Display a file dialog in which you can select the NMR dataset to open. You can open raw data (FIDs) in Bruker (fid and ser), Varian/Agilent (fid), Nanalysis (.dx), SpinIt (data.dat) and generic JCAMP (.dx) formats. You can open processed data in NMRViewJ (.nv), Sparky (.ucsf), Bruker (1r, 2rr...), JCAMP, and SpinIt formats. The opened data file will replace the current display. If the data is an unprocessed 1D or 2D (FID) file, the Processor pane will open on the right side and a list of processing operations will be generated and applied.
A menu of recently opened unprocessed (FID) or processed NMR datasets. Selecting an item from the menu will cause it to be opened, and displayed in the active spectrum window.
Open the Dataset Browser which allows you to browse directories and locate NMR datasets.
Export the current spectrum display in SVG, PDF or PNG formats. SVG and PDF are vector formats which preserve the full resolution of the graphics. PNG files are bitmaps at a fixed resolution.
Open processed datasets without displaying them in the current window. This allows you to use them in non-gui operations, or to have more control over displaying multiple datasets in windows.
NMRFx Projects are similar to NMRViewJ projects in that they consist of a main directory and a series of subdirectories. Each subdirectory contains data for a particular data type (datasets, peaks, molecules etc.). The primary storage for most information (molecular structure, peak lists, assignments etc.) is a BMRB NMR-STAR format file within the projects star subdirectory. NMRFx has a built-in copy of Git, a version control system allowing it to keep a history of project changes.
Open an existing project. Use the file browser that appears to browse to the directory containing the project directory. Select the project directory and click Open.
This is a sub-menu containing a list of recently used projects. Choose an entry from the menu to open that project. Entries in the list show the last three elements of the path to the directory to help you in recognizing projects and distinguishing projects with the same name.
Save the project into the various project sub-directories. All the component files of the project are over-written. Then a Git commit is done to maintain to record the differences from the previous state of the project.
Save the project into a new project directory. A file browser will appear that will allow you to choose a directory location in which to save the project.
Close the current project. After you confirm this action, all molecules, peaklists and assignments will be discarded. All spectral display windows, but one, will be closed.
Read a BMRB STAR3 format file.
Write project information (peaklists, assignments, molecules etc.) to a BMRB STAR3 format file.
Open a Sparky project file. Save files reference in the project file and corresponding .ucsf datasets will also be opened. This is a preliminary feature and some attributes of the Sparky files might not be imported properly or at all.
Create a new spectrum display window.
Delete the active spectrum chart from a window that has more than one chart in it. The remaining charts will be resized to fill the empty space.
Horizontal. Arrange the spectrum charts in a window with multiple charts such that they occupy a single horizontal row.
Preliminary support for synchronized axes. All the spectrum charts in a single window will be synchronized across dimensions that share the same label. Changing the x, y and plane values in one window will result in the other windows being redrawn so that they share the same values on similar dimensions. There is not currently a method to restrict the synchronization to specified axes, remove synchronization, or synchronize spectrum charts in different windows. These features will be coming in a subsequent version.
The spectral display can be copied to the clipboard as SVG (scalable vector graphics) text. The result can be pasted into some graphics applications, but at present this only works for some applications. For example, we have used this successfully with Affinity Designer on MacOS.
Adjust the referencing so spectra are aligned with each other. Alignment happens between spectra that are displayed in the same window. They can be in separate charts within the window, or multiple datasets within a single chart. Alignment occurs only between the dataset dimensions on the x and y axes (not planes). Alignment is done by peak picking the spectra (if peak picking has not already been done) and adjusting the referencing such that the distance between nearby peaks is minimized. The first dataset of the active chart is the target dataset. Other datasets are aligned to that dataset. Dataset parameter files are written to save the new referencing. This process (in current implementation) can be slow if there are a lot of peaks. Because of this it's a good idea to have the window display zoomed in somewhat.
Display the spectrum analysis window. This allow you to measure intensities in a specified region of the spectrum (area with the crosshairs).
NMRFx can read in molecular structures in several different formats, including reading in a sequence and building a molecule from a residue library, reading PDB files and reading .mol/.sdf files.
File Menu
Bring up a file selection dialog to select and open a file containing an amino acid, DNA, or RNA sequence. See the section on Molecular Structures to learn about the format of this file.
Bring up a file selection dialog to select and open a PDB format file. This is the standard way to read in pdb files. NMRFx first reads the pdb file to determine the amino acid sequence. Next, it reads the corresponding residues from the residue library. Finally, it reads coordinates from the pdb file for those atoms that have names matching the names in the residue library. Atoms, that do not have a match in the residue library will not be entered into the structure list. Atoms that are in the residue library but not in pdb file, will be included in structure list but will not be displayed. See the section on Molecular Structures to learn about using molecular structures in NMRFx.
Reads a file of atomic coordinates of a macromolecule and sets the coordinates of an existing molecule (in NMRFx) to the values found in the file. File must be stored in the PDB format as defined by the Protein Data Bank. The atoms and residues of the already in-memory molecule are not changed, only the xyz coordinates.
Reads a file of atomic coordinates of a macromolecule. File must be stored in the PDB format as defined by the Protein Data Bank (now the RCSB). This command does not also read from the residue library so no connectivity information is available. If this is needed use the pdb command instead.
Open a macromolecular structure file (the successor to PDB files). Support for mmCIF files is still under development..
Open a small molecule (.mol or .sdf) file.
Open a small molecule (.mol2) file.
Open a file containing one or more SMILE molecule descriptions.
Input a molecule in SMILE format. You will be prompted for the SMILE string and a name for the molecule. The SMILE string will be parsed and two-dimensional coordinates for the molecule generated.
Remove all existing molecules (you will be prompted to confirm this action)
Display a window in which you can enter the single letter sequence for an Protein, RNA or DNA polymer.
Select this to bring up the Assignments Panel that is used to keep track of chemical shift assignments.
Display the molecular viewer. This can be used to display the 3D structure, a 2D RNA secondary structure, or a flat (2D) view of a small molecule.
Display the RDC Analysis window
Show a window that can be used to specify the isotopic labeling scheme for RNA molecules.
Display the Console window. The console can be used in Jython (Java version of Python) or R (statistical language) modes.
Display the Log Console window. The Log Console shows error, information and warning messages that might be generated during various actions.
Show a table of currently opened datasets. Each row of the table shows the dataset name, number of dataset dimensions, default contour level, scale value, default contouring parameters and reference information. Reference information is displayed for a single dimension at a time. A pop-up menu on the DimN header allows you to choose the display dimension. The Draw menu at top of the Dataset Table window allows you to draw selected datasets in a variety of arrangements.
Show a table of spectral regions. The tool has actions for saving, loading, adding, removing and integrating regions.
The Peak tool allows the user to work with peaks and their peak lists. Users of NMRViewJ will recognize it as being similar to the Peak Inspector and having capabilities of the Peak Reference tool.
The Peak Table shows a table of all the peaks in a particular list.
The Peak List Table shows a table of all the current Peak Lists. The table includes information on what dataset the peak list is associated with, the assignments, the number of peaks in the list and the number of peaks that have been marked for deletion or assigned.
This menu action will link peaks that have common labels. Once linked they will move in synchrony when using the Peak Slider, and changing the label for one peak will change the label for all linked peak dimensions.
Display a window containing tools for analyzing shifted peaks including minimum chemical shift changes and PCA analysis.
Display a window containing tools for calibrating and exporting NOE constraints.
Display a window containing tools for fitting ZZ (chemical exchange) datasets .
Assign Tools
These are all prototypes of new tools for assigning proteins and RNA. Under rapid development
If this is active then when you pick a peak (in cursor peak-pick mode) you will be prompted for an assignment of the peak. The chemical shift of the pick position will be shown and if that positon overlaps existing assignments you will be given a list of assignments to choose from. If you close the window without clickign the Assign button the peak will be removed.
Experimental tool for RNA assignments
Various menu items for showing windows. The menu items available are platform dependent.
Open the default web browser and display the online documentation.
Open the default web browser and display the NMRFx web site.
Open the default web browser and display the NMRFx mailing list site.
Open the default web browser and display the first NMRFx Processor publication. Please cite this reference when publishing manuscripts describing research that used NMRFx Processor in the analysis.
Check the NMRFx web site to see what the latest version of NMRFx is.
NMRFx uses various open-source libraries. Open the default web browser and display information on the open source libraries used by NMRFx