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The CARA repository

• The repository contains all data relevant to your project. This includes any reference libraries, like chemical shifts statistics, residue types, spin systems, NMR spectra types, and Scripts ... Furthermore the repository contains one or more projects that all use the same set of libraries.
• All Libraries can be edited inside of CARA. There is no need to use text editors to change hard-to-find configuration files. For most tasks, graphical editors are provided. It is however possible to edit the repository in a text editor if necessary.
• The Libraries are needed to make use of all the powerful features of CARA. The simplest way to get started is to read in a template repository which contains a library for standard applications.
• For each project, the repository keeps track of all data used during the assignment process and all the knowledge accumulated by the user about the chemical shift assignments.

Template repositories

• Template Repositories can be found at the TemplatesPage. Be sure to use the most recent template release when starting new projects.

Tutorials to help you work with repositories:

• Importing a template into a Repository
• Working with other programs: Import and Export to and from XEASY, MAPPER, DYANA, ...

Manual editing of the repository (advanced users)

The repository resides in a single XML file with a .cara extension. It can be edited with a common text editor or a special XML-aware editor like Microsoft Excel / Access or XML-Spy.

Note that in XML like in HMTL information is structured using tags which indicate the type of information. Tags usually bracket the information in question. For example: <something > information </something>. In some cases a compact version <something /> is used. Any tag can be equipped with attributes of the form attribute=value. Here is a typical block of XML from a CARA repository:

    <spectrum-type name=3D N15-NOESY>
    <dim name=H atom=H>
    <label tag=HN off=0 final=1/>
    </dim>
    <dim name=H atom=H/>
    <dim name=N atom=N>
    <label tag=N off=0 final=1/>
    </dim>
    <step text=N atom=N dim=2 hops=0 rep=0/>
    <step text=H atom=H dim=0 hops=1 rep=0/>
    <step text=H atom=H dim=1 hops=-1 rep=0/>
    </spectrum-type>
    

Note that all elements are either bracketed with <xxx> and </xxx> or are of the form <xxx /> . The above block is the definition of an NMR experiment.

Be aware that CARA checks a repository when it is opened. If an inconsistency is found, an error message will show you the line number where the problem occurred. Sometimes you can fix a corrupted repository by completing the XML brackets or copy-pasting the missing part from another intact repository. See FAQ and the following issues from IssueTracker for examples:

• http://tracker.cara.nmr.ch/0624
• http://tracker.cara.nmr.ch/0700

EditingRepositories: some examples of how to edit repositories

NEXT: ImportingTemplate

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