Yang's Lab > Software > NMRspy

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Frequently Asked Questions

 

How to label HSQC peaks with its residue and index no (e.g. S120)?

How to output assignments for DYANA or CYANA calculation?

 

How to label HSQC peaks with its residue and index number (e.g. S120)?

You will have to manually edit under “Custom Label” in the Peak Editor. The Peak Editor is opened by left click to select the peak then press enter. The Peak Editor may have to be maximized to show the “Custom Label” and “Label Display” options.

 

How to output assignments for DYANA or CYANA calculation.

NMRspy allow users to output the assignments as DYANA format for structure calculation (Analysis -> NOEs). The DYANA format is also compatible with CYANA 2.l or later. For every spectrum saved under its specified dataset, a peaklist named after this dataset, containing all the assignments will be created. Users are advised to select the peaklist and the appropriate NOE axes for extraction. The number of assignments extracted will thus be indicated as number of peaks extracted.

To calibrate the NOE distance restraints based on data height intensity, users may click “Guess Bins” to create a preliminary estimation, which has to be refined later by the user himself. Then click “Calibrate”.

To save the calibrated assignments as DYANA format, click “Output” which will generate three files, the .upl, .lol and .seq files for DYANA or CYANA calculation.

Note: The Cysteine residues in .upl, .lol and .seq are abbreviated as CYS (assumed as Reduced Cysteine). User has to manually correct Oxidized Cysteine residues as CYSS using any text editor for CYANA calculation.