11.1 The Graph Editor

The Graph Editor allows to show and manage data sets calculated by VEGA ZZ and/or by other external programs. It's possible to load data in some different file formats in order to support the largest number of software packages. All functions are accessible through the menu bar, tool bar and mouse. More than one Graph Editors can be opened selecting Tools GraphED main menu item or clicking the graph icon of the VEGA ZZ tool bar.


Graph editor


11.1.1 File menu

Item Accelerator Description
New Ctrl+N Clean all data.
Open Ctrl+O

Open a new data set. The same operation can be performed by drag & drop operations of files on the Graph Edtor window. The supported file formats are: CHARMM .ene, Comma Separated values .csv, Data Interchange Format .dif, NAMD output .out, Quanta .plt and Custom.  Use the Autodetect function of the file requester to activate the automatic recognition system.   If your data set format is not supported, but is ASCII, you can select the Custom filter, that shows the following dialog window:


Custom filter


The central box shows the first lines of the selected file. In the Skip Lines field, you can specify the number of lines that will be skipped starting from the beginning of file.  Checking the Separator checkbox, you can insert the character used as column separator. The X Column field, if checked, allows to indicate the column number to associate with the X values and Y Column filed allows to indicate the column number to associate with Y values. Clicking  Ok button, you confirm the loading operation.

Save As ... Ctrl+S Save the data set. The supported output formats are: Comma Separated Values .csv, Data Interchange Format .dif, and Quanta .plt
Export to Excel Ctrl+E

Export the data directly to Microsoft Excel by OLE interface. Excel must be installed on the PC.

Print Ctrl+P Print the chart, showing the printer requester.
Exit - Close the window without saving.


11.1.2 Edit menu

Item Subitem Accelerator Description
Labels Title - Change the chart title.
X axis - Change the X axis label.
Y axis - Change the Y axis label.
Copy   Ctrl+C Copy the selected graph to the clipboard as windows metafile.
Sel. conformation   Ctrl+F Select the conformation associated to the plot clicking on the trace area. The conformation will be changed automatically and shown in the main window. This item is disabled if the graph isn't generated from the trajectory analysis.


11.1.3 Zoom menu

Item Accelerator Description
In - Zoom in.
Out - Zoom out.
Reset - Reset to the original scale.
Animation - If checked (default), activates the zoom animation.

Please note that to zoom-in on the graph area you can use the mouse pressing the left button and drawing a box.


11.1.4 Calculate menu

Item Subitem Accelerator Description
Cluster Chart   - Open the cluster analysis dialog:


Number Clustering Mode: Number

selecting Number from Clustering Mode radiobox, it's possible to specify the number of clusters. The default number of clusters is 5 and the range of each cluster is automatically calculated. Clicking Show, the histogram graph is shown:


Cluster graph


Each histogram is a cluster and its height is the number of value contained in the cluster, like shown in the little box on the top. Clustering Mode: Ranges

This operation mode consists in a user defined list of rages. Each range is the upper and lower limit of a cluster.




You can define a new range (cluster) typing in Min and Max fields the limits and pressing the Add button. To remove a single range, you must highlight it clicking on the list, and press the Remove button. If you want remove all ranges, click on Remove All and if you want change a range, highlight it, type the new limits and press Update.
The compiled list of ranges can be saved (Save button)  if you think that it should be useful. Use the Load button to reload the list in the memory. Please note that the folder where the ranges should be saved is ... \VEGA\Chart\Ranges and the file format is CSV with the semicolon as separator (;), like in the following example:

  0;  30
 30;  90
 90; 150
150; 210
210; 270
270; 330
330; 360

Freq. spectrum   -

Calculate the DFT (Discrete Fourier Transformation) frequency spectrum. It's useful to highlight the most significant wave components and their frequency and amplitude:


Frequency spectrum


The frequency spectrum is indicated in percent. Please remember that the Shannon's sampling theorem says that maximum frequency in the spectrum (100%) is half the sampling rate. The Amplitude has got the same measure unit of the starting wave. 

Noise reduction 95 -

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. Consider the following plot:


Original signal


Suppose to apply the 90% noise reduction because you want consider the low frequency transitions (slow transitions):


Denoised signal

90 -
75 -
50 -
25 -
Derivative   -

Calculate the first derivative.

Statistical Values   - Show some statistical values related to the data set:


Satistical values