Exporting chemical shift list for TALOS+

Analysis Version 3
21

No you are doing right, I thinks its just your pipx is possibly older

could you do pipx --version

22

just had a look at the pipx change log, interpreter only appeared in version 1.5.0, if yours is older than that it won’t work…

I have have a solution though

if you do
pipx uninstall nef-pipelines
pipx install nef-pipelines
nef about --verbose

you should now get version 0.1.77 and about should give you

This is NEF-Pipelines version 0.1.77

 ... text removed for brevity!


  Environment
  -----------

  Python version:   3.11.5
  Python path:      /Users/garyt/Dropbox/nef_pipelines/nef_pipelines/venv/bin/python
  Operating system: macOS-10.16

you should now at last be able to use the path listed after Python path: as PYTHON-INTERPRETER-PATH in

PYTHON-INTERPRETER-PATH/pip install --upgrade wheel setuptools

and do

pipx uninstall nef-pipelines
pipx install nef-pipelines

again

sorry this is such a pain, I will look at modifying the program to avoid this in future…

23

Dear Gary,
Thanks a lot for the help!

We tried to install ubuntu 24.04 LTS, but the pipx version 1.4.3 doesn’t update to the version 1.5.0 that you suggested. I tried to install nef- pipelines but no success, it gives me the same error as before.

Marta

24

Hi Marta,

Will obviously be great if you can get NEF-Pipelines working as it will allow you to do lots of other things, too. But if you are only interested in TALOS, then you have another option which is to use Xplor NIH, which can essentially run Talos for you and do all NEF translations.

When you run structure calculation with Xplor NIH this is the first step in the pipeline, and most set up is done for you, but you can just run the “Talos” step few small manual steps.

You do need Xplor NIH installed on your machine, but that is easy to do.

  1. Copy an entire ‘nef’ folder from Xplor NIH distribution (/xplor-nih-3.8/eginput/pasd/nef). This folder has all the files and scripts you need (such as runTalos.sh).

  2. Export your chemical shifts to NEF file and save it in the folder you created above (include chain and make sure there is only one chemical shift list in your nef file, skip ccpn tags).

  3. Edit runTalos.sh and add path to your Talos executable.
    In my case beginning of the runTalos.sh is:

#!/bin/sh

TALOSN=/Users/Eliza/Projects/talosn/talosn

nefFilename=$1
…

  1. In terminal run:
    ./runTalos.sh myFileWithShifts.nef

(if you have any problems with permissions just do first:
chmod 777 runTalos.sh
)

You should get myFileWithShifts_new.nef with dihedral angles restrains and all other Talos files.

Any problems please let me know.

Kind regards,
Eliza

25

ok installing a virtual machine with ubuntu to see if I can fix this

26

ok, thanks
Marta

27

Thank you very much Eliza.

If I can’t solve the problem I will try your suggestions.

Regards
Marta

28

Ok I can get it to work fine for me on a ubuntu 22.04 vm

I wrote a little script to repeat what I did

#!/bin/bash
sudo apt install python3-pip
sudo apt install pipx
pip install --upgrade wheel setuptools
pipx install nef-pipelines
pipx inject nef-pipelines rich
if ! grep -q 'pipx path setup!' ${HOME}/.bashrc
then
    echo  '# pipx path setup!' >> ${HOME}/.bashrc
    echo 'export PATH=${HOME}/.local/bin:${PATH}' >> ${HOME}/.bashrc
fi

you can download it from https://raw.githubusercontent.com/varioustoxins/NEF-Pipelines/master/installation_scripts/install_nefp_ubuntu.sh

if you type

bash install_ubuntu.sh

that should do all the installation, it will prompt you for your password and will ask you a couple of questions you have to reply y to. You then need to close all terminal windows and when you open new ones the command nef should work.

hopefully that will do it, if not there is always Elisa’s method, but this has that downside you don’t get tools to reimport things back into NEF, but whatever works

Thank you for bearing with me while I sort this out

hope that helps
regards
Gary

nb I have only tried this on a normal VMware vm not a windows wsl installation, I need to get my windows machine working for that
nb I am working on a cleaner install script but this works for now

29

its now updated so you don’t have to type y as part of the installation process

regards
Gary

30

Thanks again Gary but still errors

********************************************* error in nef_pipelines.tools.about *************************************************

plugin nef_pipelines.tools.about

Traceback (most recent call last):

File “/home/marta/.local/pipx/venvs/nef-pipelines/lib/python3.10/site-packages/pynmrstar/init.py”, line 15, in 

import cnmrstar

ModuleNotFoundError: No module named ‘cnmrstar’

I did exactly as you suggested same errors as before do I need to clean the installation somehow?

Best

31

sounds like it has cached it, try

pipx uninstall nef pipelines
pip cache purge

this seems to clear things on my machine

however the weird thing is I don’t have the bad pynmrstar installation problem on my system either and I am on ubuntu 22.04

lsb_release -a

gives

No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.4 LTS
Release: 22.04
Codename: jammy

any way try the uninstall and pip cache clear let me know how it goes

also note

  1. after uninstallation check nef doesn’t work any more to make sure you haven’t managed to get multiple installations
  2. to see the pip cache you use pip cache info and pip cache list

regards
Gary

32

Gary!! It’s works :smiley:

Thank you very much for your help!

Regards
Marta

33

whooo hoooo!

Now lets hope it does what you need (but if not I can fix that ;-))

regards
gary

NB thank you for sticking with this, it has been really helpful to help me get things sorted out ;-)

1 Like
34

Dear Gary,

I have another question for you!
How can I generate a Cyana .prot file from the NEF file? I need to create a proton list in this format eg.:
241 174.110 0.300 C 1
243 55.407 0.300 CA 1
245 28.704 0.300 CB 1

(atom number - chemical shift - chemical shift variation - atom name - and sequence number)

Thanks

Regards
Marta

35

nothing directly implemented at the moment but

firstly the latest version of cyana can read some nef files [elisa maybe able to advise]

secondly

this may work

nef <your_file.nef>| nef frames tabulate <your_shift_frame> --no-title | grep -v chain_code | nl | awk ‘{print $1, $6, $7, $5, $3}’

notes

  1. you will need to replace <your_file.nef> with the name of your nef file
  2. I would run

nef <your_file.nef>| nef frames list --verbose

to find out what the name of <your_shift_frame> is
3. some of the atom names may choke cyana you can always choose what atom names to include by doing

nef nmrstar import project ubiquitin| nef frames tabulate nef_chemical_shift_list_bmr5387 --no-title | grep -v chain_code | egrep ‘CA|CB’ | nl | awk ‘{print $1, $6, $7, $5, $3}’

which will only select lines contains CA and CB using ubiquitin downloaded from the bmrb as an example…

36

if atom name are a problem I do have some translation code but it is not quite working yet…

37

finally if you

pipx install tabulate

you can do

nef nmrstar import project ubiquitin| nef frames tabulate nef_chemical_shift_list_bmr5387 --no-title | grep -v chain_code | egrep 'CA|CB' | nl | awk '{print $1, $6, $7, $5, $3}'| tabulate --format plain

which gives quite nice looking output

  1  54.5  0.05  CA   1
  2  33.3  0.05  CB   1
  3  55    0.05  CA   2
  4  30.8  0.05  CB   2
  5  59.6  0.05  CA   3
  6  42.1  0.05  CB   3
  7  55.2  0.05  CA   4
  8  41.4  0.05  CB   4
  9  60.8  0.05  CA   5
 10  33.8  0.05  CB   5
 11  54.5  0.05  CA   6
 12  36.5  0.05  CB   6
 13  60.4  0.05  CA   7
 14  70.7  0.05  CB   7
38

Dear Martha,

You can just use Cyana to read NEF file:
cyana> read myNefFile.nef
cyana> write myShift.prot

Kind regards,
Eliza

39

Dear Gary and Eliza,

Thanks a lot for your help. I will try the suggestions today.
If there are any other problems I will write to you.

Regards
Marta