Residual Dipolar Coupling (RDC) Analysis



Overview

make 4 data sets named usum.nv, udif.nv, asum.nv, and adif.nv corresponding to the sum and difference ipap spectra of unaligned and aligned, respectively.
  • for non ipap data sets, duplicate the unaligned and aligned spectra and name as above. Will still use 4 spectra but the coupled peaks will appear in same spectra. You sill have to pretend it is ipap and ignore one of the coupled peaks.
make 4 crosspeaks files named usumlist.xpk, udiflist.xpk, asumlist.xpk, and adiflist.xpk.
  • this can be done by making an empty xpk file and duplicating it
you need one master spectrum with assigned xpeaks. This will be used to make assignments of the 4 spectra.
  • use hsqc for 2D spectra, use hnco for 3D. You will have to switch y and z axes for NCo and NH. Xpeak file should be hsqclist.xpk and hncolist.xpk, respectively.
read all of above into nmrView. Can use a startup script to read files, organize windows, etc.
  • NOTE: nmrView can save your state, including open windows, so you really only have to read everything in the 1st time
  • below are example startup scripts, which should be modified for your specific data
  • 2D ipap startup script (check for latest nmrview compatibility)
  • 3D hnco ipap startup script (check for latest nmrview compatibility)
  • 3D hnco NON ipap startup script (check for latest nmrview compatibility)
read in asignment script
pick and assign peaks in the 4 spectra as outlined below
  • write the 4 xpk lists to disk (usumlist.xpk, etc.)
calculate RDC's from xpk files using perl script

Assign xpeaks

These abbreviated directions assume using one of the assignipap scripts mentioned above
select peak on master spectrum (hsqc or hnco) and press "i" to center and expand
  • pick corresponding peak in each of the 4 spectra using nmrView "cursor -> add peak" function
  • click in master spectrum and center cursor on xpk with assignment
  • press "a" to assign the last picked peak in each of the 4 spectra to the same assignment of master hsqc (or hnco)
  • pressing "n" will take to you next xpeak number (not sequence number) in master (make sure active xpk list in "assign peaks" window is the hsqc or it won't work correctly)
  • pressing "I" will zoom in a little; pressing "i" will zoom in a lot; pressing "o" will zoom out

Other useful scripts

rdc2cns (perl)
rdc2pales (perl)


RDC Software


Redcat

Module

Pales