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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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Unable to find CIF files #18

Closed Geraldene closed 2 years ago

Geraldene commented 2 years ago

I am getting the following error: ValueError: Could not find CIFs in /path/to/mmcif_files

I have checked and the files are present, is there a way around this?

sanjaysrikakulam commented 2 years ago

Hi @Geraldene

Please make sure you have the proper directory structure as described here https://github.com/deepmind/alphafold#genetic-databases and also check if your user has required read permissions to the download/data directory.

Geraldene commented 2 years ago

@sanjaysrikakulam The directory has the proper structure and the 'download/data directory' has read permissions but I am still encountering the same error

sanjaysrikakulam commented 2 years ago

Hi @Geraldene,

In that case please edit the path in the variable template_mmcif_dir in run_alphafold.sh script. The script is designed to follow the AF2's data directory structure, the simplest solution, for now, would be to manually change the path within the script. To further troubleshoot please share the tree structure of your 'data directory which contains all the downloaded databases for AF2.

Geraldene commented 2 years ago

@sanjaysrikakulam I have edited the script as suggested and it's running, thanks for your help!!