Hi,
Which Cyana version are you using?
If it is 3.98.15 you will not be able to read all spectra in one large nef file and write the outputs, you would need to read in nef files with single spectra.
For instance:
cyana> read Alt_SH2_assign_edited_15N_HSQC.nef
cyana> write Alt_SH2_assign_edited_15N_HSQC.peaks
To speed up export you can run a macro to export each spectra individually (assuming you have only one peak list in each spectra):
for peak_list in project.peakLists:
project.exportNef(path='/your/path/Documents/'+peak_list.spectrum.name+'.nef', overwriteExisting=True, skipPrefixes=['ccpn'], expandSelection=False, includeOrphans=True, pidList=['MC:A', 'CL:shifts', peak_list.pid])
Once you have those individual nef files edited for Cyana you could write a shell script to do read/write in Cyana for all those spectra (let me know if you need help with that).
If you have any question do let me know.
BW,
Eliza