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Dear Simon, Unfortunately it is not quite that simple. LinkResonances will not assign a previously unassigned spectrum for you. To do that you have to tell the program specifically what each peak should be assigned to, either by hand or by subroutine. LinkResonances only comes in as part of the format conversion process, linking the new information correctly into the existing project. When you use FormatConverter to load a peak list that is already assigned, in the external file. the program first stores the assignment strings with the peaks. These assignment strings can be quite exotic, especially for SPARKY, so ti is hard to decide up front which atoms they are supposed to match. LinkResonances then convertes the external text strings to proper CCPN assignments, complete with links to MolSystem Atoms, Resonances, etc. Loading the NMRSTAR file should give you a shift list. You can set this to be the shift list for the spectra you want, and then assign the peaks using the shift list. You can also generate synthetic peaks lists with the shift list, and use the synthetic peaks asa a guide for assignment. Etc. The process is the smae as when you acquire a new spectrum, possibly at a different temperature, and want to assign it using your previous spectra as a starting point. Yours, Rasmus --------------------------------------------------------------------------- Dr. Rasmus H. Fogh Email: [log in to unmask] Dept. of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002 On Tue, 4 Oct 2011, S.P. Skinner wrote: > Hi Rasmus, > > I already have unassigned peaks picked on the spectra, I have the sequence > loaded and I have no assignments present before importing the nmrstar file. > The file itself contains molecules and assignments. According to the > documentation, when this file is imported, you should be able to run link > resonances and I guess that would then give me an assigned spectrum, is this > correct? > > Simon > > Rasmus Fogh wrote: >> Dear Simon, >> >> Could you expand a bit: >> Do you have peaks / spectra/ assignments/ molecules in the project before >> importing the NMRSTAR? >> Do you have peaks / spectra/ assignments/ molecules in the NMR_STAR file? >> Are you saying that importing the NMRSTAR file should cause already >> existing peaks in the project to be assigned, or what? >> >> Yours, >> >> Rasmus >> --------------------------------------------------------------------------- >> Dr. Rasmus H. Fogh Email: [log in to unmask] >> Dept. of Biochemistry, University of Cambridge, >> 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002 >> >> On Tue, 4 Oct 2011, S.P. Skinner wrote: >> >>> Dear All, >>> >>> I have downloaded an NMR star 2.1 file from the BMRB and imported into >>> analysis via the project menu, however when I run Link Resonances as >>> advised by the software, even though I have peaks picked in the spectra, I >>> see no assignment appear in the peak lists or on the spectra, the terminal >>> shows no traceback, only the normal messages stating assignment. >>> >>> Any ideas what's wrong >>> >>> Regards >>> >>> Simon >>> >>> -- >>> Simon P Skinner >>> Protein Chemistry Group >>> Leiden Institute of Chemistry, Universiteit Leiden >>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349 >>> E-mail : [log in to unmask] > > -- > Simon P Skinner > Protein Chemistry Group > Leiden Institute of Chemistry, Universiteit Leiden > Phone: +31 71 527 6089 / Fax: +31 71 527 4349 > E-mail : [log in to unmask]