Creating NOESY peaklists with CARA

One can start either by creating an empty peaklist, or by exporting inferred peak and spinliks from PolyScope. After that it is possible to add peaks interactively or with a script. The fastest method seems to be picking peaks automaticaly with the 'PickAll3DNOESY' script from an empty peaklist.

Simulate short and sequential peaks

1. Run 'ExportToCSI' script to generate an input file for CSI
2. Run the CSI program
3. Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction
4. Remove all unnecessary spins, such as draft assignments (e.g. '?HA'), projected spins (e.g. 'HA-1') and GFT pseudospins (e.g. 'CApCB'). Bulk remove is possible with scripts such as RemoveSins, RemoveProjectedSpins and RemoveGFTSpins.
5. Open an HSQC spectrum in PolyScope window with the corresponding NOESY spectrum loaded in the strip. In the 'Strip' menu make sure that the 'Show Spin Links' box is checked, and the 'Show Inferred Peaks' is unchecked. Select 'File' -> 'Export...' -> 'Strip Peaks to MonoScope...' to create an initial peaklist with existing assignments.

• Note that certain spinlinks (such as HE <-> N in Lys, for example) will yield undetectable peaks. Therefore, integrate the peak list first and then use the 'PeakListReport' script to delete all peaks weaker than a certain threshold.
• Some peaks may have significant overlap, or have contributions from yet unassigned long-range peaks. Interactive refinement is necessary.

Automated peak picking

1. For each peaklist define the typical peak linewidths using Intergrate -> Tune Peak Model... in MonoScope.
2. Set 'DeafultPeaklist' and 'PeakListToSpectrumMapping' attributes of the corresponding spectrum according to the peaklist.
3. Run the 'PickAll3DNOESY' script to automatically pick peaks.
4. Run the 'PeakListReport' script to delete diagonal peaks.
5. Refine the resulting peaklist by interactivelly scanning all strips.