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CHAPTER 18: Graphic Workwindow

The Graphic workwindow displays 1D Analysis, nD Analysis, Report, and AssembleIt workwindow plot files, experimental, simulated, and residual 2D and 3D NMR spectra, as well as molecular structures saved in supported file formats. The following plot types are supported by the Graphic workwindow: (1) plots of determined 1D and 2D phase and baseline parameters with error values and interpolation functions, (2) 1D spectral plots, (3) surface ("carpet") plot of 2D fitting areas, (4) isosurface plot of 3D fitting volumes, (5) location plot of detected correlations, (6) plot of determined parameter precisions and integrals, (7) NOESY and ROESY NOE build-up curves, (8) 2D and 3D spectral plots from NMRanalyst spectrum files, (9) graph of determined molecular correlations, and (10) molecular structures in NMRanalyst plot file, Molfile, and SDfile formats.

See CHAPTER 12: "Using the Workwindows" for a general description of the function and use of a workwindow. The Graphic workwindow input screen is shown in CHAPTER 3: "Tutorial I: Using NMRanalyst". Examples of its use are described in CHAPTER 4: "Tutorial II: Setting Analysis Parameters". For the printer setup used by the graphic programs, see the Print Popup settings described in CHAPTER 9: "Using the NMRanalyst Window". This chapter describes the function of all Graphic workwindow input fields grouped into several input screen sections. To display all the input fields, select from the Edit menu [Preferences...]. Select the [Show All Input Fields] switch and click [OK].

18.1 Settings for All Plots

The entries in this input section apply to all the supported plot formats.

The only entry required for plotting pre-calculated data or 2D and 3D NMR spectra is the file name of the plot data (possibly with a path name). Program graphic determines from the format of the specified file the graphics program to use for rendering the data. If a Report workwindow molecular correlations output file, a Molfile, or a SDfile is specified, the NMRgraph application is called. If a non-existing file is specified, the NMRgraph application is started with an empty window and a warning message. For the other NMRanalyst plots, the NMRplot application is invoked. (Key: FnPlot)

All plots have a default title derived from the kind of plot requested or from the file name of the plot data. This input field can be used to overwrite the default title. (Key: pTitle)

18.2 NMRplot Specific Settings

The following input fields affect all the plots displayed by the NMRplot application.

The default axis titles can be overwritten from these input fields. (Key: xTitle, yTitle, zTitle)

A plot window size depending on plot types is supplied by default. This size can be overwritten by this entry. The relative scaling of the plot axes inside the plot window is determined by the Relative Size: input fields described below. (Key: size)

The size of plot labels and of the axial numbering is chosen relative to the plot size determined by the Size field above. The default Text Size value is 1. (Key: tSize)

The AA in this label stands for anti-aliasing. Displayed text and NMR spectra are approximated by the used screen resolution. NMRplot has no inherent plot resolution limits and increasing the plot resolution sufficiently resolves rendering problems. But given a fixed screen resolution for displaying plots, anti-aliasing can be used to increase the rendering quality. Using anti-aliasing, the requested number of frames is rendered using a displacement of less than one pixel and all frames are averaged and displayed. By default, a value of 2 is used for some anti-alias rendering improvement. For maximum rendering speed, this value can be set to 0 or 1 and displayed plots are only accurate up to the size of one screen pixel. A maximum of 20 anti-aliasing frames can be specified. (Key: AAFrames)

If no values are specified in these input fields, a X-Y (or X-Y-Z for 3D plots and 2D surface plots) ratio optimal to the plot displayed will be used. If a value is specified in at least one of the input fields, the input fields without a specified value default to 1. Two-dimensional plots (except for 2D surface plots) ignore any value specified in the Relative Size: Z field. For surface plots of 2D spectra, a specified Z value scales the displayed intensity values. Several interesting effects can be obtained by changing these aspect ratios. For example, a 3D spectrum can be projected onto the 2D F1-F3 plane by setting Y to 0. To display slices through 3D spectra, specify a small range in the F? Frequency: Min and Max fields (described below) and set the corresponding slice relative size to a small or zero value. (Key: xScale, yScale, zScale)

Several types of plots (e.g., phase function plots, 1D parameter plots, 1D spectrum plots, and build-up curves) have a legend area at the right side of the plot window. By default, the legend area is displayed. Select this switch to hide the legend area. (Key: LHideLegend)

18.3 Multidimensional Spectrum Specific Settings

Using the File With Plot Data input field described in Section 18.1: "Settings for All Plots", an experimental or simulated spectrum can be specified for plotting. The spectrum specified in this field is subtracted from the File With Plot Data spectrum before plotting. A residual spectrum can be plotted as the difference between the experimental and simulated spectra, as long as both spectra have the same file format and the same number of spectral points. (Key: FnSubtract)

Locations of detected correlations can be added to 2D contour and 3D isosurface spectral plots. Specify the name of the file containing correlation locations in this input field. (Key: FnLocation)

A 1D spectrum can be added to either the F1 or F2 dimension of a 2D contour plot. Specify the name of the file containing the 1D spectrum in these input fields. Since these input fields only apply to 2D contour plots, they are hidden when the currently selected spectrum type is 3D_SPECTRUM. (Key: Fn1DSpcF1, Fn1DSpcF2)

The 2D contour and 3D isosurface plots use the specified Contour-Lines (or Iso-Surface) values as intensity contour (or surface) values. When not specified, a Max input field value is supplied based on the standard deviation of spectral intensity values. The Min input field defaults to the negative Max input field value. For 2D surface plots, specified values define clipping planes cutting off signals exceeding the specified intensity range.

The #Steps input field is only used for 2D contour plots. Its value specifies the number of contour lines to be drawn (possible values are -1000 to 1000). The default value of 2 requests one negative and one positive contour line. If a value of -1, 0, or 1 is specified, the default value is used. If the Min value is negative and the Max value positive, contour lines are drawn outside this specified intensity range to avoid the noise level around zero intensity. If both threshold values are either negative or positive, the contour lines are drawn between the two thresholds. The 2D contour lines are color coded for easy distinction. For positive contours, orange represents the lowest intensity and yellow the highest intensity with a linear color interpolation between these values. For negative contours, blue represents the lowest absolute intensity and cyan the highest absolute intensity. Linear color interpolation is used for intensities between these values. When #Steps contains a negative number, only one negative contour line is drawn and the remaining lines are used for positive contours. This causes positive signals to be filled solidly which allows them to be distinguished from negative signals on black-and-white printouts. (Key: minV, maxV, nSteps)

Multidimensional NMR spectra are acquired with pulse sequences containing an evolution time for each spectral dimension (with the last evolution time equal to the detection time). Since the evolution times are named t1 through tn, the corresponding spectral dimensions are named F1 through Fn. Following the tradition of displaying the highest spectral dimension along the horizontal (x) axis, F2 is displayed along the x-axis and F1 along the y-axis for 2D spectra. For 3D spectra, F3 is displayed along the x-axis, F2 along the y-axis, and F1 along the z-axis. Another tradition in NMR is to reverse spectral axes for displaying NMR spectra, and NMRplot application uses this convention.

NMRanalyst does not phase correct data for the spectral analysis since frequency-dependent phase functions distort the signal lineshapes. Experimental, simulated, and the corresponding residual spectra in NMRanalyst format are saved unphased. Phase corrected data is only created for plotting. These input fields allow specifying the phase functions to be applied to the data before the data is plotted. By default, these input fields are left empty and no phase correction is applied. These fields can be set automatically by loading the Report workwindow output file in this workwindow. (Key: F1Pse0, F1Pse1, F1Pse2 through F3Pse0, F3Pse1, F3Pse2)

By default, the plot type for 2D spectra is Contour. The [Surface] option shows the surface of the 2D spectrum ("carpet plot"). The Surface plots are similar to the "whitewash" mode of displaying 2D spectra, but now the spectra are true 3D objects shown with depth perception (perspective) and can be rotated. (Key: plotType)

A phase-insensitive 2D spectrum consists of two, a phase-sensitive 2D spectrum of four, and a phase-sensitive 3D spectrum of eight phase components. NMRanalyst spectra contain these phase components. The phase component to be plotted can be selected from this menu. In the menu label, R stands for the real part containing the absorption mode signals after phasing. Label I stands for the imaginary part containing the dispersion mode signals. The first character of the label corresponds to the F1 dimension, the second one to the F2 dimension, etc. The default phase component is RR,RRR. (Key: phase)

NMRplot application supports axis labeling in ppm, Hertz (Hz), and point numbers (NP). NMRanalyst spectrum files contain the spectral referencing and can be displayed in all the three units without requiring additional information. (Key: unit)

18.4 Function of the Graphic Programs

The Graphic workwindow provides an interface for specifying initial values for the graphic program. When started, the graphic program translates the input values into the nmrgraph or nmrplot command and starts the corresponding plotting application. All plotting applications are run as background processes. It may take minutes for the plot rendering program to show the requested plot.



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