DynaMight missing python modul

[Poko18]

Problem Since last week, we had problems with running dynamight with relion 5.0. Error we get seems to be related to dynamight code installed with relion5. Has anyone experienced similar problem?

Job options:

relion_python_dynamight optimize-deformations --refinement-star-file Refine3D/run_it016_data.star --output-directory DynaMight/ --initial-model Refine3D/run_it016_half1_class001.mrc --initial-resolution 8 --n-gaussians 30000 --n-gaussian-widths 1 --n-latent-dimensions 5 --n-positional-encoding-dimensions 10 --n-linear-layers 8 --n-neurons-per-layer 32 --n-warmup-epochs 10 --consensus-update-rate 1.0 --consensus-update-pooled-particles 500 --regularization-factor 0.9 --particle-diameter 280.0 --soft-edge-width 20.0 --batch-size 256 --n-epochs 150 --n-threads 8 --n-workers 32 --combine-resolution 8.0 --use-data-normalization --kld-factor 0.01

Error message:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/conda/envs/relion-5.0/lib/python3.10/site-packages/dynamight/__init__.py", line 3, in <module>
    from .deformations import optimize_deformations, optimize_deformations_rigid
  File "/opt/conda/envs/relion-5.0/lib/python3.10/site-packages/dynamight/deformations/__init__.py", line 3, in <module>
    from. optimize_deformations_rigid import optimize_deformations_rigid
ModuleNotFoundError: No module named 'dynamight.deformations.optimize_deformations_rigid'
---------------------------------- 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/conda/envs/relion-5.0/bin/python

[biochem-fan]

Since last week

Do you mean it used to work before?

[Poko18]

Yes, It was working 10-14 days ago. We reinstalled relion with the latest changes in branch 5.0, and somehow it does not seem to work anymore. Is it possible that the recent changes broke something? Or perhaps our installation is stale?

[biochem-fan]

Probably the easiest thing to try is to remove the relion-5.0 conda environment and rebuild both RELION and the conda environment.

[Qiangong2]

@biochem-fan Having the exact same issue. Occurs even after removing and rebuilding. We're using Ubuntu 22.04.

EDIT: This only happens with the python tomo tools and dynamight

[biochem-fan]

@schwabjohannes @dkimanius Did you change something?

[Poko18]

We also tried to rebuild RELION and it did not work. Seems like dynamight.deformations.optimize_deformations_rigid module is missing, which was added recently: https://github.com/3dem/DynaMight/commit/5760613f094e17c768b6f0eec81bccfbca9cc569

[schwabjohannes]

I think it was a typo, should be fixed now.

[Poko18]

changes fixed the issue, thanks!

[Qiangong2]

@biochem-fan While dynamight is now working, we're still receiving the Python interpreter error on the python tomo tools.

[biochem-fan]

@Qiangong2 Let's discuss tomography issues on #1087.