Starting NMRmix¶
Assuming that NMRmix was installed using the installer scripts, open a terminal window and type:
nmrmix
If NMRmix was installed manually without the scripts, but all the necessary dependencies are present, then the program can be started like any other python program. Open a terminal window, change the current directory to the location of the NMRmix source files, and type:
python NMRmix.py
The NMRFAM splash screen should pop up, and NMRmix should start. On the resulting NMRmix title screen, press Continue to start using NMRmix.
Setting Default Parameters¶
The default user-defined parameters can be set and saved for future uses of NMRmix. The parameters are saved as a simple text file (parameters.txt) that is located in a directory called .nmrmix, which can be found under the user’s home directory. This file and folder is only created if the default parameters are changed and saved. If for any reason NMRmix is unable to create this directory/file, saving the default parameters will not be possible. Instead, each parameter will need to be modified manually, if necessary, for each execution of the NMRmix program.
To set the default preferences, click the Set Default Preferences button on the NMRmix title window. The Default Preferences window should appear with four tabs: Directories/Scoring; Optimizing; Refining; and Display/Statistics.
Directories/Scoring Parameters¶
- Working Directory
- For a description of this parameter, see Setting Working and Peaklist Directories.
- Local Peak List Directory
- For a description of this parameter, see Setting Working and Peaklist Directories.
- Overlap Range
- For a description of this parameter, see
- Score Scaling
- For a description of this parameter, see
- Use Intensity Scoring
- For a description of this parameter, see
- Autosave Results
- For a description of this parameter, see
Optimizing Parameters¶
- Starting Mixture Number
- For a description of this parameter, see
- Max Mixture Size
- For a description of this parameter, see
- Extra Mixtures
- For a description of this parameter, see
- Cooling Rate
- For a description of this parameter, see
- Start Temp
- For a description of this parameter, see
- Final Temp
- For a description of this parameter, see
- Max Steps
- For a description of this parameter, see
- Mix Rate
- For a description of this parameter, see
- Iterations
- For a description of this parameter, see
- Restrict by Group
- For a description of this parameter, see
- Randomize Initial Mixture
- For a description of this parameter, see
Refining Parameters¶
- Use Refinement
- For a description of this parameter, see
- Cooling Rate
- For a description of this parameter, see
- Start Temp
- For a description of this parameter, see
- Final Temp
- For a description of this parameter, see
- Max Steps
- For a description of this parameter, see
- Mix Rate
- For a description of this parameter, see
Display/Statistics Parameters¶
- Optimization Progress Bar Update (steps)
- During the optimization of the mixtures, a progress bar is used to show the number of annealing steps that have been completed. On most computers each step can happen fairly quickly. This parameter defines how often to draw an update to the progress bar. For example, the default is set to 50 steps, which indicates that the progress bar will update every 50 annealing steps. With some lower end computers, it may be useful to draw the updates less frequently (larger step size).
- Simulated Peak Width Fraction (half-width at half-maximum)
- The simulated spectra in NMRmix draws each peak using a Lorentz distribution. While the resolution and line width of NMR peaks is often dependent upon magnet strength, the simulated spectra uses a default line width for drawing. This parameter only changes the cosmetic look of the simulated peaks and does NOT affect the optimization process.
Saving Default Parameters¶
- Close
- This button closes the Default Preferences window without saving any of the changes made. This means that NMRmix will use the parameters that were loaded upon startup, whether these are the factory defaults or the parameters read from an existing parameters file.
- Reset
- This button resets all of the parameters to the factory default parameters. While this updates all the default parameter values for this open instance of NMRmix, these values are not saved as the default values in the .nmrmix/parameters.txt file. To save these values, press the Save button.
- Restore
- This button resets all of the parameters to the values found in the .nmrmix/parameters.txt file. This updates all the default parameter values for this open instance of NMRmix. Since these values are read directly from the parameters.txt file, there is no need to save unless changes are made.
- Save
This button will write the all of the parameters in the Default Parameters window to the .nmrmix/parameters.txt file. If the .nmrmix directory does not exist, NMRmix will create it and place the parameters.txt file within. A window will pop-up indicating whether the save was successful.
If saving fails (likely due to permissions issues), these current parameters will be the defaults for the currently open instance of NMRmix. In this case, subsequent launches of NMRmix will not use the updated parameters as they were not saved.