DrJesseHansen

no module named openmm

2

Hello, We are running Alphafold 2.3.1 on a Linux HPC through SLURM submission. The databases were downloaded to our cluster for AF2 to run correctly. We were able to successfully...

TypeError: tuple indices must be integers or slices, not str

10

Hi all, I have resubmitted the same job as my [previous issue](https://github.com/deepmind/alphafold/issues/742), except this time on GeForce RTX 2080 Ti rather than A10 or A40s (under the assumption that these...

ptxas fatal : Ptx assembly aborted due to errors

3

Hello all, thank you for the update! However now we are running into a new error while testing on a bunch of different GPUs. This is on our HPC. ```...

std::bad_alloc for subtomo averaging

1

hi, I am using RELION for subtomo averaging after exporting the extracted subvolumes from WARP. My box is 200 pix at 4.2A/pix. I have 4000 particles. This doesnt seem excessive....

Estimating initial noise spectra from HUGE number of particles

1

hi, I am running RELION/4.0 on cluster environment. I am doing subtomo refinement, box size 160, 38000 particles. local angular search only, at healpix 5, and a translational search of...

Label mask is not specificed

11

Dear Devs, I am using tomotwin as part of napari 0.4.18. I am running in clustering mode. The pixel size of my tomogram is 11.06, note that I did try...

No such file or directory: results

3

Hi I followed your tutorial steps except using my data. I gave it several tomograms, preprocessed as you describe, then ran refine on the HPC. It runs for about 3...

dose weighting in RELION 5

2

hi Biochemfan, I am sorry for posting this here, I'm not sure how else to contact you. I am wondering if it's possible to include a dose weighting scheme for...

relion 5 tomo error

1

Running on a Linux Deb 12 compute cluster, have tried on various GPU nodes. Running relion/5 beta-3-commit-6331fe. For example when I run the command below: relion_python_tomo_align_tilt_series AreTomo --sample-thickness-nanometers 120 --gpu...

3D refinement with subvolumes gives the error cited. Subvolumes extracted from WarpTools 2.0.0/dev28. reconstruct_particle gives a very nice reconstruction. `mpirun --np 5 --oversubscribe relion_refine_mpi --o Refine3D/job001_3D/run --auto_refine --split_random_halves --i allparticles_bin8_3D.star...