NEF export of multiple chains

Analysis Version 3
#1

Dear all,

I need to import my ccpnmr3.1 project to ccpnmr2.5 to “Make distance restraints” (this is due to calibration problems of intermolecular NOE peaklists during structure calculation cause there are no fixed reference distances in these types of peak lists).

In my ccpnmr3.1 project of a dimeric protein, I have chain A and B, and NMRChain A, B and @ (unassigned second conformation). A and B have exactly the same chemical shift, i.e. B was generated by duplicating A.

During NEF export, I choose chain A and B, and NMRChain A and B. However, upon ccpnmr2.5 import I get the error message

>>> '@-'

which I guess steams from the NMRChain @. Inspection of the NEF file shows, that indeed _nmr_atom.chain_code “@-” was also exported even though it was unchecked. [The same thing happens if I only choose chain and nmrchain “A”, all three (@-, A and B) are exported.]

After modifying the NEF file and removing all @- entries by hand, I get further errors as pop up windows that are

“There are more resonances (3) than atoms sets for 43Val CG1/CG2”

for every residue of the protein.

What can I do to import such a project to ccpnmr2.5 in order to use the function “Make distance restraints”? Is there maybe another “easier” way to achieve what I am trying to do?

Thanks and best wishes,
Max

#2

Hi Max,
Have you tried first the macro in 3.1 “calculateDistanceRestraints” ?
You can find in MainMenu > Macro > run CCPN Macros > calculateDistanceRestraints.

The requirement is that you set the Reference Experiment type for the source spectrum. Can do by double click on the spectrum on sidebar. Dimensions tab: set Reference Experiment type to 13C HSQC-NOESY (which I think is the only implemented/tested so far).

We will look into 2.5 error. Thanks for reporting this.

#3

Hi Max,

I am struggling to reproduce this error, would you be able to send us your project and/or NEF file you are trying to load to v2? (eapa2@leicester.ac.uk or support@ccpn.ac.uk)

Kind regards,
Eliza

#4

Thanks, I have sent you the file!

#5

Hi Luca,

thanks for the suggestion. I have tried the macro, however, if I understand correctly, it requires me to assign all peaks before, i.e. it does not do at chemical shift matching towards the assigned chemical shifts?

Best,
Max