shift import nmrview format

Analysis Version 3
#1

Hello,

I just spent the better part of a day trying to import chemical shifts in NMRView, SPARKY and XEASY formats into Analysis v. 3. I tried the STARch tool at bmrb, exporting and reading star files, manually editing star files, using ccpn v2 format converter, no progress. SURELY, this problem has been encountered and solved many times already. I saw several threads here dealing with the topic of shift import but nothing definitive that I could get to work.

Any streamlied tips would be most appreciated – thanks!

-M

#2

Hi Mark,

Would it be possible for you to send us your BMRB generated NMR Star file and your .prot file (support@ccpn.ac.uk) so we can have a look what errors you are encountering? Usually when there is a problem with NMR Star import it is the lack of some tags in the file.

Kind regards,
Eliza

#3

hi mark

you may want to look at nef pipelines

this can read chemical shifts from nmrview and sparky into nef which you can then read into assign.The software is new and there will still be bugs, but the author is me so there is someone to talk to.

full disclosure nmr atom name conversion is still rudimentary at best

what is your original input format and source of data?

regards
Gary

#4

Hi Gary,

I got the NEF pipeline tools to work (starting from nmrview files), an successfully loaded the resulting nef file into ccpnmr3.

My original ppm.out file had stereo codes of 0 or 1, while the converter was expecting 1,2 or 3. I couldn’t find documentation on these but the output file from nmrfx uses the 1-3 codes. That, and a seq file, worked to generate a nef file that was read in, with proper residue numbers.

Thanks!

-M

#5

Hi Mark

really glad to hear you got it to work, you are my first real user outside of kent and ccpn!

some requests if you have time

  1. please star the project on GitHub (GitHub - varioustoxins/NEF-Pipelines: Nef tools) if you have an account!
  2. could you share what commands you ran?
  3. would you able to share directly with me a snippet of the file with the interesting stereo codes (suitably anonymised if needed and just a few relevances residues )

regards
Gary

#6

Hi Gary,

#7

Hi Mark

The reply seemed to be truncated!

regards
Gary

#8

Strange that my response was truncated. I had to enter this response on the form, not via email.

Hi Gary,

  1. I starred the project on GitHub
  2. To generate the nef file I ran:

~/.local/bin/nef nmrview import sequence …/file.seq
| ~/.local/bin/nef nmrview import shifts test-ppm.txt > file.nef

In that regard, let me add that this is the first time I’ve used pipx, but if I understand it, this tool by default places files in ~/.local , which is non-intuitive to me, since those files will be invisible unless one goes looking for them. Until now I have executables in /Applications, ~/Applications, ~/bin, /usr/local/bin, and /usr/local/nmr//bin. Now I have to remember that I also have apps in ~/.local/bin and ~/.local/pipx/. I assume there’s a good reason for this, but I can imagine forgetting those files are there.

  1. Regarding the 1/0 stereo code, I assume it’s an old format. The file I started with was generated by a prior lab member who was using CARA for sequential assignments, so perhaps the nmrview format changed since CARA was last updated. A snippet is here:

128.CA 45.253 1
128.HA2 3.925 0
128.HA3 3.925 0
128.C 174.224 1
129.N 121.098 1
129.H 8.641 1
129.CA 57.179 1
129.HA 4.225 1
129.CB 29.973 1
129.HB2 2.000 1
129.HB3 1.956 1

The same snipped saved from nmrfx:

128.CA 45.253 1
128.HA2 3.925 2
128.HA3 3.925 2
128.C 174.224 1
129.N 121.098 1
129.H 8.641 1
129.CA 57.179 1
129.HA 4.225 1
129.CB 29.973 1
129.HB2 2.000 2
129.HB3 1.956 2

  1. I should add that I haven’t yet had a change to work through the complete workflow with the imported assignments, so I’ll let you know if I encounter any hiccups.

Thanks again!

-M