Exporting or converting peaklist til NMRstar for CSI 2.0 analysis

Analysis Version 3
1

Hi there!

I’m in the process of making a secondary chemical shift analysis and want to use CSI 2.0 (CSI 2.0: Prediction of Secondary Structure from Backbone Chemical Shifts and Sequence.) to analyse changes to secondary structure. However, the analysis tool accepts only NMRstar or Shifty formats. Is there any way for me to export my Peaklist as NMRstar or Shifty or any way to convert the NEF files?

Thanks in advance.

2

Hi

you should be able to use nef-pipelines to do this.

  1. to install run the script install_nef_pipelines in the ccpn/bin directory
  2. this should give you a command called nef if you run it you get this
Usage: main.py [OPTIONS] COMMAND [ARGS]...

Options:
  --install-completion  Install completion for the current shell.
  --show-completion     Show completion for the current shell, to copy it or
                        customize the installation.
  --help                Show this message and exit.

Commands:
  about      - info about NEF-Pipelines
  chains     - carry out operations on chains
  csv        - read [rdcs]
  echidna    - read echidna data [peaks]
 ...
  xplor      - read xplor [sequences, dihedral & distance restraints]

one of the things it supports is export of shifty files

  1. export you data from assign as a nef file. xxx.nef
  2. run this

nef stream xx.nef|nef shifty export shifts

this will produce a file called <entry_id>.shifty where entry_id is the name of your nef entry and cccp project

when I run this on Sec5Part4.nef which is the nef exported from one of the ccpn demo projects I get

Sec5Part4.shifty which contains

#NUM  AA     HA      HN      N15      CA      CB     CO
3     R   0.000   8.446  122.019  55.551  31.219  0.000
4     Q   0.000   8.379  121.418  53.532  29.263  0.000
7     L   0.000   8.688  126.114  53.996  45.397  0.000
8     V   0.000   8.663  127.613  63.568  32.661  0.000
9     T   0.000   8.990  116.934  60.533  70.168  0.000
10    G   0.000   7.914  110.000  46.275   0.000  0.000
11    I   0.000   8.389  120.492  59.923  41.475  0.000
12    S   0.000   8.257  119.603  54.585  65.743  0.000
14    N   0.000   8.360  112.221  53.066  38.204  0.000
15    E   0.000   7.288  114.885  53.038  32.933  0.000
....
87    S   0.000   8.098  115.333  56.718  66.321  0.000
88    F   0.000   8.931  121.922  56.762  43.057  0.000
89    K   0.000   6.862  127.675  54.686  34.067  0.000
90    L   0.000   8.185  128.944  53.784  43.198  0.000
91    L   0.000   8.037  126.831  53.304  43.211  0.000
92    K   0.000   8.227  121.217  53.610  32.935  0.000
94    E   0.000   8.507  121.524  56.734  30.609  0.000
95    K   0.000   7.834  125.927  57.617  33.854  0.000

note the columns HA and CO are zero because there is no data this still seems to work with CSI 2.0

note if you want a different output destination you can just add the name of the file to the command

e.g nef stream xx.nef|nef shifty export shifts my_directory/my_file.shifty

also if you have more than one chain you will be asked to name a chain e.g. use

e.g nef stream xx.nef|nef shifty export shifts --chain B my_directory/my_file.shifty

if you had a chain A and a chain B

note we can’t currently import ss structure into assign but its hopefully on its way…

regards
gary

3

nota bene if you already have NEF-Pipelines installed you will meed to update to this evening’s version to make this work by running install_nef_pipelines again

to check the version run nef about you should see version 0.1.57 if the upgrade worked…

4

nb if this works for you give the project a star on GitHub! GitHub - varioustoxins/NEF-Pipelines: Nef tools if not let me know what else you need ;-0