Tutorials ========= Visualize spectra --------------------------- A tutorial on how to load and display 1D NMR spectra is presented in :ref:`Getting started `. Here, we load and inspect 2D relaxation spectra of glycine and L-histidine hydrochloride monohydrate with magic angle spinning solid-state NMR spectroscopy. The data folders for glycine and histidine are in the GLY and HISTCM folders. Drag and drop both folders to the Workflow of EasyNMR. Two transient Folder objects are created. Extract experiments 401 and 412 from the GLY and HISTCM folders, respectively, by clicking on the `Extract` button. These two experiments are marked as *Bruker 2D spectrum*. .. figure:: images/easynmr_tutorial_2d_histgly_loaded.jpg :align: center :width: 800 Loading two 2D relaxation spectra for glycine and L-histidine hydrochloride monohydrate. Double click on the glycine Plot object. You can see the :sup:`15`\N chemical shift in the horizontal axis and delay time in the T\ :sub:`1` measurement method of Torchia (`J. Magn. Reson. 30 (3): 613-616 `_) in the vertical axis. The glycine signal at :math:`\delta_{Gly} = 32.9 \textrm{ ppm}` disappears in approximately 2 seconds - five times that of the T\ :sub:`1` value for this amine site - with an approximate relaxation time of T\ :sub:`1, Gly` = 0.4 s. .. figure:: images/easynmr_tutorial_2d_histgly_plotglycine_time.jpg :align: center :width: 800 Two-dimensional :sup:`15`\N relaxation ordered spectroscopy of glycine with solid-state NMR. The vertical axis is delay time for T\ :sub:`1` relaxation measurement, while the horizontal axis is the :sup:`15`\N chemical shift. Now, double click on the histidine Plot object. There are three nitogen sites in L-histidine hydrochloride monohydrate: :math:`\delta_{A} = 47 \textrm{ ppm}` for the amine nitrogen, :math:`\delta_{\epsilon} = 176 \textrm{ ppm}` for the nitrogen nuclei farthest from the branch, and :math:`\delta_{\delta} = 189 \textrm{ ppm}` for the imidazole nitrogen closest to the branch. With the default magnification, in the 2D :math:`t_{Delay} - \delta` plot, you can only see the :math:`\textrm{N}^{\delta}` and :math:`\textrm{N}^{\epsilon}` peaks. .. figure:: images/easynmr_tutorial_2d_histgly_plothistidine_time.jpg :align: center :width: 800 Two-dimensional :sup:`15`\N relaxation ordered spectroscopy of histidine with solid-state NMR. The vertical axis is delay time for T\ :sub:`1` relaxation measurement, while the horizontal axis is the :sup:`15`\N chemical shift. The :math:`\textrm{N}^{\delta}` and :math:`\textrm{N}^{\epsilon}` sites have long relaxation times. Their signal was not completely relax, even after 8000 seconds! In fact, :math:`T_{1, \delta} = 3120 \textrm{ s}` and :math:`T_{1, \epsilon} = 2720 \textrm{ s}`. Use the Zoom tool in the Plot toolbar to inspect the amine peak. Magnify the area around the amine region and repeat this process until you see the amine peak. .. figure:: images/easynmr_tutorial_2d_histgly_plothistidine_zoomcropped.jpg :align: center :width: 300 Use the Zoom tool to magnify the amine region of the plot. .. figure:: images/easynmr_tutorial_2d_histgly_plothistidine_zooming.jpg :align: center :width: 800 Zooming into the amine region. The amine peak in histidine disappears in approximately 8 seconds with :math:`T_{1, A} = 1.8 \textrm{ s}` .. figure:: images/easynmr_tutorial_2d_histgly_plothistidine_aminepeak.jpg :align: center :width: 800 Amine regione of histidine data. You can fit the time domain data to extract :math:`T_1` values using a combination of Trace and Model objects. .. Spectrum modelling --------------------------- In this tutorial, we fit the :sup:`13`\C chemical shift anisotropy (CSA) pattern of Hexamethylbenzene at magic angle spinning (MAS) conditions. Starting from an empty workflow, load the experimental data Hexamethylbenzene.csdf by drag and dropping it into the Workflow. A plot object will be automatically attached to the Data object. Click on the Model object icon on the toolbar. A Model object will be added to the workflow with a Plot object already attached to it. Click on the Connect icon in the toolbar. This enables the Connect mode. Now click on the CSDM anchors of the Data and Model objects. These two objects should be connected now. Click on the connect icon again to deactivate the Connect mode. Click on the Plot object attached to the Data and click on the Delete Object icon in the Toolbar. This should delete the Plot object. In the Lines pane of the Model Object Properties, click on ``Add line`` → ``CSA`` → ``CSA MAS``. A new CSA MAS line with default parameters will be added to the Model. Press on ``Calculate`` to calculate a line shape with Line Parameters of the active model. After computations, a green checkbox appear on the Model object and a root mean square is returned for the difference between the model and data. Double click on the Plot object to see the results. Click on the 1D Plot Type, and enable both datasets: the model and experimental data. Since we did not optimize the model, computations do not match experimental data. Get back to Model parameters by double clicking on the Model Object. Edit Values and Controls of Line Parameters by clicking on ``Edit``. By visually inspecting the data, we can start with educated guesses of :math:`\delta_{\textrm{iso}} = 150 \textrm{ppm}`, :math:`\delta_{\textrm{iso}} = 50 \textrm{ppm}`, :math:`{\textrm{Line width}} = 5 \textrm{ppm}`, and :math:`\textrm{Gauss/Lorentz fraction} = 1`. Set these parameters in the Value edit boxes and set the *Control* of :math:`\textrm{Gauss/Lorentz fraction}` to *Fix*. Note that you need to enter the units as well, with as space separated from numbers - :math:`\textrm{ppm}` in this case. We would like to fit the model only on :sup:`13`\C site of the aromatic ring. Therefore, we limit the optimization only to the Fit range of [25 ppm, 250 ppm]. Set the Fit range in *Dataset Parameters* and confirm your choices by clicking on ``Done``. Don't forget to put in the :math:`\textrm{ppm}` units! Click on the ``Calculate`` button and inspect the Model output in the Plot module. You can see that the model matches some of the peak positions. Now, return back to the Model and perform a parameter-estimation simulation by clicking on the ``Fit`` button. A progress bar on the right corner of EasyNMR shows the progress. .. Working with molecules ---------------------- Thomas should advise what example to put here. .. Creating your own workflow -------------------------- [REDOR Example. Need REDOR Data with permission to share to be added to the documentation.] [For now, I will write the procedure based on the video and data we already have. We will later change images.] .. Tutorial for the calculator object ---------------------------------- [We can add the histidine cross relaxation example.] Numerical simulations with SIMPSON ---------------------------------- SIMPSON tutorials may be accessed from `here `_, where you can choose between nine basic examples, four examples for proteins, and two advanced examples. These tutorials are published in `Annu. Rep. NMR 100, 1, 2020 `_ (`open access preview `_).