereRes <= 24).
SphereScale Sphere scale (10 <= SphereScale <= 50).
CylinderRes Cylinder resolution (8 <= CylinderRes <= 24).
CylinderRad Cylinder radius (0.05 <= CylinderRad <= 0.5).

Return values:
Error code if it fails.

 

Example:
BALLSTICKPROP    16   20   10   0.10
(Default settings).

 

See also:
CPKPROP, STICKPROP, TRACEPROP, TUBEPROP, WIREPROP, mShowSettings.


BEGINCALC
This command notifies to VEGA ZZ that a new asynchronous calculation being to start. VEGA ZZ locks the workspace and disables the menus. To check if the calculation is running, read the ISRUNNING variable.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
BEGINCALC

 

See also:
ENDCALC.


BIODOCK   (CHAR)FileName
Use this command to start a BioDock background calculation. To check if the calculation is running, read the ISRUNNING variable.

Parameters:
FileName    the file name of the BioDock input file. The .bp extension can be omitted.

Return values:
Error code if it fails.

 

Example:
BIODOCK    "C:\My Documents\MyDocking.bp"

 

See also:
MOPAC.


BUILD3D   (INT)Flags
Convert a 1D/2D structure to 3D. To check if the calculation is running, read the ISRUNNING variable. Remember to add the hydrogens and to fix the atom charges (BUILD3D_CHARGE flag) before the conversion, if it's required.

Parameters:
Flags   Control flags that can be combined by OR logical operator or sum:
     
   
Flag Value Description
BUILD3D_CHARGE 1 Assign the atom charges.
BUILD3D_CONJUGATE 2 Perform the conjugate gradients minimization.
BUILD3D_FIXAROM 4 Fix the aromatic rings and the carboxylate groups.
BUILD3D_FIXCHIR 8 Adjust the chiral centers if they are wrong.
BUILD3D_FIXGEOM 16 Adjust the E/Z geometry if it's wrong.
BUILD3D_GSDG 32 Perform the Gauss-Siedel distance geometry optimization.
BUILD3D_NORMALIZE 64 Normalize the atom coordinates.
BUILD3D_STEEPEST 128 Perform the steepest descent minimization.

Return values:
Error code if it fails.

 

Example:
BUILD3D    63

 

See also:
None.


COLOR   (MCHAR)Color
Change the color of the current selection.

Parameters:
Color    Color name: black, white, red, green, cyan, yellow, firebirck, magenta, pink, violet, ghostgray, gray, darkgray, orange, darkgreen, blue, darkyellow, brown, skyblue, ghostpink, ghostgreen, ghostblue, ghostyellow and sand.

Return values:
Error code if it fails.

 

Example:
COLOR    Blue

 

See also:
mColorByAtom, mColorByChain, mColorByCharge, mColorByMol, mColorByRes, mColorSel.


CONCLRHIST
Clear the command history buffer of the console.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
CONCLRHIST

 

See also:
CONCLS, CONGETLINE, CONSET, CONSAVE, CONWIN, mConsole.


CONCLS
Clear the console window.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
CONCLS

 

See also:
CONCLRHIST, CONGETLINE, CONSET, CONSAVE, CONWIN, mConsole.


CONGETLINE   (INT)LineNumber
Get a text line from the console.

Parameters:
LineNumber   

Number of the line from which to retrieve the text. Positive values get the text from the top and negative values get the text from the bottom. The line numbering starts from 1, thus 1 indicates the first line and -1 the last one. Values out of range of available lines are allowed, but an empty line is obtained.

Return values:
Error code if it fails.

 

Example:
CONGETLINE  3

 

See also:
CONCLS, CONCLRHIST, CONCLS, CONSET, CONWIN, mConsole.


CONSAVE   (CHAR)FileName
Save the console output to a text file.

Parameters:
FileName    Full path and file name of the output file.

Return values:
Error code if it fails.

 

Example:
CONSAVE "C:\Temp\Output.txt"

 

See also:
CONCLRHIST, CONCLS, CONGETLINE, CONSET, CONWIN, mConsole.


CONSET   (UINT)BufferSize   (UINT)HistorySize
Set the console buffer size (in lines) and the command history size.

Parameters:
BufferSize    Output buffer size in lines (BufferSize > 20, default 200).
HistorySize History size in number of commands (HistorySize> 0, default 20).

Return values:
Error code if it fails.

 

Example:
CONSET   1000   40

 

See also:
CONCLRHIST, CONCLS, CONGETLINE, CONSAVE, CONWIN, mConsole.


CONWIN   (UINT)PosX   (UINT)PosY   (UINT)SizeX   (UINT)SizeY
Change position and size of the console window, undocking it if it's required.

Parameters:
PosX    X position.
PosY Y position.
SizeX Width.
SizeY Height.

Return values:
Error code if it fails.

 

Example:
CONWIN   0   0   640   300

 

See also:
CONCLRHIST, CONCLS, CONGETLINE, CONSAVE, CONSET, mConsole.


COPY   (MCHAR)Format
Copy the molecule to clipboard, converting it to the specified format. To paste use the mPaste menu command. For more information, click here.

Parameters:
Format    Clipborad format: VEGA (Molecule object), Bitmap, Sketch, Biosym, InChI, Mol2, Mopac, PDB, PDBF, XYZ.

Return values:
Error code if it fails.

 

Example:
COPY   Bitmap

 

See also:
COPYTEXT, mCopy, mCopySpecial, mCut, mPaste.


COPYTEXT   (CHAR)String
Copy the specified string to clipboard.

Parameters:
String    String that will be copied to clipboard.

Return values:
Error code if it fails.

 

Example:
COPYTEXT   "Hello World !"

 

See also:
COPY, mCopy, mCopySpecial, mCut, mPaste.


CPKPROP   (UINT)SphereRes    (UINT)DotSize
Change the CPK visualization properties.

Parameters:
SphereRes    Sphere resolution (12 <= SphereRes <= 36).
DotSize Dot size (1 <= DotSize <= 4).

Return values:
Error code if it fails.

 

Example:
CPKPROP   20   2

 

See also:
BALLSTICKPROP, STICKPROP, TRACEPROP, TUBEPROP, WIREPROP, mShowSettings.


CTORCLEAR
Clear all torsions

 

Parameters:
None.

 

Return values:
None.

 

Example:
CTORCLEAR

 

See also:
CTORFIND.


CTORFIND   (MCHAR)Mode
Find all torsions that can be used for a calculation (e.g. AMMP's conformational search, AutoDock 4 calculations, trajectory analysis, torsion adjustment).

Parameters:
Mode    Mode to find the torsions:
     
   
Mode Description
All All torsions.
AutoDock Torsions required by AutoDock to perform the in situ conformational search.
Flex Flexible torsions only.

Return values:
None.

 

Example:
CTORFIND   FLEX

 

See also:
CTORCLEAR.


CTORGET   (BOOL)Number
Get the properties of a torsion angle that can be used for a calculation (e.g. AMMP's conformational search, trajectory analysis, torsion adjustment).

Parameters:
Number    Torsion number. It must be greater than zero and less than the total number of defined torsions (use Get TotCTor to obtain is).

Return values:
If the Number argument is valid, the atom ID defining the torsion, the base torsion value (in degree), the number of steps used in the systematic conformational search, the torsion window value (in degree) used in Boltzmann jump and in random conformational search and the activation status (0 or 1) are returned:

15 17 18 23 0.000000 6 360.000000 1

If the Number is less or equal to zero, an error message is shown. If it's greater than total number of torsions a null result is returned:

0 0 0 0 0.0 0 0.0 0

Example:
CTORGET   2

 

See also:
CTORCLEAR, CTORFIND.


CURSOR   (MCHAR)CursorImage
Change the mouse cursor image. You could use this command to notify a calculation.

Parameters:
CursorImage    The cursor image. It can be: default, none, arrow, busy, cross.

Return values:
None.

 

Example:
CURSOR   busy

 

See also:
None


DEPTHCUE   (BOOL)Mode
Enable/disable the depth cueing.

Parameters:
Mode    If Mode is 1, the depth cue is enabled, otherwise if it's 0, the depth cueing is disabled.

Return values:
Error code if it fails.

 

Example:
DEPTHCUE    1

 

See also:
ANTIALIAS, SMARTMOVE, mLight, mShowSettings.


DISTANCE   (CHAR)Atom1   (CHAR)Atom2   (INT)Flags
Measure the distance between two atoms.

Parameters:
Atom1    Atoms defining the bond. See SELECT for the correct syntax.
Atom2
Flags Control flags that can be combined by OR logical operator or sum:
  
Flag Value Description
MEAS_3DOBJ 1 Show the measure indicator in the main window.
MEAS_3DTXT 2 Show the measure value in the main window.
MEAS_CONTXT 4 Show the measure value in the console window.

Return values:
The command returns the measure value and if it fails, the error code is reported.

 

Examples:
DISTANCE    CA:ALA:25   O:ASP:42   0
DISTANCE    10   36   4

 

See also:
ANGLE, PLANEANG, SELECT, TORSION.


ENDCALC

This command notifies to VEGA ZZ that the asynchronous calculation is finished. VEGA ZZ unlocks the workspace and enables the menus. To check if the calculation is stopped, read the ISRUNNING variable.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
ENDCALC

 

See also:
BEGINCALC.


GRAPHACTIVATE
Activate the current graph window, giving the input focus to it.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHACTIVATE

 

See also:
GRAPHCLOSE, GRAPHOPEN, GRAPHWIN, mGraphEd.


GRAPHADD    (FLOAT)XValue   (FLOAT)YValue
Add a point value to the current chart.

Parameters:
XValue    X value.
YValue Y value.

Return values:
Error code if it fails.

 

Example:
GRAPHADD   1.5   0.25

 

See also:
GRAPHDELETE, GRAPHGET, GRAPHSET, mGraphEd.


GRAPHBEGINUPDATE
This command notifies to the current chart window that it will be massively updated. It speeds-up the next graph commands. Remember to call GraphEndUpdate at the end of the update.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHBEGINUPDATE

 

See also:
GRAPHADD, GRAPHDELETE, GRAPHENDUPDATE, GRAPHGET, GRAPHSET, mGraphEd.


GRAPHCALC    (MCHAR)ClacType
Calculate a statistical value using the chart dataset.

Parameters:
ClacType    It's the keyword for the selection of the calculation type:
  
Keyword Description
AverageVal Average value.
MaxVal Maximum value.
MinVal Minimum value.
StdDev Standard deviation.

Return values:
This function returns the result of the requested calculation. If no data is present in the chart, the return value is zero.

 

Example:
GRAPHCALC    StdDev

 

See also:
GRAPHDERIVATIVE, GRAPHGET, GRAPHNR, GRAPHSPECTRUM, mGraphEd.


GRAPHCLOSE
Close the Graph Editor (GraphED) window.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHCLOSE

 

See also:
GRAPHACTIVATE, GRAPHLOAD, GRAPHNEW, GRAPHOPEN, GRAPHSAVE, GRAPHWIN, mGraphEd.


GRAPHDELETE   (UINT)PointIndex
Delete a single dataset point.

Parameters:
PointIndex    Point index (0< PointIndex < GraphPoints). To obtain the total number of points (GraphPoints), use GET or PLUGINGET commands.

Return values:
Error code if it fails.

 

Example:
GRAPHDELETE    3

 

See also:
GRAPHADD, GRAPHGET, GRAPHSET, mGraphEd.


GRAPHDERIVATIVE
Calculate the derivative of the current plot opening a new window.

 

Parameters:
None.

 

Return values:
The function returns zero if it fails, otherwise the window  ID of the derivative plot.

 

Example:
GRAPHDERIVATIVE

 

See also:
GRAPHCALC, GRAPHGET, GRAPHNR, GRAPHSPECTRUM, mGraphEd.


GRAPHENDUPDATE
This command notifies to graph window that the update operation is finish and all changes can be shown. It must be called after the GraphBeginUpdate command.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHENDUPDATE

 

See also:
GRAPHADD, GRAPHBEGINUPDATE, GRAPHDELETE, GRAPHGET, GRAPHSET, mGraphEd.


GRAPHEXCEL
Export the data to Microsoft Excel by DDE interface.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHEXCEL

 

See also:
GRAPHLOAD, GRAPHNEW, GRAPHOPEN, GRAPHSAVE, GRAPHTOCLIP, mGraphEd.


GRAPHGET    (UINT)PointIndex
Get the Cartesian coordinates of a dataset point.

Parameters:
PointIndex    Point index (0< PointIndex < GraphPoints). To obtain the total number of points (GraphPoints), use GET or PLUGINGET commands.

Return values:
This function returns the X and Y floating point values separated by a space. If PointIndex exceeds the total number of points, no values are returned.

 

Example:
GRAPHGET    5

 

See also:
GRAPHADD, GRAPHDELETE, GRAPHSET, mGraphEd.


GRAPHLABELX   (CHAR)Label
Set the label of X axis.

Parameters:
Title    X axis label.

Return values:
Error code if it fails.

 

Example:
GRAPHLABELX    "Time (ps)"

 

See also:
GRAPHLABELY, GRAPHTITLE, GRAPHTYPE, GRAPHWIN, mGraphEd.


GRAPHLABELY   (CHAR)Label
Set the label of Y axis.

Parameters:
Title    Y axis label.

Return values:
Error code if it fails.

 

Example:
GRAPHLABELY    "Energy (Kcal/mol)"

 

See also:
GRAPHLABELX, GRAPHTITLE, GRAPHTYPE, GRAPHWIN, mGraphEd.


GRAPHLOAD    (CHAR)FileName
Load the graph data from file.

Parameters:
FileName    Name of the file to load. The supported file formats are: CHARMM .ene, Comma Separated Values .csv, Data Interchange Format .dif, NAMD output .out and Quanta .plt .

Return values:
Error code if it fails.

 

Example:
GRAPHLOAD    "MyGraph.csv"

 

See also:
GRAPHCLOSE, GRAPHEXCEL, GRAPHNEW, GRAPHOPEN, GRAPHPRINT, GRAPHSAVE, GRAPHTOCLIP, mGraphEd.


GRAPHMAXIMIZE
Maximize the graph window.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHMAXIMIZE

 

See also:
GRAPHCLOSE, GRAPHMINIMIZE, GRAPHOPEN, GRAPHRESTORE, mGraphEd.


GRAPHMINIMIZE
Minimize the current graph window.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHMINIMIZE

 

See also:
GRAPHCLOSE, GRAPHMAXIMIZE, GRAPHOPEN, GRAPHRESTORE, mGraphEd.


GRAPHNEW
Clear all data in the chart.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHNEW

 

See also:
GRAPHCLOSE, GRAPHEXCEL, GRAPHLOAD, GRAPHOPEN, GRAPHPRINT, GRAPHSAVE, GRAPHTOCLIP, mGraphEd.


GRAPHNR    (UINT)Percent
Remove the noise applying a DFT (Discrete Fourier Transformation) low-pass filter. As first step it creates the frequency spectrum, it removes the high frequencies and finally it rebuilds the filtered wave using the inverse DFT

Parameters:
Percent    It's the spectrum range (percentage) that will be removed by the low-pass filter.

Return values:
The function returns zero if it fails, otherwise the window  ID of the noise-reduced plot.

 

Example:
GRAPHNR    80

 

See also:
GRAPHCALC, GRAPHDERIVATIVE, GRAPHGET, GRAPHSPECTRUM, mGraphEd.


GRAPHOPEN    (UINT)Flags
Open the Graph Editor (GraphED) window and it came automatically the current window.

Parameters:
Flags    Control flags:
  
Flag Value Description
GRAPHOPEN_CENTER 1 Center the window in the screen.

Return values:
The ID of the window or an error code if it fails.

 

Example:
GRAPHOPEN    1

 

See also:
GRAPHACTIVATE, GRAPHCLOSE, GRAPHEXCEL, GRAPHLOAD, GRAPHNEW, GRAPHPRINT, GRAPHSAVE, GRAPHSETCUR, GRAPHTOCLIP, mGraphEd.


GRAPHPRINT    (BOOL)ShowDialog
Print the current chart.

Parameters:
ShowDialog    If it's true (1), the print dialog is shown, otherwise the plot is sent to the predefined printer.

Return values:
Error code if it fails.

 

Example:
GRAPHPRINT    1

 

See also:
GRAPHLOAD, GRAPHNEW, GRAPHSAVE, GRAPHTOCLIP, mGraphEd.


GRAPHRESTORE
Restore the size an the position of  the graph window (maximized or minimized).

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHRESTORE

 

See also:
GRAPHCLOSE, GRAPHMAXIMIZE, GRAPHMINIMIZE, GRAPHOPEN, mGraphEd.


GRAPHSAVE    (CHAR)FileName   (MCHAR)Format   (CHAR)Compression
Save graph data to file.

Parameters:
FileName    Chart title.
Format Output format. The supported formats are:
  
Keyword Description
CSV Comma Separated Values.
DIF Data Interchange Format (Microsoft Excel).
PLT Quanta plot.
RAW Raw float format.
Compression Compression mode (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS).

Return values:
Error code if it fails.

 

Example:
GRAPHSAVE    "C:\My Documents\Graph.csv"   CSV   NONE

 

See also:
GRAPHCLOSE, GRAPHEXCEL, GRAPHLOAD, GRAPHNEW, GRAPHOPEN, GRAPHPRINT, GRAPHTOCLIP, mGraphEd.


GRAPHSET    (UINT)PointIndex   (FLOAT)XValue    (FLOAT)YValue
Set/change the dataset values. To add a new point, use GRAPHADD command.

Parameters:
PointIndex    Point index (0< PointIndex < GraphPoints). To obtain the total number of points (GraphPoints), use GET or PLUGINGET commands.
XValue X value.
YValue Y value.

Return values:
Error code if it fails.

 

Example:
GRAPHSET    5   3   4.34

 

See also:
GRAPHADD, GRAPHDELETE, GRAPHGET, mGraphEd.


GRAPHSETCUR    (UINT)WindowID 
Set/change the current Graph Editor window. When you use this functions, all graph commands are sent to the Graph Editor window with the specified window ID. To obtain the ID of the current window, use the GRAPHID variable.

Parameters:
WindowID    The ID of the Graph Editor window.

Return values:
Error code if the ID is wrong or if no graph windows are opened.

 

Example:
GRAPHSETCUR    1

 

See also:
GRAPHOPEN, mGraphEd.


GRAPHSPECTRUM
Calculate the spectrum frequency using the Discrete Fourier Transformation (DFT). The results are shown in a new bar graph. For more information, see the Graph Editor section.

 

Parameters:
None.

 

Return values:
The function returns zero if it fails, otherwise the window  ID of the derivative plot.

 

Example:
GRAPHDSPECTRUM

 

See also:
GRAPHCALC, GRAPHDERIVATIVE, GRAPHGET, GRAPHNR, mGraphEd.


GRAPHTITLE   (CHAR)Title
Change the chart title.

Parameters:
Title    Chart title.

Return values:
Error code if it fails.

 

Example:
GRAPHTITLE    "This is my chart"

 

See also:
GRAPHLABELX, GRAPHLABELY, GRAPHTYPE, GRAPHWIN, mGraphEd.


GRAPHTOCLIP
Copy the current graph to clipboard in Enhanced Meta File (EMF) format.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
GRAPHTOCLIP

 

See also:
GRAPHCLOSE, GRAPHEXCEL, GRAPHLOAD, GRAPHNEW, GRAPHOPEN, GRAPHPRINT, GRAPHSAVE, mGraphEd.


GRAPHTYPE   (UINT)ChartType
Change the type of the current chart.

Parameters:
ChartType    Type of chart. It can be:
ChartType Description
0 Bar (histogram).
1 Line.
2 Pie.
3 Mass (for mass spectrometry).

Return values:
Error code if it fails.

 

Example:
GRAPHTYPE   2

 

See also:

GRAPHLABELX, GRAPHLABELY, GRAPHTITLE, GRAPHWIN, mGraphEd.


GRAPHWIN   (UINT)PosX   (UINT)PosY   (UINT)SizeX   (UINT)SizeY
Change position and size of the current Graph Editor (GraphED) window.

Parameters:
PosX    X position.
PosY Y position.
SizeX Width.
SizeY Height.

Return values:
Error code if it fails.

 

Example:
GRAPHWIN   50 50 300 300

 

See also:
GRAPHACTIVATE, GRAPHCALC, GRAPHLABELX, GRAPHLABELY, GRAPHTITLE, GRAPHTYPE, mGraphEd.


LIGHT   (BOOL)Enable
Enable/disable the lighting.

Parameters:
Enable    1 (true) enables the lighting; 0 (false) disables the lighting.

Return values:
Error code if it fails.

 

Example:
LIGHT    0
(disables the lighting).

 

See also:
LIGHTAMB, LIGHTCUR, mLight.


LIGHTAMB   (BOOL)Enable
Enable/disable the ambient light.

Parameters:
Enable    1 (true) enables the ambient light; 0 (false) disables it.

Return values:
Error code if it fails.

 

Example:
LIGHTAMB    0
(Disable the ambient light).

 

See also:
LIGHT, LIGHTAMBCOLOR, mLight.


LIGHTAMBCOLOR   (UINT)Color
Change the ambient light color.

Parameters:
Color   

Color in RGB format (0 <= Color <= 16777215).

Return values:
Error code if it fails.

 

Example:
LIGHTAMBCOLOR    16777215
(sets the ambient light color to white).

 

See also:
LIGHT, LIGHTAMB, mLight.


LIGHTCUR   (UINT)LightSource
Set the current light source. After the call of this command, all light functions are referenced to the new light source.

Parameters:
LightSource    Number of the light source from 1 to 4 (default 1).

Return values:
Error code if it fails.

 

Example:
LIGHTCUR    2
(sets the current light source to the number two).

 

See also:
LIGHT, LIGHTCURDIFCOL, LIGHTCUREN, mLight.


LIGHTCURDIFCOL   (UINT)Color
Change the diffuse light color of the current light source.

Parameters:
Color    Color in RGB format (0 <= Color <= 16777215).

Return values:
Error code if it fails.

 

Example:
LIGHTCURDIFCOL    8355711
(sets the diffuse light color to gray).

 

See also:
LIGHT, LIGHTCUR, LIGHTCUREN, LIGHTCURSPECCOL, mLight.


LIGHTCUREN   (BOOL)Enable
Enable/disable the current light source.

Parameters:
LightSource    1 (true) switches on the current light source; 0 (false) switch off it.

Return values:
Error code if it fails.

 

Example:
LIGHTCUREN    1
(enables the current light source).

 

See also:
LIGHT, LIGHTCUR, mLight.


LIGHTCURPOS   (float)PosX   (float)PosY   (float)PosZ
Set the position of the current light source.

Parameters:
PosX
PosY,
PosZ
   Coordinates of the current light source. The allowed values are: -1, 0 and 1.

Return values:
Error code if it fails.

 

Example:
LIGHTCURPOS    1   1   1
(sets the position of the current light to top-right-back position).

 

See also:
LIGHT, LIGHTCUR, mLight.


LIGHTCURSPECCOL   (UINT)Color
Change the specular light color of the current light source.

Parameters:
Color   

Color in RGB format (0 <= Color <= 16777215).

Return values:
Error code if it fails.

 

Example:
LIGHTCURSPECCOL    16777215
(sets the specular light color to white).

 

See also:
LIGHT, LIGHTCUR, LIGHTCURDIFCOL, LIGHTCUREN, mLight.


LOGOPOS   (UINT)Position
Enable/disable the VEGA ZZ logo visualization and set its position. The logo is shown only if a molecule is present in the workspace.

Parameters:
Position    Logo position (0 <= Position <= 9). For the position codes, see GET  LogoPos.

Return values:
Error code if it fails.

 

Example:
LOGOPOS    9
(bottom right position)

 

See also:
LOGOSCALE.


LOGOSCALE   (FLOAT)ScaleFactor
Set the scale factor of the VEGA ZZ logo.

Parameters:
ScaleFactor    Scale factor. Negative values are allowed.

Return values:
Error code if it fails.

 

Example:
LOGOSCALE    0.5 (default value)

 

See also:
LOGOPOS.


MAINWIN   (UINT)PosX   (UINT)PosY   (UINT)SizeX   (UINT)SizeY
Change position and size of the main window.

Parameters:
PosX    X position.
PosY Y position
SizeX Width.
SizeY Height.

Return values:
Error code if it fails.

 

Example:
MAINWIN   0 0 800 600

 

See also:
wMaximize, wMinimize, wRestore.


MATSHINY   (UINT)Shininess
Change the material shininess.

Parameters:
Shininess    Material shininess (from 0 to 100).

Return values:
Error code if it fails.

 

Example:
MATSHINY   15
(sets the material shininess to 15%)

 

See also:
MATSPECULAR, MATVECTSPEC.


MATSPECULAR   (UINT)Specularity
Change the material shininess.

Parameters:
Specularity    Material specularity (from 0 to 100).

Return values:
Error code if it fails.

 

Example:
MATSPECULAR   80
(sets the material specularity to 80%)

 

See also:
MATSHINY, MATVECTSPEC.


MATVECTSPEC   (BOOL)Enable
Enable/disable the vector specularity

Parameters:
Enable    1 (true) enables the vector specularity, 0 (false) disables it.

Return values:
Error code if it fails.

 

Example:
MATVECTSPEC   1
(enables the vector specularity)

 

See also:
MATSHINY, MATSPECULAR.


MENUENABLE   (MCHAR)Status
Enable/disable the main menu.

Parameters:
Status   

It can be All (enable all menu items depending on the VEGA ZZ status) or Calc (enable the menu items for calculation only).

Return values:
Error code if it fails.

 

Example:
MENUENABLE   All
(enables all menu items)

 

See also:
None.


MONITORPOWER   (BOOL)Status
Change the monitor power status (CRT).

Parameters:
Status    1 (true) switches off the monitor (stand-by mode); 1 (true) switches on it.

Return values:
Error code if it fails.

 

Example:
MONITORPOWER   0
(switches off the monitor)

 

See also:
SHUTDOWN.


MOPAC   (CHAR)FileName   (CHAR)Keywords
Use this command to start a Mopac background calculation. To check if the calculation is running, read the ISRUNNING variable.

Parameters:
FileName    It's the full path file name of the input file that VEGA ZZ creates to start Mopac (the .dat extension is optional).
Keywords Mopac keywords. If the CHARGE keyword isn't specified, VEGA ZZ calculates automatically the total charge and it adds this for you.

Return values:
Error code if it fails.

 

Example:
MOPAC "C:\Molecules\a3" "AM1 CHARGE=0 PRECISE"

 

See also:
mCalcMoPac.


MOVIEADD
Add a new video frame to the movie opened by MOVIECREATE command.

 

Parameters:
None.

 

Return values:
0 if it fails, 1 if no error occurs.

 

Example:
MOVIEADD

 

See also:
MOVIECLOSE, MOVICREATE.


MOVIECLOSE
Close the movie file previously created by MOVIECREATE command. Remember that the movie stream is automatically closed when VEGA ZZ exits or when you save a trajectory file in video format.

 

Parameters:
None.

 

Return values:
0 if it fails, 1 if no error occurs.

 

Example:
MOVIECLOSE

 

See also:
MOVIEADD, MOVICREATE.


MOVIECREATE   (CHAR)FileName
This command creates a new movie file. The file extension allows to select the video format that can be: AVI file (.avi), MPEG1 stream (.mpeg or .mpg), MPEG2-VOB (.vob). Calling this command, video encoding window is shown as when you save the MD trajectories in video format.

Parameters:
FileName    File name of the movie that you intend to create.

Return values:
0 if it fails, 1 if no error occurs.

 

Example:
MOVIECREATE "C:\MyMovie.avi"

 

See also:
MOVIEADD, MOVIECLOSE.


OPENDATADIR
Explore the data directory.

 

Parameters:
None.

 

Return values:
None.

 

Example:
OPENDATADIR

 

See also:
None


PLANEANG   (CHAR)Atom1   (CHAR)Atom2   (CHAR)Atom3   (CHAR)Atom4   (CHAR)Atom5   (CHAR)Atom6   (INT)Flags
Measure the angle between two planes defined by two triplets of atoms.

Parameters:
Atom1    Atoms defining the first plane. See SELECT command for the correct syntax.
Atom2
Atom3
Atom4 Atoms defining the second plane.
Atom5
Atom6
Flags Control flags that can be combined by OR logical operator or sum:
  
Flag Value Description
MEAS_3DOBJ 1 Show the measure indicator in the main window.
MEAS_3DTXT 2 Show the measure value in the main window.
MEAS_CONTXT 4 Show the measure value in the console window.

Return values:
The command returns the measure value and if it fails, the error code is reported.

 

Example:
PLANEANG    C1   C3   C5   C29   C31   C33

 

See also:
ANGLE, DISTANCE, SELECT, TORSION.


PLUGINABOUT   (CHAR)PluginName
Show the about information of the specified plug-in.

Parameters:
PluginName    Name of the plug-in.

Return values:
Error code if it fails.

 

Example:
PLUGINABOUT    PowerNet

 

See also:
PLUGINCONFIG, PLUGINCALL, PLUGINGET, PLUGINHELP.


PLUGINCALL  (CHAR)PluginName    (UINT)FunctionNumber
Call a plug-in user function by function number.

Parameters:
PluginName    Name of the plug-in.
FunctionNumber Function number (from 1 to 100).

Return values:
Error code if it fails.

 

Example:
PLUGINCALL    PowerNet   1

 

See also:
PLUGINABOUT, PLUGINCONFIG, PLUGINGET, PLUGINHELP.


PLUGINCONFIG   (CHAR)PluginName
This command opens the plug-in configuration dialog.

Parameters:
PluginName    Name of the plug-in.

Return values:
Error code if it fails.

 

Example:
PLUGINCONFIG    PowerNet

 

See also:
PLUGINABOUT, PLUGINCALL, PLUGINGET, PLUGINHELP.


PLUGINGET   (CHAR)Variable
As the standard GET command, it returns the value of a specific internal variable, but without using the inter-process communication system (e.g. clipboard). It's strongly recommended to use in the plug-in code. For more information see the GET command.

Parameters:
Variable    Variable name.

Return values:
The value of the specified variable.

 

Example:
PLUGINGET   CURLANG

 

See also:
GET.


PLUGINHELP   (CHAR)PluginName
Show the plug-in help.

Parameters:
PluginName    Name of the plug-in.

Return values:
Error code if it fails.

 

Example:
PLUGINHELP    PowerNet

 

See also:
PLUGINABOUT, PLUGINCALL, PLUGINCONFIG, PLUGINGET.


REFRESH
Force the main window refresh.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
RERESH

 

See also:
None.


ROTATE   (FLOAT)X    (FLOAT)Y   (FLOAT)Z
Rotate the active object around X, Y and Z axis.

Parameters:
X    X rotation (degree).
Y Y rotation (degree).
Z Z rotation (degree).

Return values:
Error code if it fails.

 

Example:
ROTATE   90   45.5   0

 

See also:
TRANSLATE, ZOOM.


SAVEIMG   (CHAR)FileName
Save the current view as bitmap or vector file.

Parameters:
FileName   

The name name of the output file. Choose the appropriate extension to select the file format, according to the following table:

   
Extension Format
.bmp Windows Bitmap
.eps Encapsulated PostScript
.gif Compuserve GIF
.jpg JPEG
.pcx ZSoft PCX
.pdf PDF
.png Portable Network Graphics
.pnm PNM
.pov Persist of Vision Raytracer (POV-Ray)
.ps PostScript
.raw Raw data
.svg Scalable Vector Graphics
.sgi Silicon Graphics
.tex LaTex
.tga Targa
.tif Tiff
.wrl VRML
.wrz VRML gzipped

Return values:
Error code if it fails.

 

Example:
SAVEIMG   "C:\SnapShot.gif"

 

See also:
SAVE.


SAVEIMG2D   (CHAR)FileName   (UINT)Width   (UINT)Height
Save the current molecule as 2D sketch.

Parameters:
FileName   

The name name of the output bitmap. Choose the appropriate file extension to select the format, according to thefollowing table:

   
Extension Format
.bmp Windows Bitmap
.emf Enhanced Metafile
.jpg JPEG
.pcx ZSoft PCX
.pdf PDF
.png Portable Network Graphics
.pnm PNM
.raw Raw data
.sgi Silicon Graphics
.svg Scalable Vector Graphic
.tga Targa
.tif Tiff
Width   Image width (ignored by vector formats as EMF and SVG).
Height   Image height (ignored by vector formats as EMF and SVG).

Return values:
Error code if it fails.

 

Example:
SAVEIMG2D   "C:\MySketch.png"

 

See also:
SAVE, SAVEIMG.


SELECT   (CHAR)Selection
With this command it's possible to show/hide (see UNSELECT command) the atoms.

Parameters:
Selection   

The selection uses the following format:

ATOM_NAME:RESIDUE_NAME:RESIDUE_NUMBER:CHAIN_ID:MOLECULE_MUMBER

Each argument of the selection is optional and the maximum length of each field is four characters for the ATOM_NAME, RESIDUE_NAME, RESIDUE_NUMBER, MOLECULE_MUMBER and one character for the CHAIN_ID. The selection is case-sensitive and you can use wildcards (?, *). The SELECT command can be used also to select by atom number.

Return values:
Error code if it fails.

 

Examples:

SELECT    H*    Select all hydrogens
SELECT    C*:ALA    Select all carbons of all alanines
SELECT    CA:*:*:B    Select all alpha carbon of the chain B
SELECT    *:VAL:?    Select all valines in the first 9 residues
SELECT    10    Select the atom number 10

See also:
SELPROX, SELRANGE, UNSELECT, UNSELPROX, UNSELRANGE, mSelectAll, mSelectCustom, mSelectNone, mSelectInvert, mSelectBackbone, mSelectNoHyd, mSelectNoWater.


SELPROX   (MCHAR)Mode   (CHAR)Selection   (UFLOAT)Radius
Show (to hide use UNSELPROX) atoms or residues included in a sphere around specified atom selection.

Parameters:
Mode    Selection mode (ATOM, RESIDUE).
Selection Atom selection. For more detail, see SELECT.
Radius Radius of the spheroid including at least one atom.

Return values:
Error code if it fails.

 

Examples:

SELPROX    ATOM   *:GLY:45   3.0   Show atoms included in a sphere of 3.0 radius around GLY 45
SELPROX    RESIDUE   *:*:*:*:2   4.5   Show residues which at least one atom is included in a sphere of 4.5 around the molecule # 2.

See also:
SELECT, SELRANGE, UNSELECT, UNSELPROX, UNSELRANGE, mSelectAll, mSelectCustom, mSelectNone, mSelectInvert, mSelectBackbone, mSelectNoHyd, mSelectNoWater.


SELRANGE   (MCHAR)Mode   (UINT)Start   (UINT)End
Show atom or residue ranges specifying the starting and the ending atom/residue number (to hide use UNSELRANGE).

Parameters:
Mode    Selection mode (ATOM, RESIDUE).
Start Staring atom/residue number.
End Endig atom/residue number.

Return values:
Error code if it fails.

 

Examples:

SELRANGE    ATOM   45   101    Show atoms from 45 to 101
SELRANGE    RESIDUE   70   75    Show residues from 70 to 75

See also:
SELECT, SELPROX, UNSELECT, UNSELPROX, UNSELRANGE, mSelectAll, mSelectCustom, mSelectNone, mSelectInvert, mSelectBackbone, mSelectNoHyd, mSelectNoWater.


SELSMARTS   (CHAR)SmartsString

Show atoms according to the SMARTS string (to hide use UNSELSMARTS). When you use this command, you must pay attention, because SMARTS language assumes that the bond order is correctly assigned to the molecule. If this condition is not satisfied, you may obtain wrong selections.

Parameters:
SmartsString    SMARTS string.

Return values:
Error code if it fails.

 

Examples:

SELSMARTS    C=O    Show the carbonylic groups

See also:
SELECT, SELPROX, SELRANGE, UNSELECT, UNSELPROX, UNSELRANGE, UNSELSMARTS, mSelectAll, mSelectCustom, mSelectNone, mSelectInvert, mSelectBackbone, mSelectNoHyd, mSelectNoWater.


 

SETLASTFILENAME   (MCHAR)FileName
Set the pre-defined name used to open a file.

Parameters:
FileName    File name without path and extension.

Return values:
Error code if it fails.

 

Example:

SetLastFileName   "My file"

 

See also:
None


SHUTDOWN
Shutdown (power off) the system, showing a count down window to abort the operation.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
SHUTDOWN

 

See also:
MONITORPOWER.


SMARTMOVE   (BOOL)Mode
Enable/disable the SmartMove rendering mode (see View settings).

Parameters:
Mode    If it's true (1), it enables the SmartMove, or if it's false (0), it disables it.

Return values:
Error code if it fails.

 

Example:
SMARTMOVE   0

 

See also:
ANTIALIAS, DEPTHCUE, SMARTMOVEATM, mLight, mShowSettings.


SMARTMOVEATM   (UINT)Atoms
Change the atom threshold to auto enable the SmartMove (see View settings).

Parameters:
Atoms    Number of atoms. If it's null (0), the SmartMove is always active.

Return values:
Error code if it fails.

 

Example:
SMARTMOVEATM   700

 

See also:
ANTIALIAS, DEPTHCUE, SMARTMOVE, mLight, mShowSettings.


SOUNDEFFECTS   (BOOL)Enable
Enable/disable the sound effects for event notifications.

Parameters:
Enable    I1 (true), it enables the sound effects; 0 (false), it disables them.

Return values:
The previous status of the sound effects status: 1 (true) enabled or 0 (false) disabled.

 

Examples:
SOUNDEFFECTS   1

 

See also:
None.


SRFALPHA   (BOOL)Enable
Enable/disable the alpha blending (transparency) of the current surface.

Parameters:
Enable    If it's 1 (true), it enables the alpha blending, or if it's 0 (false), it disables it.

Return values:
Error code if it fails.

 

Examples:
SRFALPHA   1
(Enable the alpha blending).

 

See also:
SRFALPHAVAL, SRFCOLOR, SRFCOLORBY, SRFCUR, SRFDOTSIZE, mSurface.


SRFALPHAVAL   (UINT)AlphaValue
Set the alpha blending value (transparency level) to the current surface. The alpha blending must be enabled to see the effect of this command (SRFALPHA command).

Parameters:
AlphaValue    Alpha blending value. It must be between 0 (invisible) to 255 (opaque).

Return values:
Error code if it fails.

 

Examples:
SRFALPHAVAL   128

 

See also:
SRFALPHA, SRFCOLOR, SRFCOLORBY, SRFCUR, SRFDOTSIZE, mSurface.


SRFCOLOR   (UINT)Color
Change the color of the current surface using the RGB format.

Parameters:
Color    Color in RGB format (0 Color 16777215).

Return values:
Error code if it fails.

 

Examples:
SRFCOLOR   255
(Color the surface in red).

SRFCOLOR   65535
(Color the surface in yellow)

 

See also:
SRFCOLORBY, SRFCOLORGRAD, SRFCUR, mSurface.


SRFCOLORBY   (MCHAR)Method
This command changes the color of the current  surface by a specific method.

Parameters:
Method    Coloring method (ATOM, RESIDUE, CHAIN, SEGMENT, MOLECULE and SURFACE).

Return values:
Error code if it fails.

 

Example:
SRFCOLORBY   RESIDUE
(Color the surface by residue).

 

See also:
SRFCOLOR, SRFCUR, SRFCOLORGRAD, mSurface.


SRFCOLORGRAD  (UINT)Colors
Color the current surface using a gradient of colors. The color assignment is based on the surface property calculated for each dot (e.g. MEP, MLP, ILM, PSA). To define a new gradient of colors, see SRFGRAD.

Parameters:
Colors    Number of gradient colors. It can be from 2 to 6.

Return values:
Error code if it fails.

 

Example:
SRFCOLORGRAD   4
(Color the surface using a gradient defined by four colors).

 

See also:
SRFCOLOR, SRFCOLORBY, SRFCUR, SRFGRAD, mSurface.


SRFDOTSIZE  (UINT)DotSize
Change the dot size of the current surface. The effect of this command is available only with dotted surfaces.

Parameters:
DotSize    Dot size: values between 1 to 4 are for dots and between 5 to 10 are for small spheres.

Return values:
Error code if it fails.

 

Example:
SRFCOLORGRAD   5
(Change the dot size to 5 and, more in detail, switch the visualization from dots  to small spheres).

 

See also:
SRFALPHA, SRFALPHAVAL, SRFCOLOR, SRFCOLORBY, SRFCUR, mSurface.


SRFGRAD  (UINT)Color1   (UINT)Color2   (UINT)Color3   (UINT)Color4   (UINT)Color5   (UINT)Color6
Color the current surface using a gradient of colors. The color assignment is based on the surface property calculated for each dot (e.g. MEP, MLP, ILM, PSA).

Parameters:
Color1
Color2
Color3
Color4
Color5
Color6
   Colors in RGB format (0 Color 16777215) defining the gradient. Unused color must be set to 0.

Return values:
Error code if it fails.

 

Example:
SRFGRAD   65535   255   0   0   0   0
(It defines a two color gradient from yellow to red).

 

See also:
SRFCOLORGRAD, SRFCUR, SRFGRADAUTORNG, SRFGRADRANGE, mSurface.


SRFGRADAUTORNG  (BOOL)Enable
Enable/disable the automatic property range detection used by SRFGARD command. When this function is enabled, VEGA ZZ searches the maximum and the minimum value of the property calculated for each surface dot, in order to use all gradient colors. If you want to use a standardized gradient, you must disable this function and define the property range values by SRFGRADRANGE command.

Parameters:
Enable    If it's 1 (true) or 0 (false), the automatic range will be enabled or not.

Return values:
Error code if it fails.

 

Example:
SRFGRADAUTORNG   0
(It disables the automatic range detection).

 

See also:
SRFCOLORGRAD, SRFCUR, SRFGRAD, SRFGRADRANGE, mSurface.


SRFGRADRANGE  (FLOAT)MinVal   (FLOAT)MaxVal
This command defines the range of the property values that will be used to color the current surface by gradient (see SRFGARD command). It doesn't have effects if the automatic range detection is enabled (see SRFGRADAUTORNG command to disable it). This function is useful to obtain surface maps colored with standardized color gradients.

Parameters:
MinVal    Lower bound of the range of property values.
MaxVal Higher bound of the range of property values.

Return values:
Error code if it fails.

 

Example:
SRFGRADRANGE   -0.5   0.5
(Set the property range from -0.5 to +0.5).

 

See also:
SRFCOLORGRAD, SRFCUR, SRFGRAD, SRFGRADAUTORNG, mSurface.


SRFVISIBLE   (BOOL)Enable
Show/hide the current surface.

Parameters:
Enable

  

If it's 1 (true), the surface is visible, or if it's 0 (false), the surface is invisible.

Return values:
Error code if it fails.

 

Example:
SRFVISIBLE   0
(Disable the surface making it invisible).

 

See also:
SRFCUR, mSurface.


STICKPROP   (UINT)Resolution   (FLOAT)CylinderRad
Change the stick visualization properties.

Parameters:
Resolution    Resolution (8 SphereRes 24).
CylinderRad Cylinder radius (0.05 CylinderRad 0.5).

Return values:
Error code if it fails.

 

Example:
STICKPROP    12   0.20
(Default settings).

 

See also:
BALLSTICKPROP, CPKPROP, TRACEPROP, TUBEPROP, WIREPROP, mShowSettings.


TORSION   (CHAR)Atom1   (CHAR)Atom2   (CHAR)Atom3   (CHAR)Atom4   (INT)Flags
Measure the torsion angle defined by four atoms.

Parameters:
Atom1    Atoms defining the torsion. See SELECT command for the correct syntax.
Atom2
Atom3
Atom4
Flags Control flags that can be combined by OR logical operator or sum:
  
Flag Value Description
MEAS_3DOBJ 1 Show the measure indicator in the main window.
MEAS_3DTXT 2 Show the measure value in the main window.
MEAS_CONTXT 4 Show the measure value in the console window.

Return values:
The command returns the torsion value in degrees and if it fails, the error code is reported.

 

Example:
TORSION    1   2   3   4
(Measure the torsion defined by first, second, third and forth atoms).

 

See also:
ANGLE, DISTANCE, SELECT, PLANEANG.


TRACEPROP   (UINT)CylinderRes    (FLOAT)CylinderRad
Change the trace visualization properties.

Parameters:
CylinderRes     Cylinder resolution (3   CylinderRes 30).
CylinderRad Cylinder radius (0.1 CylinderRad 1.0).

Return values:
Error code if it fails.

 

Example:
TRACEPROP   10   0.4
(Set the trace visualization properties to default).

 

See also:
BALLSTICKPROP, CPKPROP, STICKPROP, TUBEPROP, WIREPROP, mShowSettings.


TRANSLATE   (FLOAT)X    (FLOAT)Y   (FLOAT)Z
Translate the active object along X, Y and Z axis.

Parameters:
X    X translation.
Y Y translation.
Z Z translation.

Return values:
Error code if it fails.

 

Example:
TRANSLATE   90   45.5   0

 

See also:
ROTATE, ZOOM.


TRJANIMPLAY
Start the trajectory animation playback.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
TRJANIMPLAY

 

See also:
OPEN, TRJANIMSET, TRJANIMSPEED, TRJANIMSTOP, TRJOPEN, TRJSEL, TRJSELFIRST, TRJSELLAST, mOpen, mAnalysis.


TRJANIMSET   (UINT)Start    (UINT)End   (BOOL)Loop
Set the trajectory animation range.

Parameters:
Start    Starting frame.
End Ending frame.
Loop If it's 1 (true), the animation is played endlessly, or if it's 0 (false), the animation is played one time only.

Return values:
Error code if it fails.

 

Example:
TRJANIMSET   12   40   1

 

See also:
OPEN, TRJANIMPLAY, TRJANIMSPEED, TRJANIMSTOP, TRJOPEN, TRJSEL, TRJSELFIRST, TRJSELLAST, mOpen, mAnalysis.


TRJANIMSPEED   (UINT)Speed    (UINT)Skip
Set the trajectory animation speed and the number of frames to skip for each animation step.

Parameters:
Speed    Animation speed (0 Speed 500).
Skip Number of frames to skip for each animation step (Skip 0).

Return values:
Error code if it fails.

 

Example:
TRJANIMSPEED   200   0

 

See also:
OPEN, TRJANIMPLAY, TRJANIMSET, TRJANIMSTOP, TRJOPEN, TRJSEL, TRJSELFIRST, TRJSELLAST, mOpen, mAnalysis.


TRJANIMSTOP
Stop the animation playback.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
TRJANIMSTOP

 

See also:
OPEN, TRJANIMPLAY, TRJANIMSET, TRJANIMSPEED, TRJOPEN, TRJSEL, TRJSELFIRST, TRJSELLAST, mOpen, mAnalysis.


TRJGRAPHENE
Show the energy data in the Graph Editor, if the energy values match the trajectory file.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
TRJGRAPHENE

 

See also:
OPEN, GRAPHCLOSE, TRJOPEN, mOpen, mAnalysis.


TUBEPROP   (UINT)SplineRes   (UINT)CylinderRes    (FLOAT)CylinderRad   (BOOL)BiquadInter
Change the trace visualization properties.

Parameters:
SplineRes    Spiline sesolution (1 SplineRes 20).
CylinderRes  Cylinder resolution (3   CylinderRes 30).
CylinderRad Cylinder radius (0.1 CylinderRad 1.0).
BiquadInter If it's true (1), the biquadratic interpolation is performed; if it's false (0), the cubic interpolation is performed.

Return values:
Error code if it fails.

 

Example:
TUBEPROP   5   10   0.4   0
(Set the tube visualization properties to default).

 

See also:
BALLSTICKPROP, CPKPROP, STICKPROP, TRACEPROP, WIREPROP, mShowSettings.

 


TURBO   (BOOL)Enable
Enable/disable the turbo mode. This function increases the computational speed when you need to process a large number of molecules (e.g. databases and trajectories). The refresh of OpenGL window is synchronized to the monitor vertical scan (usually 60 Hz for LCD monitors) and, for this reason, the processing speed is limited to that frequency. The turbo mode disables the OpenGL update of the main window and in this way the computational thread doesn't need to wait the window refresh.

Parameters:
Enable    If it's true (1), the turbo mode is enabled; if it's false (0), the turbo mode is disabled.

Return values:
None.

 

Example:
TURBO   1
 

See also:

TURBOEX.


TURBOEX   (CHAR)Message
Enable the turbo mode (see TURBO), changing the default message. Use TURBO 0 to revert to the normal mode.

Parameters:
Message    IMessage to be shown in VEGA ZZ main window.

Return values:
None.

 

Example:
TURBOEX   "Hello World !"
 

See also:

TURBO.


UNDOENABLE   (BOOL)Enable
Enable/disable the undo/redo buffer.

Parameters:
Enable    If it's true (1), the undo buffer is enabled; if it's false (0), the undo buffer is disabled.

Return values:
Error code if it fails.

 

Example:
UNDOENABLE   0
 

See also:

UNDOPUSH, mRedo, mUndo.


UNDOPUSH   (CHAR)Message
Push the current molecule to the undo buffer, specifying the message to revert to previous status.

Parameters:
Message    Message to revert the operation.

Return values:
Error code if it fails.

 

Example:
UNDOPUSH   "Undo the last operation"
 

See also:

UNDOENABLE, mRedo, mUndo.


UNSELECT   (CHAR)Selection
Hide atoms using pattern matching. See SELECT command.


UNSELPROX   (MCHAR)Mode    (CHAR)Selection   (UFLOAT)Radius
Hide atoms or residues included in a sphere around specified atom selection. See SELPROX command.


UNSELRANGE   (MCHAR)Mode    (UINT)Start   (UINT)End
Hide an atom or a residue range. See SELRANGE command.


UNSELSMARTS   (CHAR)SmartsString
Hide atoms according to the SMARTS string. See SELSMARTS command.


UPDATELASTFILE   (BOOL)Enable
Enable/disable the automatic update of last file in the main menu.

Parameters:
Enable   

If it's true (1), the update of the last file menu is enabled (default status), otherwise if it's false (0), the menu update is disabled. This status is useful if a script is performing a job in which several files are loaded and/or saved, avoiding to loose the history of last files.

Return values:
Error code if it fails.

 

Example:
UPDATELASTFILE   0

 

See also:
OPEN, SAVE, mOpen, mSave.


WIREPROP   (UINT)Thickness    (BOOL)SmoothMode
Change the wireframe visualization properties.

Parameters:
Thickness    Bond thickness (1   Thickness 5).
SmoothMode Smoothing of bond colors (1 = enabled, 0 = disabled).

Return values:
Error code if it fails.

 

Example:
WIREPROP   2   0

 

See also:
BALLSTICKPROP, CPKPROP, STICKPROP, TRACEPROP, TUBEPROP, mShowSettings.


WKSCHANGE   (UINT)WorkspaceNumber 
Change the current workspace.

Parameters:
WorkspaceNumber    Workspace number. It must be grater or equal to 0 and 0 is the main workspace.

Return values:
True (1), if the workspace is correctly changed or false (0), if the specified workspace doesn't exist.

 

Example:
WKSCHANGE   3

 

See also:
WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSCPYATM   (UINT)DestinationWorkspaceNumber    (UINT)SourceWorkspaceNumber
Copy the atoms from a workspace to another one.

Parameters:
DestinationWorkspaceNumber    Destination workspace ID.
SourceWorkspaceNumber   Source workspace ID.

Return values:
True (1), if the copy is successfully completed or false (0), if an error occurs.

 

Example:
WKSCPYATM   0   1

 

See also:
WKSCHANGE, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSLOCK
Lock the current workspace. Until the workspace is locked, it can't be changed. To check the workspace lock status, get the value of WKSLOCKED variable.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
WKSLOCK

See also:
WKSCHANGE, WKSCPYATM, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSNEW
Create a new workspace and change the current to it.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
WKSNEW

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSNEXT
Select the next workspace.

 

Parameters:
None.

 

Return values:
True (1), if the workspace is correctly changed or false (0), if the current workspace is the last and there aren't other workspaces.

 

Example:
WKSNEXT

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSPREV
Select the previous workspace.

 

Parameters:
None.

 

Return values:
True (1), if the workspace is correctly changed or false (0), if the current workspace is the first (main).

 

Example:
WKSPREV

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSREM   (UINT)WorkspaceNumber   (BOOL)Ask
Remove the specified workspace. All contained data are lost.

Parameters:
WorkspaceNumber    Workspace number. It must be grater to 0. The main workspace (0) can't be removed.
Ask If it's true (1) and if the workspace isn't empty, a requester is shown to confirm the operation. If it's false (0), the requester isn't shown.

Return values:
True (1), if the workspace is removed without errors or false (0) if the specified workspace doesn't exist or it's the main workspace (0) or the user aborts the operation.

 

Example:
WKSREM   2   1

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSREMALL   (BOOL)Ask
Remove all workspaces deleting all contained data. The main workspace (0) remains unchanged.

Parameters:
Ask    If it's true (1) and if the workspace isn't empty, a requester is shown to confirm the operation. If it's false (0), the requester isn't shown.

Return values:
True (1), if all workspaces are removed without errors or false (0), if the user aborts the operation.

 

Example:
WKSREMALL   0

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMCUR, WKSSETNAME, WKSUNLOCK.


WKSREMCUR   (BOOL)Ask
Remove the current workspace deleting all contained data. The main workspace (0) can't removed.

Parameters:
Ask    If it's true (1) and the workspace isn't empty, a requester is shown to confirm the operation. If it's false (0), the requester isn't shown.

Return values:
True (1), if the workspace is removed without errors or false (0), if the user aborts the operation or if the current workspace is the main one (0).

 

Example:
WKSREMCUR   1

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSSETNAME, WKSUNLOCK.


WKSSETNAME   (CHAR)NewName
Change name of the current workspace.

Parameters:
NewName    New workspace name.

Return values:
Error code if it fails.

 

Example:
WKSSETNAME   "My molecule"

 

See also:
WKSCHANGE, WKSCPYATM, WKSLOCK, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSUNLOCK.


WKSUNLOCK
Unlock the workspace, allowing to change the current workspace. To check the workspace lock status, get the value of WKSLOCKED variable.

 

Parameters
None.

 

Return values:
Error code if it fails.

 

Example:
WKSUNLOCK

 

See also:
WKSCHANGE, WKSCPYATM, WKSNEW, WKSNEXT, WKSPREV, WKSREM, WKSREMALL, WKSREMCUR, WKSSETNAME, WKSLOCK.


ZCLIP   (UINT)Value
This command sets the Z clipping.

Parameters:
Value    Z clipping value (1 Value 300).

Return values:
Error code if it fails.

 

Example:
ZCLIP   200

 

See also:
ANTIALIAS, DEPTHCUE, mShowSettings.


ZOOM   (UINT)Ratio
Set the zoom ratio.

Parameters:
Ratio    Zoom ratio (Ratio > 0).

Return values:
Error code if it fails.

 

Example:
ZOOM   200

 

See also:
ROTATE, TRANSLATE, mShowSettings.


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