Projects are managed as a set of folders (directories) under one root directory. By default the root of the project directories is the folder nvprojects within your HOME directory. You can locate this directory somewhere else, or have multiple project directory roots. The location of the current project root is displayed in the Projects Directory entry. Click the browse button to find a different subdirectory. If you want to create the project root just enter the path, for example "/Users/brucejohnson/nvprojects", and hit the Enter/Return key. If the directory doesn't exist you'll be prompted to create a new one.
Create or open a project before you start working with a analyzed data. That is, don't read in molecular structures or pick peaks, and then open a project. Create and open the project first (if you ignore this, or already have such data you can save a STAR file, create a project, then copy the STAR file into the new projects STAR directory).
The Available Projects list simply lists all folders contained within the projects root folder. If you've just created the project root, this list will of course be empty. Click the button to create a new project. You'll be prompted for a project name. Enter a new name, which will be come a sub-folder of the projects root directory. Next you'll be prompted for whether or not to use IUPAC nomenclature for this project. When a project is loaded this value will override the value in the Paths and Filenames section of the Preferences interface.
Next you'll be prompted for whether to link to another directory. You may already be storing a project directory in some other location. If you answer yest, you'll be able to create a link to that other directory. For most users, just say NO. Finally, you'll be asked to create the new project folder if it doesn't exist (as will generally be the case). When you say Yes, the project folder will be created along with a set of project specific sub-folders. The structure of the project root and one example project folder as will be created in this process are shown here.
Six different sub-folders will be found in each project:
- datasets
Any NMR datasets readable by NMRViewJ that are in this folder will be opened automatically whenever the project is opened, if the Datasets check button is selected.
- star
When you save a project, a STAR 3 format file will be created here containing the molecular topology, peak lists, atomic assignments, distance and dihedral constraints, and other information. When you open a project, the latest STAR file as defined by the numerical extension (file1.str, file2.str etc.) will be opened, if the STAR check button is selected.
- list
The default directory when you read and write peak lists is this directory. But, please remember, you shouldn't need to explicitly write peak lists as all peak information will be stored in the STAR file.
- win
You can save the state of any opened spectral window by clicking the Spectrum icon bar Favorites icon. The window state will be saved in this folder.
- tcl
Any Tcl scripts that are stored in this folder will be sourced in when the project is opened. This is the appropriate place to put any project specific scripts.
- structures
The default directory when you read and write structure (PDB) files is this directory.
When a project is loaded datasets are automatically opened from a a set of specified directories. The project's own dataset directory is always scanned and you can add additional directories in the Data Dirs section of the Project Browser. Click the button in this section to select directories you wish to include. As you select directories they will appear in the list. You can remove a directory by highlighting the entry in the list and clicking the Delete key.
When NMRViewJ scans the listed directories it looks not only in each specified directory, but recursivelyy through any sub-folders. Thus it will fid any datasets contained anywhere below the listed directories.
A new project is not ready to be used until you click the button. At this time all the project folders that don't exist will be created along with a project file (project.txt) containing the state of various parameters. A typical project file is shown here and contains parameters specifiying whether to load datasets, load the latest STAR file, and whether to use IUPAC mode for atomnomenclature. Note that by default, the if the dataPath entries refere to folders in your HOME directory they will be specified relative to the symbolic home locatio. That way you can copy the project folder to another computer where you have datasets in a similar relationship to the home directory.
loadStar 1
loadDatasets 1
useIUPAC 1
dataPath {$env(HOME)/nvprojects2/test2/datasets}
dataPath {$env(HOME)/data/titrationkg}
You actually open a project (including newly created ones) by selecting the project in the Available Projects list and clicking the button. If you have any existing project data open (peak lists and molecular structures) you will get a warning and a request that data needs be be cleared first. You can explicitly remove any existing project data by clicking the the button located next to the name of the Active Project. Note you can use this button even if you're not working with a project and simply want to remove data such as molecules and peak lists so that you can, for example, load a new STAR file.
When you open the project all appropriate datasets will be loaded, the latest STAR file will be read and the project window description file will be processed so that all spectral windows should be displayed as they were when you saved the project.
As you work with a project you should periodically use the → → menu item to save the project data. Each time you do this a new STAR file will be written to the projects' star folder and the state of all windows will be saved.
When you're working with a project you can take advantage of the Favorites
system. This lets you save and reload the state of any windows (this is separate
from the saving of all window states that happens when you save the whole project).
Just click the 
button on the Spectrum window's icon bar to save state of the
currently active window. You'll be prompted for a window name and then the window
data will be written into a ".nvw" file in the win folder of the current project.
You can retrieve the window state by selecting the the → menu item. When you do this a list of all available window files for
that project will be displayed. Just select one and click the
button.