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CHAPTER 9: Using the NMRanalyst Window

The shown NMRanalyst window provides the user interface for the automated analysis of multidimensional NMR spectra. Its function is to display and control the subwindows of the software: the Help system, the Directory Editor, the UNIX shell window, the graphic windows, and the workwindows managing all computations.

9.1 Starting NMRanalyst

To start NMRanalyst on MS Windows, from the menu click , click , and then click . On Linux, start NMRanalyst from a shell window using:

 % analyst
 Starting NMRanalyst 3.6 from /usr/local/ANALYST.LINUX...

The above command starts NMRanalyst as a background process to free the terminal for further input. Optionally, a spectrum type can be specified as a command line parameter. For example, analyst HMBC starts NMRanalyst with HMBC (instead of the default last used spectrum type) as the selected spectrum type. The following three sections (SECTION 9.2: "Error Message "analyst: not found"", SECTION 9.3: "Error: Incorrectly Set DISPLAY Variable", and SECTION 9.4: "NMRanalyst Cannot Find Its Installation Directory") provide information on correcting problems that may be encountered during the start of NMRanalyst. Should no problems be encountered at this stage, skip to SECTION 9.5: "Structure and Function of the Application Window".

9.2 Error Message "analyst: not found"

This error message indicates your shell cannot locate the analyst program. This is caused by an incorrectly set PATH variable or incorrectly installed software. Try to find program analyst in default locations for system wide installation: /usr/local/bin, /bin, /usr/bin, and for local installations: $HOME/bin and other users bin directory. On MS Windows, also search the various top level directories of disk drives. If the analyst program cannot be found in program directories, try to locate the NMRanalyst installation directory called ANALYST.WIN or ANALYST.LINUX, depending on platform. Default installation locations are /usr/local, $HOME, /opt, /export/home, /usr, /home, and the top level directories of PC drives. If the installation directory can be found, start analyst from its bin subdirectory.

If the installation directory cannot be found either, then determine if the analyst program is accessible anywhere on the computer using the Bourne and Korn shell command:

 % find / -type f -name analyst -print 2> /dev/null

If this step fails, NMRanalyst is not installed or not accessible from the current user account. In either case, consult your system administrator. If the analyst program can be found, the problem with locating the analyst program is caused by an incompletely set PATH variable. A UNIX shell only automatically searches for a program in the directories which are listed in the shell's PATH variable. The current value of the PATH variable (with directories separated by colons) can be displayed by:

 % echo $PATH

Add the directory in which you found the analyst program, say /usr/local/bin, to the PATH variable for the Bourne and Korn shells with:

 % PATH=$PATH:/usr/local/bin; export PATH

To avoid having to retype these settings after every login, the above PATH extension command should be added to the user's .profile file for the Bourne and Korn shells.

9.3 Error: Incorrectly Set DISPLAY Variable

On Linux, the NMRanalyst application needs to establish a display connection to the X Window display server. The Windows version simply uses the local display in case of connection problems. All NMRanalyst versions show a message indicating a DISPLAY error if no connection to the screen can be established. The following list provides reasons and corrective actions:

1. The most common problem is an unset or incorrectly set DISPLAY shell variable. The DISPLAY variable identifies the display server, the display number, the type of network connection, and optionally the screen number to be used. Whenever program analyst detects problems with opening the display connection, the following message is displayed:

 % analyst                      
 Starting NMRanalyst 3.6 from /usr/local/ANALYST.LINUX...
 Exception in thread "main" java.lang.InternalError: Can't connect to X11 window
 server using 'localhosti:0.0' as the value of the DISPLAY variable.

On a properly configured network, a specified computer name gets automatically translated into the corresponding network (IP) address. Should this name resolution fail, either specify the network (IP) address or have the system administrator add the mapping between the name of your display computer and its IP address in the file /etc/hosts. Program analyst assumes by default a TCP/IP connection1 with both the display and the screen number of zero.

The DISPLAY variable can also be set manually. To display the current value of the DISPLAY variable, use:

 % echo $DISPLAY

on the client side (where the analyst program should be run). This shell variable setting can be changed for the Bourne and Korn shells with:

 % DISPLAY=host:0; export DISPLAY

where "host" is the network node name (such as hydrogen.company.com) or the IP network address (such as 123.456.789.01) of the computer on which you want to display the windows. Since standard Linux workstations have only one display per CPU, the display number will always be 0. The colon in the example specifies a TCP/IP connection. When the client and server are running on the same computer, the special DISPLAY value :0 or localhost:0 or unix:0 can be used. Note that a DISPLAY value specified inside NMRanalyst is only valid for the current NMRanalyst session. A DISPLAY value specified from the Linux command line is active only for the programs started from that shell.

2. The analyst program does not have the permission to display the application window on the X Window server identified by the DISPLAY variable. The X Window server must grant permission to other computers to display windows on it. So the owner of the X Window server process (the user who started the server) should issue the command:

 % xhost +host

where "host" is the name or network (IP) address of the computer on which the analyst application is running. It is also possible to use the "xhost +" command (no "host" name specified), which allows all computers to display windows on the display server.2

3. The X Window server identified by the DISPLAY variable is not running. The X Window system can normally be started with:

 % xinit

In case of further problems, consult the system administrator.

9.4 NMRanalyst Cannot Find Its Installation Directory

NMRanalyst only loads the currently needed programs and help files in computer memory. When further information is needed, it is loaded from the installation directory at run-time. Upon startup, NMRanalyst tries to locate the installation directory by inspecting the NMRDIR shell variable, and by searching standard installation locations for the installation directory. If these attempts fail, the Directory Editor rather than the NMRanalyst application window is shown with a popup explaining the problem encountered. Set the correct installation directory in the Directory Editor, possibly using the Filebox popup, and click the Directory Editor [OK] button to start the NMRanalyst application window. See CHAPTER 10: "Using the Directory Editor" for details on using the Directory Editor.

9.5 Structure and Function of the Application Window

The application window provides access to all NMRanalyst functions. The window consists of the following parts:

The window title displays the currently selected spectrum type and workwindow, and a short explanation of the function of the selected workwindow.

At the top right corner of the application window is the NMRanalyst logo. When the currently selected workwindow is computing, the logo is animated.

At the top of the application window is a row of pull-down menus providing access to all application window functions. The menus can alternatively be accessed through the keyboard keys. The [F10] key makes the pull-down menus accessible from the keyboard and the [File] menu button is highlighted. The other menus can be accessed with the [Left] or [Right] cursor key. The [Down] or [Up] cursor key selects items in the currently opened menu.

At the bottom of the application window is a row of workwindow tabs. The analysis of multidimensional NMR spectra is controlled by workwindows, displayed in the application window. Each workwindow provides the user interface for one analysis step. See CHAPTER 12: "Using the Workwindows" for details. The desired workwindow can be selected by clicking on the corresponding tab. Each workwindow tab has a keyboard mnemonic, that is, typing [Alt] (or [Ctrl]) and the underlined character (e.g. [T] for the FFT workwindow) simultaneously is equivalent to clicking the tab. Only one workwindow can be displayed at a time, but NMRanalyst allows all workwindows to perform computations simultaneously.

9.6 The Workwindow Tabs

The workwindows provide access to the analysis software and appear as a stack of "folders" in the application window. Clicking on a folder tab displays the corresponding workwindow. SECTION 9.5: "Structure and Function of the Application Window" shows the row of folder tabs for the analysis of 2D spectra. For the analysis of 3D spectra, the tabs appear as shown in SECTION 9.1: "Starting NMRanalyst". The position of the tabs and associated workwindows (from left to right) corresponds to the order in which a typical analysis is performed.

When a workwindow is selected, the corresponding tab is displayed in front of the others. When the computation of the workwindow is started, the tab displays a clock icon to the left of the workwindow name (e.g., ). The clock icon disappears as soon as the computation is completed.

Right clicking on a workwindow tab shows the popup menu , which allows repositioning the stack of workwindow tabs toward the top of the application window. After the workwindow tabs are moved to the top, right clicking on a tab again brings up the popup menu , which allows moving the workwindow tabs back to the bottom of the application window.

9.7 The Speed Button Panel

The pull-down menus described in SECTION 9.8: "The Application Window Menus" provide access to all NMRanalyst functions. The upper section of the application window contains speed buttons for convenient access to frequently used functions. The underlined letter in a button label indicates the keyboard mnemonic, that is, typing [Alt] (or [Ctrl]) and the underlined letter simultaneously is equivalent to clicking the button.

This button toggles the workwindow display area between the Input Screen and the Output Screen by moving the separating sash. Starting a computation with the [Start] button toggles the display area to the output screen.

Clicking this button starts a Filebox popup for loading a *.txt, *.log, *.plot, Varian procpar, or Bruker acqu* file. The *.txt files are the native parameter files of NMRanalyst. The other file formats are converted to *.txt format by this load procedure by calling (in this order) the varian2txt, bruker2txt, log2txt, and plot2txt shell scripts. The varian2txt script extracts for the 1D Analysis and FFT workwindows the relevant information from Varian VNMR parameter files (named procpar). The bruker2txt script extracts for the 1D Analysis and FFT workwindows the relevant information from Bruker parameter files.

The log2txt script provides a mechanism to transfer output from one workwindow to another workwindow input screen. The script supports the transfer of linear phase functions from the Report workwindow output screen to the nD Analysis or the Graphic workwindow input screen and the transfer of signal description from the 1D Analysis workwindow output screen to the signal table in its input screen. The plot2txt script extracts linear phase function parameters from a phase function plot file. This information is used by the nD Analysis and Graphic workwindows. If none of the scripts generate information appropriate for the current workwindow, the following popup shows. [Cancel] aborts the loading process.

All the format conversions are provided as shell scripts for easy customization. The conversion scripts can be called interactively from the Linux command line, for example:

 % varian2txt 1d.fid/procpar > 1d_analysis.txt

This button shows the deactivated (dimmed) [Pause] label if no computation is in progress. When a computation is started, this button shows the activated [Pause] label. Clicking this button suspends (pauses) the computation, and the button label changes to [Resume]. Clicking this button again continues the computation from the point where it was suspended and changes the button label to [Pause]. A suspended computation can be terminated using the [Stop] button.

To start a workwindow computation requires write permissions on the spectrum specific subdirectory under the NMRDATA directory and the corresponding *.log file and its backup file *.log.bck. NMRanalyst obtains write permissions on the directory and files when possible. The following popup window appears if NMRanalyst cannot obtain write access to the spectrum specific subdirectory:

[Cancel] removes the popup window. Directory permissions can only be changed by the directory owner or a user with system privileges. To manually add write permissions to a directory (e.g., $NMRDATA/INADEQUATE), type the following command from the NMRanalyst UNIX Shell window:

 % chmod u+w $NMRDATA/INADEQUATE

In case that the *.log file and its backup file *.log.bck have no write permissions and NMRanalyst fails to obtain write access on these files, the following popup window is shown:

[Cancel]
removes this popup window. Change the file permissions and try again.

When [Start] is clicked and no permission problems exist, the workwindow input screen changes to the output screen to show the output of the computation. The computation can be terminated using the [Stop] button. This [Start] / [Stop] button is set as the default button so that typing the [Enter] key is equivalent to clicking the button.

This button starts a popup from which the directories used by the NMRanalyst software can be changed. See CHAPTER 10: "Using the Directory Editor" for details.

Clicking the [UNIX Shell] button opens a UNIX shell window for command line input.

Clicking this button exits from NMRanalyst.

If no computations are in progress, the shown popup is displayed. [Exit] terminates NMRanalyst, [Cancel] returns to the NMRanalyst application window.

The shown popup is displayed if any workwindow is computing. [Terminate] aborts the computations and exits from NMRanalyst. [Cancel] causes the exit request to be ignored. [Background] causes the computations to continue in the background while NMRanalyst exits.

Backgrounding allows exiting from the application workwindow and on Linux even logging out without interfering with ongoing computations. A background process competes with interactive users for computer cycles. Hence, a slider is provided to set the priority of the background process created through the [Background] button. The left side of the slider corresponds to the lowest possible priority (Slow) that the background process can be given. At this lowest priority, the background process should not interfere with the interactive use of the computer. The right side of the slider corresponds to the highest priority (Fast) a user can give background processes.

9.8 The Application Window Menus

Functions available through the speed buttons and the workwindow tabs are also available as menus. They are located at the top of the application window. The NMRanalyst functions are available through pull-down menus: File, Edit, SpectrumType, Workwindow, Process, Tools, and Help.

[Load...] reads a file into the selected workwindow input screen. [Print...] starts the Print popup described in SECTION 9.9: "The Print Popup". [Exit...] exits from the software. The [Load...] and [Exit...] items can also be found as speed buttons in the application window. The [Load...] item has an accelerator, that is, typing [Ctrl][L] is identical to opening the File menu and selecting the [Load...] menu item. Similarly, typing [Ctrl][I] is equivalent to selecting the [Exit...] menu item. An underlined letter in a menu item indicates the keyboard mnemonic: When a menu is opened, typing the underlined letter is equivalent to selecting the corresponding menu item.

[Cut] cuts and [Copy] copies the selected text to the CLIPBOARD. The CLIPBOARD content is accessible to other applications. [Paste] copies the CLIPBOARD content to the text field with the input focus.

To search text in the output screen, click [Find in Output Screen] from the Edit menu. The shown popup is then displayed. Enter the text to be searched in the Find Text input field. Select the [Match Case] check box for case-sensitive search. Click the [Find] button to start searching from the top of the output screen. The first match, if any, is then highlighted. To continue searching for the next match, select [Find Next] from the Edit menu (or hit the F3 short-cut key). [Cancel] closes the popup without searching.

Selecting [Preferences...] from the Edit menu brings up the shown popup. In the Full NMRanalyst mode, all the six workwindows (1D Analysis, FFT, nD Analysis, Report, AssembleIt, and Graphic) are displayed. If the FindIt & VerifyIt mode is selected, only the three relevant workwindows, 1D Analysis, AssembleIt, and Graphic, are displayed. For the routine use of the software, many input fields are not needed and hence are hidden by default. Select the [Show All Input Fields] check box to display all the available fields.

Clicking on the [Color] tab switches to the shown display. From here, choose the background color to identify interface widgets (such as text fields) with non-default values. The preview area updates with each color selection. Click [OK] to set the current selections (in both the [General] and [Color] tabs) as the preferences. The preferences are used by NMRanalyst until they are altered again. [Defaults] restores the preferences to the initial values. [Cancel] closes the popup without applying any change.

The [Spectrum Type] menu displays the 2D spectrum types for which specialized analysis settings are available. Other 2D spectrum types can likely be analyzed by one of the provided ones. All phase sensitive 3D spectra can be analyzed with the provided heteronuclear 3D spectrum type by selecting the [3D_SPECTRUM] menu item.

[Make Default] erases all history information of the selected workwindow input screen. Hence, the current values of all input screen items in the selected workwindow become the default values, and all input fields and buttons return to their default (background) color. [Clear History] deletes the old analysis parameter values which accumulate whenever workwindow input screen values are changed. [Restore To Default] resets the current values of all input screen items to their default values without erasing any history information. The remaining items correspond to the functions described in SECTION 9.6: "The Workwindow Tabs" and in SECTION 9.7: "The Speed Button Panel". For a full description of each workwindow, see CHAPTER 3: "Tutorial I: Using NMRanalyst" and CHAPTER 7: "Tutorial V: Additional NMRanalyst Features".

From the Process menu, [Start] runs the current workwindow. The [Pause] item is dimmed if no computation is in progress. As soon as a computation is started, this item is activated. See SECTION 9.7: "The Speed Button Panel" for the description of its functions.

The [Directory Editor...] and [UNIX Shell...] menu items start the Directory Editor and the UNIX shell window respectively. The functions are identical to those described in SECTION 9.7: "The Speed Button Panel".

Selecting [FindIt Database Manager...] starts the shown popup for adding, extracting, or removing user structures from the FindIt database. To add structures, select the [Add User Structures] switch. Then specify either a file or a directory containing the structures to be added. If a directory name is specified, all files in the directory are processed, but sub-directories are ignored. The supported file formats include NMRgraph native structure files (.plot), Molfiles (.mol), and SDfiles (.sdf). To remove a structure, select the [Remove User-Added Structure] switch and specify the structure ID to delete. Only user-added structures can be removed. When adding a structure to the database, the assigned structure ID is displayed in the progress message. The ID can later be used to remove the structure. To remove all the user-added structures, select the [All] switch. To extract structures from the FindIt database, select [Extract User-Added Structures] and specify a directory to store extracted structures in. Extracting structures does not remove the structures from the FindIt database. Only user-added structures can be extracted. Each extracted structure is saved in a SDfile. Click [OK] to start adding, removing, or extracting structures. [Cancel] closes the popup without applying any changes.

When adding (removing, or extracting) structures, the shown popup with progress information is displayed. If a structure is already contained in the FindIt database, its ID is displayed and it won't be added again. During the adding process, the [Abort] button allows stopping the process. When the adding (removing, or extracting) process is completed, the [Done] and [Continue] buttons are enabled. [Done] closes the popup. [Continue] brings up the FindIt Database Manager popup for further structure processing. The complete progress messages are saved in the file findit.log in the current NMRDATA directory.

After upgrading to a new version of NMRanalyst, the user-added structures in the FindIt database will be out-of-date. To upgrade the user structures, follow these steps: First, extract all the user structures to an empty directory. Next, delete all the user structures from the FindIt database. Finally, re-add the saved user structures to the FindIt database.

The Help menu provides fast access to several important manual chapters. The NMRanalyst software reuses an existing Help window whenever possible. Hence, it is not necessary to quit the Help window manually since this window may be reused and is removed when the NMRanalyst application exits. For details see CHAPTER 8: "Using the Help System". [About NMRanalyst...] shows program version information.

9.9 The Print Popup

The shown popup is started from the [Print...] item in the File menu. It can be used to print a specified file or to adjust the current printer settings. It provides the printer drivers: PostScript, bj10e, bj200, bjc600, bjc800, cdeskjet, cdj550, cdjcolor, cdjmono, deskjet, djet500, epson (Windows only), epsonc (Windows only), laserjet, lbp8 (Windows only), ljet3, ljet4, ljetplus, pjxl300, r4081 (Windows only), stcolor (Windows only), and uniprint. NMRanalyst creates print and plot output in PostScript format. Program gs (Ghostscript) is used for conversion to other printer formats. See http://www.cs.wisc.edu/~ghost/doc/printer.htm for further information on the functionality and printer compatibility of gs supplied printer drivers. Since a user may not know the correct printer driver, Other Printer in the To: pull-down menu is selected by default, which invokes the Windows native dialog or Linux kprinter dialog for printing.

Specify in the To: text field the printer to use. By default, the first available value from the last used entry (stored in file .analyst), the LPDEST shell variable, the PRINTER shell variable, or the system default printer is shown. Under Windows, if a specified printer name does not work, specify the printer's port name in this field instead. See SECTION 21.9: "How can I get NMRanalyst printing to work?" for further printer setting information. The Pages/Sheet menu allows printing multiple text pages on a single sheet of paper.

Button [Print] saves the printer settings and prints the specified file, [Apply Settings] only saves the current printer settings, [Cancel] removes the dialog without printing.

9.10 Copyright Enscript Program

Copyright (c) 1995 Markku Rossi.

Author: Markku Rossi <mtr@iki.fi>

This file is part of GNU enscript.

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

This program 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 General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; see the file COPYING. If not, write to the Free Software Foundation, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

(The file COPYING can be found in directory $NMRDIR/enscript/ and the enscript source code can be downloaded from http://people.ssh.fi/mtr/genscript/ or can be ordered from ScienceSoft, LLC for the cost of distribution. Enscript is not an integral part of NMRanalyst, nor does ScienceSoft, LLC support it. It is provided AS IS in the hope that its conversion of text into formatted PostScript will be found helpful.)

9.11 Copyright GNU Ghostscript Program

GNU Ghostscript is distributed under the GNU General Public License (GPL), which allows free use, and free copying and redistribution under certain conditions (including, in some cases, commercial distribution). See file $NMRDIR/enscript/COPYING or http://www.gnu.org/copyleft/gpl.html for details.

(The source code can be downloaded from http://www.gnu.org or can be ordered from ScienceSoft, LLC for the cost of distribution. The GNU Ghostscript software is not an integral part of NMRanalyst, nor does ScienceSoft support it. It is provided AS IS in the hope that its PostScript to Printer Control Language (PCL) document conversion will be found helpful.)

9.12 Copyright Java Runtime Environment

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D. Source Code. Software may contain source code that, unless expressly licensed for other purposes, is provided solely for reference purposes pursuant to the terms of this Agreement. Source code may not be redistributed unless expressly provided for in this Agreement.

E. Third Party Code. Additional copyright notices and license terms applicable to portions of the Software are set forth in the THIRDPARTYLICENSEREADME.txt file. In addition to any terms and conditions of any third party opensource/freeware license identified in the THIRDPARTYLICENSEREADME.txt file, the disclaimer of warranty and limitation of liability provisions in paragraphs 5 and 6 of the Binary Code License Agreement shall apply to all Software in this distribution.

F. Termination for Infringement. Either party may terminate this Agreement immediately should any Software become, or in either party's opinion be likely to become, the subject of a claim of infringement of any intellectual property right.

G. Installation and Auto-Update. The Software's installation and auto-update processes transmit a limited amount of data to Sun (or its service provider) about those specific processes to help Sun understand and optimize them. Sun does not associate the data with personally identifiable information. You can find more information about the data Sun collects at http://java.com/data/.

For inquiries please contact: Sun Microsystems, Inc., 4150 Network Circle, Santa Clara, California 95054, U.S.A. (LFI#143333/Form ID#011801)

9.13 Copyright PC Cygwin UNIX Toolset

Most of the provided UNIX tools are covered by the GNU General Public License (GPL), though some are public domain, and others have a Berkeley-style copyright. See http://cygwin.com for the source code, a verbatim copy of the GPL license, and the available documentation about this tool set. The Cygwin software is not an integral part of NMRanalyst, nor does ScienceSoft support it. It is provided AS IS in the hope that its UNIX-like commands will be found helpful.

1TCP/IP stands for Transfer Control Protocol / Internet Protocol.

2This convenient approach can compromise the computer security in an unsafe network environment.



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