Import CARA assignment to ccpn

NEF
1

Hi everyone, I’ve started my backbone assignment using CARA, but it couldn’t be finished because the protein has an intrinsically desordered region. Anyways, I’d like to show the peaks I could assign in a graph with good resolution, but as I don’t know how to do this using CARA, I’d like to import the assignment to CCPN. I’ve tried to import the .peaks file I exported from CARA, but it didn’t work. Any ideas on how could I import the CARA assigned peaks?

PS.: I’m using “analysis” in the nmrbox.

2

Hi Cynthia

I think you should be able to import your CARA assignments into NEF using the xeasy importer in NEF-Pipelines https://github.com/varioustoxins/NEF-Pipelines

I would installl nef pipelines as follows rather the information on the NEF-Pipelines page [note NEF-Pipelines is mostly supported on Linux and Max but Windows sort of works and WSL unix distributions should work]

  1. Install the UV package manager following these instructions [https://docs.astral.sh/uv/getting-started/installation/#installation-methods]

    1. Use uv to install nef pipelines using the following command in a shell

uv tool install nef-pipelines --python 3.12 --with rich

  1. Check the program is installed by typing nef you should get something along the lines of

nef

Usage: main.py [OPTIONS] COMMAND [ARGS]…

╭─ Options ───────────────────────────────────────────────────────────────────────────────╮
│ --install-completion [bash|zsh|fish|powershell|pw Install completion for the │
│ sh] specified shell. │
│ [default: None] │
│ --show-completion [bash|zsh|fish|powershell|pw Show completion for the │
│ sh] specified shell, to copy it │
│ or customize the │
│ installation. │
│ [default: None] │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────╮
│ chains - carry out operations on chains │
│ csv - read [rdcs] │
…
│ xplor - read xplor [sequences, dihedral & distance restraints] │
╰─────────────────────────────────────────────────────────────────────────────────────────╯

  1. This shows nef is working

  2. Export your peaks and shifts to xeasy format using

  • WriteProtonList.lua : Writes out an xeasy-formatted proton list for a project (no unassigned “999.000” atoms included)
    • NOTE A more sophisticated script for this purpose is WriteAssignments.lua (see ATNOS/CANDID section above)
  • PeakListNumberedByResidue.lua : : Write out a peaklist where the peaknumber corresponds to the residue number for a specific atom in each dimension. E.g. you want to write out a peaklist for an HSQC15N where each residue gives rise to a peak (HN/N) whose peaknumber corresponds to the residue number. This is useful for plotting the results of NH dynamics or exchange vs. sequence. Note that you can load this peaklist back into CARA from MonoScope. Because the list is numbered by residue, this makes it convenient to use the peaklist navigator in MonoScope (pl) or the shortcut goto peak gp to find the signal from a given residue.

Using the scripts from http://cara.nmr.ch.nmr.kasserver.com/old_cara_wiki/ScriptsToExportFileToProgram.html

  1. Find your self a fasta sequence file for your protein

5.You should then be able to do something like

nef fasta import sequence my_protein.fasta | nef xeasy import peaks my_protein.peaks | nef xeasy import my_protein.prot > my_protein.nef

This should give you a NEF file with shifts, peaks and a sequence you can import into CCPN

You may need to a translation step for atom names in there too if you do come back to me, the translation engine in NEF-pipelines is written but not currently that well exposed

If this isn’t work for you you can either

  1. Export data to another format e.g sparky, talos may also work, though I can’t read the nmrstar2 files that the script WriteAssignments.lua gives you
  2. Get in touch with your cara project and I will see what I can put together later this week

Note if you can send me on a copy of your cara project anyway (suitably obfuscated if you wish) I can have a go at making a direct CARA reader for the future

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

:telephone::01227 82 7117
:envelope:: g.s.thompson@kent.ac.uk
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