ScienceSoft, LLC
www.ScienceSoft.net
TOC PREV NEXT INDEX


CHAPTER 20: NMRplot: Plotting Multidimensional Spectra

NMRanalyst automates the analysis of multidimensional NMR spectra. The NMRplot application provides the link between the visual and NMRanalyst's automated analysis. The quality of NMRanalyst results can be visualized using experimental, simulated, and residual 1D through 3D spectra. Derived information such as phase functions, correlation locations, NOE build-up curves, and detailed area plots can also be visualized. This chapter describes the NMRplot application with its interactive features.

20.1 Spectral Phasing

NMRplot can be started by the Graphic workwindow. If the specified plot file is in NMRanalyst spectral file format, the spectrum is phase corrected by the phase functions specified in the F1 Phase =, F2 Phase =, and F3 Phase = input fields in the Graphic workwindow before plotting. See CHAPTER 16: "Report Workwindow" and SECTION 18.3: "Multidimensional Spectrum Specific Settings" for details.

20.2 Mouse Interactions

The NMRplot application supports the following mouse interactions:

Left mouse button
select (rubber-band) area in 2D plots to redisplay as enlarged spectral plot; rotate spectrum for 3D and 2D surface plots,
Middle mouse button
move spectrum,
Right mouse button
enlarge or reduce (zoom) spectrum, and
[Ctrl] left button
spin 3D spectrum and 2D surface plots.

On a two-button mouse, the missing middle mouse button is emulated by holding the [Shift] keyboard key and pressing the left mouse button. Two-dimensional contour, 2D location plots of correlation signals, precision distribution, integral values, phase function, 1D parameter, 1D spectrum, and build-up curve plots support zooming and moving, but not rotating or spinning. For these 2D plots, pressing and dragging the left mouse button draws a rectangular box (rubber-band) over the displayed spectrum; upon release of the left mouse button, the spectral area inside the rubber-band is enlarged. To abort a rubber-band zooming, type the [Esc] keyboard key before releasing the left mouse button. The display of these 2D plots can be shifted to a different area. Press the middle mouse button over the displayed area and drag the mouse in the desired direction. The edge of the acquired spectrum is indicated by a red dashed line. Upon the completion of a rubber-band zoom or shift, the axis labels update.

20.3 Pull-Down Menus

Pull-down menus are located at the top of the NMRplot window. Besides mouse interactions, the menus and menu items can be activated by typing the F10 keyboard key and navigated through the left, right, up, and down arrow keys. Not all menus and menu items apply to each plot type. So only applicable menus and menu items are shown for a displayed plot. Details of each menu and menu item are discussed below:

[Save PostScript...] saves the displayed plot as a color PostScript file. It starts a Filebox popup for specifying the file name. The Ctrl+S displayed at the right hand side is the keyboard short-cut for this menu item. [Print] sends the color PostScript file of the displayed plot to the printer specified in the NMRanalyst Print Settings popup. [Exit] exits the displayed NMRplot application.

[Reset] returns to the display with which NMRplot started.[Previous Zoom] restores the previous rubber-band zooming level. [Black Background] and [White Background] switch the background color for displayed and saved plots. [Parallel Projection] and [Perspective Projection] switch perspective for the plot off and on, respectively. [Surface] renders the displayed surface or iso-surface plot as filled surfaces. [Wireframe] shows such plot in wireframe representation. For 2D contour plots, [Horizontal F1] and [Horizontal F2] display F1 and F2 respectively along the horizontal (i.e., X) axis. For 2D surface plots, [F1 Side] and [F2 Side] reorient the spectrum to show the corresponding side of the spectrum. For 3D spectral displays, [F3-F2 Side], [F3-F1 Side], and [F2-F1 Side] show the corresponding spectrum surface.

[Overlay] menu applies to 2D contour, 3D isosurface, 1D spectrum, and phase function plots. The items in this menu selectively switch the visibility of displayed components on and off. For 2D contour and 3D isosurface plots, [nD Positive Signals], [nD Negative Signals], and [nD Correlation Locations] (if specified) display/hide the positive signals, negative signals, and correlation locations respectively.

For 1D spectrum plots, [1D Experimental Spectrum], [1D Simulated Spectrum] and [1D Residual Spectrum] plot the selected spectra. The residual spectrum is the difference between experimental and simulated spectra. [1D Component Resonances] plots the individual overlapping signals of which the sum is equal to the simulated spectrum.

If a 1D spectrum is added to the F1 or F2 dimension of a 2D contour plot, [1D Experimental Spectrum], [1D Simulated Spectrum] and [1D Residual Spectrum] menu items are shown for displaying/hiding the selected 1D spectra.

For phase function plots, F1, F2, and F3 (for 3D spectra only) phase components can be displayed or hidden by toggling [F1 Phases], [F2 Phases], and [F3 Phases] respectively.

[Component] menu applies to 1D spectrum plots, 2D contour plots, 2D surface plots, surface plots of 2D fitting areas, and isosurface plots of 3D fitting volumes. For the 1D plots, the selected item determines whether the absorption or the dispersion mode of a 1D spectrum is displayed. For the 2D and 3D plots, the selected item determines the displayed phase component. A phase component is specified in the order F1 F2 F3, and R stands for real and I for imaginary. After phase correction, R contains the absorption mode and I the dispersion mode resonances. For 2D F1 phase-insensitive spectra, the [IR] and [II] items in this menu are deactivated.

[Unit] menu applies to 2D contour, 2D surface, 3D isosurface, 2D and 3D correlation location, 1D spectrum, and 1D parameter plots. The selected item determines the unit displayed along the spectral axes.

[Build-up Curves] menu is only shown for plots of build-up curves. [Previous Plot] and [Next Plot] menu items can be selected to scroll through all build-up curves.

The [Help] menu [Nmrplot...] displays the current manual chapter. [Tutorial...] shows Tutorial II with application examples. The NMRplot application is started by the Graphic workwindow. Files displayed by NMRplot can be created by the 1D Analysis, nD Analysis, and Report workwindows. The menu items [1D Analysis Workwindow...], [nD Analysis Workwindow...], [Report Workwindow...], and [Graphic Workwindow...] display the manual chapters on the 1D Analysis, nD Analysis, Report, and Graphic workwindows, respectively. [About NMRplot...] shows program version information.

20.4 Copyright Mesa

Copyright (C) 1999-2005 Brian Paul All Rights Reserved.Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL BRIAN PAUL BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

20.5 Copyright OpenGL to PostScript Printing Library GL2PS

GL2PS, an OpenGL to PostScript Printing LibraryCopyright (C) 1999-2002 Christophe Geuzaine

E-mail: geuz@geuz.orgURL: http://www.geuz.org/gl2ps/

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details.

You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

(For a verbatim copy of the GNU LIBRARY GENERAL PUBLIC LICENSE, please see file $NMRDIR/enscript/LGPL. The source code can be downloaded from http://www.geuz.org/gl2ps/ and can be ordered from ScienceSoft, LLC for the cost of distribution.)

20.6 Copyright Visualization Toolkit (VTK)

Copyright (c) 1993-1998 Ken Martin, Will Schroeder, Bill Lorensen.

This software is copyrighted by Ken Martin, Will Schroeder and Bill Lorensen. The following terms apply to all files associated with the software unless explicitly disclaimed in individual files. This copyright specifically does not apply to the related textbook "The Visualization Toolkit" ISBN 013199837-4 published by Prentice Hall which is covered by its own copyright.

The authors hereby grant permission to use, copy, and distribute this software and its documentation for any purpose, provided that existing copyright notices are retained in all copies and that this notice is included verbatim in any distributions. Additionally, the authors grant permission to modify this software and its documentation for any purpose, provided that such modifications are not distributed without the explicit consent of the authors and that existing copyright notices are retained in all copies. Some of the algorithms implemented by this software are patented, observe all applicable patent law.

IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.



ScienceSoft, LLC
www.ScienceSoft.net
TOC PREV NEXT INDEX