NEF export not grouping spin systems by residue

Analysis Version 3
,
1

I’m working with CCPNMR Analysis (v3.3.4), and I’m having trouble with spin system grouping during NEF export while I exactly follow the tutorial related to exporting NEF for BMRB.

My assigned residues (like Lys135, Tyr136, etc.) are split into separate spin systems (135, 135-1, 136, 136-1, etc.) in the exported .nef file, while for example, 136-1 should be merged with the 135 spin system. I expected that residues with assigned HN, N, CA, CB, etc. would be exported under a single spin system per residue, but this doesn’t seem to be happening.
Can you please help me with that?

2

Hi,

you can merge your i and i-1 NmrResidues if you like. The only thing to bear in mind is that you can’t undo this operation.
So make sure you save and archive your project or do this in a separate new project.

Then you can simply use this macro:

# Macro to merge "-1" NmrAtoms with the actual i-1 NmrAtoms
# Make sure the correct NmrChain has been selected in the first line
 
nmrChain = project.getByPid('NC:A')
 
with undo():
  for nmrRes in nmrChain.nmrResidues:
      if nmrRes.relativeOffset == -1:
          if nmrRes.mainNmrResidue:
              if nmrRes.mainNmrResidue.previousNmrResidue:
                  newSeqCode = nmrRes.mainNmrResidue.previousNmrResidue.sequenceCode
                  for nmrAtom in nmrRes.nmrAtoms:
                      nmrAtom.assignTo(sequenceCode=newSeqCode, mergeToExisting=True)
                  project.deleteObjects(nmrRes)

(Taken from the post at Synthetic peak list and merging i and i-1 - #3 by VickyH)

For information about running macros go to

Vicky

3

Hi Vickey,

Thank you very much. It works, really appreciate it!

Best,
Mahdi