The nmrManage program is designed to group sets of related procTool files and sample files in one place in so-called projects, without actually moving or copying data. Thus, it is an indirection mechanism (pointer mechamism). Using nmrManage, one can quickly view, modify, or list the different experiments or samples.
Throughout this text, a menu-item will be denoted <item>. A cascaded menu-item by <item>-<sub-item>. A button will be denoted by [button-item]. {entry} denotes an entry field for a specific parameter; Italics denote a value entered by the user in an entry field, or the value of an option such as a radio-button or a check-button.
If procTool has been properly installed it can be started at the command line by typing:
nmrManage
The nmrManage interface-window will pop up (see Fig. 1).
Fig. 1: The nmrManage window.
On top is a menu-bar with <File> and <Tools> . There are also three shortcut [buttons] on the righthand side of the menubar. Below the menu-bar is a general window area, that displays information about the current project. Below that, 3 tabs (Samples, Experiments, and History) are located which each contain entry fields for various parameters as well as buttons. The tabs can be closed or opened by clicking on the open/close buttons on the right side. Finally, at the bottom a help bar is present. Moving the mouse over specific items in the procTool window, displays a short help text in this bar.
nmrManage uses text with red fonts for important information relating
to the current status. Text with steel-blue fonts is used for giving information,
text with green fonts indicates 'action' (usually on buttons). All other
text is black. Entry fields can be activated by moving over the appropriate
box and clicking the mouse. Sometimes, entry fields contain a cascade pulldown
with options to choose from.
NmrManage will restore its previous state. A new start can be made by choosing <File>-<New>. An existing project can be opened by using <File>-<Open> or by using the [Open-File] icon-button in the menu barThe program can be quit by choosing <File>-<Quit> or by using the [Quit] icon-button in the menu bar.
nmrManage is designed to work together with two additional programs (i.e.
samples and procTool) to achieve a simple form of project management.
The Samples and Experiments tabs of nmrManage allow the user to group
specific sample files and procTool files describing specific experiments
together as one entity. Note that a samples-file or procTool file can occus
in multiple projects if needed.
Four buttons describe the actions possible for the Samples tab
[add sample] Allows selection of a specific sample
file to the project. Note that sample files can also be added to a project
from within the samples program.
[remove] Removes selected sample file from the
project. Select sample file by clicking the appropriate entry.
[xwsh] Opens a shell in the directory of the selected sample file. Select sample file by clicking the appropriate entry.
[run samples] Runs the samples program on the
selected sample file. Select sample file by clicking the appropriate entry.
Seven buttons describe the actions possible for the Experiments tab
[add experiment] Allows selection of a specific
procTool file to the project. Note that procTool files can also be added
to a project from within the procTool program.
[remove] Removes selected procTool file from
the project. Select procTool file by clicking the appropriate entry.
[xwsh] Opens a shell in the directory of the selected procTool file. Select procTool file by clicking the appropriate entry.
[summary] Generate a summary of the selected
procTool file. Select procTool file by clicking the appropriate entry.
[run procTool] Runs the procTool program on the
selected procTool file. Select procTool file by clicking the appropriate
entry.
[run nmrDraw] Runs the procTool program and starts
nmrDraw on the selected procTool file. Select procTool file by clicking the
appropriate entry.
[remove data] Runs the file removal tool of the
procTool program on the selected procTool file. Select procTool file by clicking
the appropriate entry.
The history tab contains a logging of the nmrFile file and actions. The history can be cleared with <Tools>-<History>-<Clear> . Contents of the tab can be edited by the user; information can be appended. To add a time stamp use <Tools>-<History>-<Append timestamp>.
The <Tools> menu contains miscaleneous menu commands to view directories, remove files from the DATA directory, setup additional nmrManage parameters, view the source code, etc.
The expression editor can be used to calculate any arbitrary expression.
Enter the expression and press return, the result will show next to the
entry field.
There is an internal help facility: button [Help]-<Commands> (on the far right in the menubar) gives an overview of the commands and the parameters, <Help>-<About> shows the about text, <Help>-<Version> shows the version history, and <Help>-<Tutorial> shows the tutorial through your web-browser.
Version 1.5.1: No bugs reported. Undoubtly this will change!
This program and its related software is provided "as is". The author makes no warranties, either express or implied, as to any matter whatsoever with respect to the software. In particular, any and all warranties of merchantability and fitness for any particular purpose are expressly excluded. In no event will the KUN, the Laboratory of Biophysical Chemistry, the NSRIM Center, or the author be liable for any loss of profits, any incidental, special, exemplary, or consequential damages of any nature whatsoever (including without limitation, loss of use or other commercial or research loss) arising out of or relating to the use or performance of the software.
This program may not be distributed without prior permission.
(C) Geerten W. Vuister 1999-2003
Laboratory of Biophysical Chemistry NSRIM Center, University of Nijmegen, The Netherlands Email: vuister@nmr.kun.nl http://www.nmr.kun.nl
Last update: 14 Oct 2003