Chemical Shift List Export

Analysis Version 3
1

Hi,

I would like to export my chemical shift list in a shifty format. What would be the best way to do that ?

Thank you.

Best,
Kleopatra

2

Hi Kleopatra,

The only way to export chemical shifts from CCPN V3 project is the NEF format.

You may be able to convert NEF format to shifty with:

perhaps dr Gary Thompson @varioustoxins will be able to comment on that.

BW,
Eliza

3

looks like it should be possible, I will reply with some details later tonight

4

Great thank you both.

5

Hi

installation

to install nef-pipelines download the install script using the following link [you might need to right click it and select download linked file or equivalent]

then run

bash install.sh

using the downloaded file install.sh file in a terminal and wait for the installation to complete [note this won’t work on windows but nef-pipelines is on nmr box]

nef export from ccpn

export your file from ccpn analysis assign using the menu file->export nef file

or the two letter command EX

conversion

to do the conversion do the following in the terminal

nef stream ubi.nef | nef shifty export shifts

notes:

  1. in this case the file has one chemical shift frame called bmr5387 so this is saved to a file called bmr5387_A.shifty, the A is the chain and bmr5387 is the name of the shift frame. Multiple shift frames and chains get stored in separate files

  2. if you just want to see the output in the terminal use

    nef stream ubi.nef | nef shifty export shifts -

  3. there is an option to set the templates for the filenames, so

    nef shifty export shifts --file-name-template 'garys_shifts_{nef_entry_id}_{chain_code}.shifty'

    would give garys_shifts_bmr5387_A.shifty instead

    where {nef_entry_id} and {chain_code} are place holders [in this case for bmr5387 and A ]

  4. you can select which frames and chains to export using the --chain and --frame options

  5. a handy way to list all the frames in a file is the following

    nef frames list ubi.nef

    again using using ubi.nef as an example

regards
Gary

6

Thank you Gary.

Best,
Kleopatra

7

Hi Kleopatra

do let me know if it works, and I not get back and I will sort any problems…

regards
Gary

8

Hi Gary,

Thank you for the help. I was able to convert the nef files into the shifty using nmr box.

Best,
Kleopatra