Augustin Žídek
Augustin Žídek
Is this still an issue with the latest version of AlphaFold? Also, does it help to run without relax (`--run_relax=false`)?
Hi, thanks for the additional information, we will investigate and let you know.
Is this an issue for all 5 predictions or just some of them?
Could you try adding this code just before the problematic line is called? ```python import os del os.environ['LC_ALL'] ``` Also, is this issue happening in the AlphaFold Colab, or is...
Hi @Ezio0o, I can't unfortunately reproduce that with `gsutil` 5.10, the command runs fine for me and downloads the file. Two questions: 1. Is it possible that access to Google...
Hi, could you try setting `run_relax=false`? This means the relaxation step will be skipped (and there might be some clashes in the output structure), but might help with your issue.
Relax has problems usually if there is large number of clashes in the predicted structure, so this should happen only occasionally. With the newly release v2.2.0 the clashes in AlphaFold-Multimer...
Closing this issue for now, feel free to reopen if this is still a problem.
Currently AlphaFold saves the output only in the PDB format, but we would like to add support ModelCIF-compliant mmCIF output. We will keep this issue open until it is added.
HHBlits doesn't use GPUs, so it is definitely something else about the machines that is causing the difference. The most common HHBlits error is running out of RAM.