Virtual NMR Spectrometer: The Main Window
  1. Directory edit box: Use this box to type in a new directory where pulse programs might be located.
  2. Help button: Using this button to get link to help files. Currently available: info about the version, authors, and acknowledgements.
  3. Number of Spins pulldown menu: Click the downward pointing arrow and drag to change the number of spins in the system that will be used for simulation. After selecting the desired number of spins, click the Spin Setup button (4). Note: if you change already selected number of spins, you will have to click this button twice (not double-click!): once to recalculate the spin density operator for the new number of spins, again to open the Spin Setup window and configure the spin system.
  4. Spin Setup button: Click this button to open the Spin Setup window. This window allows the user to configure a particular spin system for a simulation - type of nuclei (1H,15N,13C) and relevant parameters such as chemical shift, relaxation and cross-relaxation rates, scalar coupling, etc. This window also can be used to toggle the projection tracing mode and to select basis operators for tracing spin-density components during the experiment. Also features Relaxation Calculator, a built-in tool for calculating relaxation rates for a given nuclear pair.
  5. Program Parameters button: Click this button after translating a pulse program (17) to open the Program Parameters window. This window allows the user to define and modify the variables used in the pulse program that has been translated.
  6. ZG button: Click this button after setting all parameters (e.g. spin system, experimental, and pulse sequence parameters) to begin the simulation. This button appears dark until a valid pulse sequence has been translated into a matlab script, then it turns green, indicating that the pulse sequence has been translated and you can now proceed with the simulation. If there was an error in pulse program execution (e.g. some of the params were not defined etc), this button will turn blue; usually, an explanatory message will be displayed in the matlab window in this case. You can click on the blue ZG button to start the simulation (after fixing the problem of undefined experimental parameters). (See (17) in this window for instructions on translating a pulse sequence).
  7. Experimental Setup button: Click this button to open the Experimental Setup window. This window allows the user to set parameters such as the spectral width, carrier offset, resolution, etc.
  8. Progress display counter: This counter displays the progress of the simulation. The denominator is the total number of rows of data to be simulated. The numerator is the number of rows already simulated.
  9. Simulation Parameters button: Click this button to open the Simulation Parameters window. This window allows the user to set parameters such as the spectral width, carrier offset, resolution, etc.
  10. Number of Pathways display This counter will display the total number of coherence transfer pathways (for all of the spherical basis operators) during a simulation in which CTP approach was selected in the Simulation Parameters window.
  11. Data Processing button: Click this button to open the Data Processing window. This window provides all of the standard tools to process "raw" acquisition data and display it as a spectrum.
  12. Projections button: This button opens the Projection Display window to show the projection of the spin density onto selected basis operators during a simulated pulse sequence. In order for this window to contain information, prior to starting the simulation, the user must select the projections to be analyzed in the Spin Operator Tracing edit window of the Spin Setup window.
  13. Shape Generator: This button opens the Shape Generator window to design/visuallize standard or used-defined shapes for shaped pulses of PFG.
  14. EXIT button: Using this button to exit the virtual spectrometer is preferable to simply closing the main pannel by clicking the 'x' in the upper right corner of the window because clicking the EXIT button will close other subordinate windows and clear temporary files and workspace variables.
  15. Save button: Click this button to save the results of current session or the experimental settings. Opens Save Data Window.
  16. Load button: Click this button to read in the results of previous sessions or experimental settings. Opens Load Data Window.
  17. Translate Pulse Program button: Click this button after selecting a pulse program in the Pulse Program Selection edit window(18) to translate the pulse program into a simulation script that matlab can execute.
  18. Pulse Program Selection edit window: Click this window and use the arrow keys or the mouse to select a pulse program from the active directory. To change the active directory, use either: the Directory Selection edit window & Go button (23 & 21), or the Directory edit box & Change Directory button (25 & 1).
  19. Display Pulse Program button: Click this button to open a new window to display the pulse program selected in the Pulse Program Selection edit window (18).
  20. Pulse Program display: This text displays the name of the pulse program that has most recently been translated into a matlab script (i.e. the one that will be run if the ZG button (6) is pressed).
  21. Go button: Click this button to change to the directory selected in the Neighbor Directory edit window (23).
  22. Refresh button: Click this button to refresh (re-read) the content of the selected directory: this could be useful if the content of this directory has been changed after it was displayed.
  23. Neighbor Directory edit window: Click on this window and use the arrow keys or the mouse to select a directory. Use this window to navigate towards a directory that contains pulse programs that can be translated.
  24. Current Directory display: This text display indicates the current active directory. Files containted in the active directory are diplayed in the Pulse Program Selection edit window (18).
  25. Change Directory button: Click this button to change the active directory to the one in the Directory edit box (1).

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Page designed by Peter Nicholas. Last modified 12/26/03 by David Fushman.