Creating Peaklist in NCO Experiments

Analysis Version 3
#1

Hi There!

I am just wondering if there is anyway to transfer chemical shift values and generate a peaklist in a 2D NCO spectrum. I am familar with the macro that will place the peaks in a CC spectrum - But I cannot seem to get it to work for an NCO spectrum.

Is there a macro that can do the same? I hope that makes sense

#2

Hi

I should be able to make nef pipelines do that, I will left you know when I have had a hack at it

Regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & working group member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:phone::01227 82 7117
:email:: g.s.thompson@kent.ac.uk
orchid: ORCID

#3

NEF-pipelines now has support for making synthetic spectra for 13C detect IDP directed experiments . NEF-Pipelines can be installed and upgraded using the script bin/install_nef_pipelines in the ccpnmr distribution. The you should be able to do the following

  1. export a nef file with from ccpn assign File->Export-> NEF File and save as my_protein.nef or your choice of name
  2. run the following command
nef stream my_protein.nef | nef shifts make-peaks --spectra NCO > my_protein_cdetect.nef
  1. import the nef file back into ccpn assign either by dragging it in the program or using File -> Import -> NEF File

PLEASE NOTE

  1. the c detect IDP experiments are a new feature, as always please do check that you are getting what you expect!. If you aren’t please contact me or put a ticket on GitHub see nef about for details and I will try and fix it as soon as possible.
  2. the shifts make-peaks command may move to something like nef simulate peaks sometime in the near future
  3. there are quite a lot of spectra you can simulate run nef shifts make-peaks --help for a complete list. The current list is

N_HSQC, C_HSQC, HNCA, HNcoCA, HNCACB,
HNcoCACB, CBCAcoNH, HNCO, HNcaCO, CON, NCO,
CAN, CACO, CBCACO, CACON, CBCACON, caNCO,
CANCO, COCON, NcaNCO, CBCANCO, COCA,
CDETECT, TRIPLE [default: N_HSQC]

note CDETECT and TRIPLE expand to multiple experiments…
4. if you like the software give it a star on GitHub again see nef about for information

#4

Hi,

if you right-click on a Chemical Shift List in the sidebar, you should be able to select Simulate Spectrum and then select NCO from the drop-down menu. That should create an NCO PeakList from shifts for you.

Vicky

#5

well that’s quicker than my solution… but I think I have a few extra spectra

#6

Hi there,

thank you both for this. Do either of these methods simulate the i-1 or are they restricted to intra-residue connections?

#7

Hi,

I think my method will only give you the N(i)-CO(i-1) peaks.

Vicky

#8

Oh that is fantastic! That is exactly what we need, Thank you!

1 Like
#9

mine does as well, the complete lists of connections for the spectra I have are

N_HSQC
((0, ‘N’), (0, ‘H’))

HNCA
((0, ‘CA’), (0, ‘N’), (0, ‘H’))
((-1, ‘CA’), (0, ‘N’), (0, ‘H’))

HNcoCA
((0, ‘H’), (0, ‘N’), (-1, ‘CA’))

HNCACB
((0, ‘H’), (0, ‘N’), (0, ‘CA’))
((0, ‘H’), (0, ‘N’), (-1, ‘CA’))
((0, ‘H’), (0, ‘N’), (0, ‘CB’))
((0, ‘H’), (0, ‘N’), (-1, ‘CB’))

HNcoCACB
((0, ‘H’), (0, ‘N’), (-1, ‘CA’))
((0, ‘H’), (0, ‘N’), (-1, ‘CB’))

CBCAcoNH
((0, ‘H’), (0, ‘N’), (-1, ‘CA’))
((0, ‘H’), (0, ‘N’), (-1, ‘CB’))

HNCO
((0, ‘H’), (0, ‘N’), (-1, ‘C’))

HNcaCO
((0, ‘H’), (0, ‘N’), (0, ‘C’))
((0, ‘H’), (0, ‘N’), (-1, ‘C’))

CON
((-1, ‘C’), (0, ‘N’))

NCO
((0, ‘N’), (-1, ‘C’))

CAN
((0, ‘N’), (0, ‘CA’))

CACO
((0, ‘CA’), (0, ‘C’))

CBCACO
((0, ‘CA’), (0, ‘C’))
((0, ‘CB’), (0, ‘C’))

CACON
((-1, ‘CA’), (-1, ‘C’), (0, ‘N’))

CBCACON
((-1, ‘CA’), (-1, ‘C’), (0, ‘N’))
((-1, ‘CB’), (-1, ‘C’), (0, ‘N’))

caNCO
((0, ‘N’), (0, ‘N’), (-1, ‘C’))
((1, ‘N’), (0, ‘N’), (-1, ‘C’))

CANCO
((0, ‘CA’), (1, ‘N’), (0, ‘C’))
((1, ‘CA’), (1, ‘N’), (0, ‘C’))

COCON
((-1, ‘C’), (-1, ‘C’), (0, ‘N’))
((-1, ‘C’), (0, ‘C’), (1, ‘N’))
((1, ‘C’), (0, ‘C’), (1, ‘N’))

NcaNCO
((0, ‘N’), (0, ‘N’), (-1, ‘C’))
((1, ‘N’), (0, ‘N’), (-1, ‘C’))
((-1, ‘N’), (0, ‘N’), (-1, ‘C’))

CBCANCO
((0, ‘CA’), (0, ‘C’), (0, ‘N’))
((0, ‘CB’), (0, ‘C’), (0, ‘N’))
((0, ‘CA’), (0, ‘C’), (1, ‘N’))
((0, ‘CB’), (0, ‘C’), (1, ‘N’))

where
((0, ‘CB’), (0, ‘C’), (1, ‘N’))
says peak with
CA shift at residue offset i=0
C shift at residue offset i=0
N shift at residue offset i=+1

if that helps