Relion5.0 tomo

[nbcronin]

Installed Relion5.0. with no problem. Runs with programs in the environment.yml (relion_blush; topaz etc)

Currently want to run relion --tomo ( Relion-5.0-beta-1-commit-b75b38) and get the error

---------------------------------- PYTHON ERROR --------------------------------- Has RELION been provided a Python interpreter with the correct environment? The interpreter can be passed to RELION either during Cmake configuration by using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.

Using python executable: /opt/anaconda3/envs/relion-5.0/bin/python

ModuleNotFoundError: No module named 'tomography_python_programs'

The path for the python executable is correct - is there a module named tomography_python_programs?

Thanks

Nora

[nbcronin]

I can see the tomo programs are located - in a relion/src/tomography_python_programs - ie there an environment variable to point to this? Currently it is looking at the conda environment to locate the programs.

nora

[LIjieHan]

I'm having the same problem, did you figure out how to fix it?

[nbcronin]

Hi

Yes the problem has been resolved. The advice I received is very simple:

"Before running cmake, you must have conda in your path (but not activated relion-5.0 env). Cmake will create Python files inside the bin directory."

Once you have created the environment place the path in your profile.d (or local equivalent) eg a python.sh file:

export PATH=/opt/anaconda3/envs/relion-5.0/bin/:$PATH

ie wherever your path to the relion-5.0 environment is located.

Then run cmake etc

The difference between correct and incorrect is that you will now see the tomo executables in the conda bin area above.

Best

Nora

Nora Cronin LonCEM Facility Manager

The Francis Crick Institute

1 Midland Road

London NW1 1AT

T: +442037965225

E: @.**@.>

W: www.crick.ac.ukhttp://www.crick.ac.uk/

---

From: Lijie Han @.> Sent: Wednesday, March 20, 2024 11:29 PM To: 3dem/relion @.> Cc: Nora Cronin @.>; Author @.> Subject: Re: [3dem/relion] Relion5.0 tomo (Issue #1087)

External Sender: Use caution.

I'm having the same problem, did you figure out how to fix it?

— Reply to this email directly, view it on GitHubhttps://github.com/3dem/relion/issues/1087#issuecomment-2010899186, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2HDYEUH6ARJJ3PQJPOCRTTYZILUPAVCNFSM6AAAAABECB56JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJQHA4TSMJYGY. You are receiving this because you authored the thread.Message ID: @.***>

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[Qiangong2]

The files are successfully made in the bin directory, but we still get the python error.

[nbcronin]

Hi

You are attempting to use Dynamight ? Do you see it in the conda path (/opt/anaconda3/envs/relion-5.0/bin - this is my one):

-rwxr-xr-x. 1 croninn 256 Mar 19 15:08 relion_tomo_denoise -rwxr-xr-x. 1 croninn 266 Mar 19 15:08 relion_tomo_align_tilt_series -rwxr-xr-x. 1 croninn 253 Mar 19 15:08 relion_tomo_view -rwxr-xr-x. 1 croninn 253 Mar 19 15:08 relion_tomo_pick -rwxr-xr-x. 1 croninn 267 Mar 19 15:08 relion_tomo_import -rwxr-xr-x. 1 croninn 267 Mar 19 15:08 relion_tomo_get_particle_poses -rwxr-xr-x. 1 croninn 268 Mar 19 15:08 relion_tomo_exclude_tilt_images -rwxr-xr-x. 1 croninn 231 Mar 19 15:08 dynamight

Try running from the cmd line:

relion_python_dynamight --help

(base) @.*** Jie]$ relion_python_dynamight --help

Usage: -c [OPTIONS] COMMAND [ARGS]...

╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─ Commands ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ compute-masks-for-rigid-transforms │ │ compute-rigid-transforms │ │ deformable-backprojection │ │ deformable-backprojection-correction │ │ deformable-backprojection-single │ │ deformable-backprojection-single-deformation │ │ explore-latent-space │ │ optimize-deformations │ │ optimize-deformations-rigid │ │ optimize-deformations-single │ │ optimize-inverse-deformations │ │ optimize-inverse-deformations-single │ ╰─

The python error indicates that the program is not correctly installed?

Best

Nora

Nora Cronin LonCEM Facility Manager

The Francis Crick Institute

1 Midland Road

London NW1 1AT

T: +442037965225

E: @.**@.>

W: www.crick.ac.ukhttp://www.crick.ac.uk/

---

From: Kurt @.> Sent: Friday, March 22, 2024 5:46 PM To: 3dem/relion @.> Cc: Nora Cronin @.>; Author @.> Subject: Re: [3dem/relion] Relion5.0 tomo (Issue #1087)

External Sender: Use caution.

The files are successfully made in the bin directory, but we still get the python error.

— Reply to this email directly, view it on GitHubhttps://github.com/3dem/relion/issues/1087#issuecomment-2015608878, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2HDYEUU6Y3TNK6VSIN4V23YZRVA3AVCNFSM6AAAAABECB56JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJVGYYDQOBXHA. You are receiving this because you authored the thread.Message ID: @.***>

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[Qiangong2]

Hi @nbcronin, No, dynamight is functional, but the other tomo python programs do not. The conda paths are fine, Relion is able to find the correct python path during compilation and any other tools except for the tomo tools.

[Qiangong2]

@biochem-fan Any ideas?

[EricDeveaud]

hello, had the same problem with relion-5.0 and found that among this python module some other are missing, I fixed it by.

    # used by relion_python_tomo_align_tilt_series
    cd $(SOFT)/src && cp -r tomography_python_programs $(PYLIB)
    $(PIP) install makefun yet_another_imod_wrapper lil_aretomo
    # used by relion_python_tomo_get_particle_poses
    $(PIP) install morphosamplers
    # used by relion_python_tomo_pick
    $(PIP) install napari_threedee
    # used by relion_python_tomo_pick relion_python_tomo_view relion_python_tomo_exclude_tilt_images
    $(PIP) install lru-dict

NB installation performed out of conda.

[nbcronin]

Hi

I found the solution to this problem entails installing in the correct order. Starting from scratch - new relion install and conda environment not installed; before creating the conda environment, create the 'build' subdirectory. Then create the conda environment running the environment.yml file from the ~/relion repository - you will see the 'tomography_python_programs' directory appearing in the build 'lib' subdirectory:

cd /home/supervisor/relion-5.0/relion/build/lib

drwxr-xr-x. 6 supervisor 4.0K Apr 10 14:49 acc/ drwxr-xr-x. 2 supervisor 4.0K Apr 10 14:49 apps/ drwxr-xr-x. 3 supervisor 4.0K Apr 10 14:49 Eigen/ drwxr-xr-x. 19 supervisor 4.0K Apr 10 14:49 jaz/ drwxr-xr-x. 2 supervisor 143 Apr 10 14:49 lbfgs/ -rw-r--r--. 1 root 6.8M Apr 10 17:09 librelion_gpu_util.a -rw-r--r--. 1 root 2.3M Apr 10 17:05 librelion_gui_lib.a -rw-r--r--. 1 root 14K Apr 10 17:09 librelion_jaz_gpu_util.a -rw-r--r--. 1 root 39M Apr 10 17:05 librelion_lib.a drwxr-xr-x. 2 supervisor 116 Apr 10 14:49 spherical-harmonics/ drwxr-xr-x. 13 supervisor 4.0K Apr 10 14:49 tomography_python_programs/

Then proceed with cmake etc. with the conda python environment in the path (but not activated).

Best

Nora

Nora Cronin LonCEM Facility Manager

The Francis Crick Institute

1 Midland Road

London NW1 1AT

T: +442037965225

E: @.**@.>

W: www.crick.ac.ukhttp://www.crick.ac.uk/

---

From: Eric Deveaud @.> Sent: Monday, April 22, 2024 11:50 AM To: 3dem/relion @.> Cc: Nora Cronin @.>; Mention @.> Subject: Re: [3dem/relion] Relion5.0 tomo (Issue #1087)

External Sender: Use caution.

hello, had the same problem with relion-5.0 and found that among this python module some other are missing, I fixed it by.

# used by relion_python_tomo_align_tilt_series
cd $(SOFT)/src && cp -r tomography_python_programs $(PYLIB)
$(PIP) install makefun yet_another_imod_wrapper lil_aretomo
# used by relion_python_tomo_get_particle_poses
$(PIP) install morphosamplers
# used by relion_python_tomo_pick
$(PIP) install napari_threedee
# used by relion_python_tomo_pick relion_python_tomo_view relion_python_tomo_exclude_tilt_images
$(PIP) install lru-dict

NB installation performed out of conda.

— Reply to this email directly, view it on GitHubhttps://github.com/3dem/relion/issues/1087#issuecomment-2069081160, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2HDYETJTS4DD56J3Z4KGKTY6TTOPAVCNFSM6AAAAABECB56JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGA4DCMJWGA. You are receiving this because you were mentioned.Message ID: @.***>

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[Qiangong2]

Hi @nbcronin

Unfortunately, it still doesn't work.

---------------------------------- PYTHON ERROR ---------------------------------
   Has RELION been provided a Python interpreter with the correct environment?
   The interpreter can be passed to RELION either during Cmake configuration by
     using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.
---------------------------------------------------------------------------------

The above error appears specifically on relion_python_tomo_import, relion_python_tomo_denoise, relion_python_tomo_exclude_tilt_images, relion_python_modelangelo, relion_python_topaz, and relion_python_tomo_align_tilt_series. The other python tools are fine.

@biochem-fan Can you please provide an update on this?

[biochem-fan]

@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.

[Qiangong2]

@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.

@biochem-fan Who is then?