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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
90 stars 18 forks source link

[Question] How to get the FastA formatted file for all sequences in this databank? #17

Closed agdiaz closed 1 year ago

agdiaz commented 1 year ago

Hello everyone there, thank you very much for this tool!

I'm trying to install it locally and after installing all the dependencies, now I'm about to run the command:

alphafill prepare-pdb-list --pdb-dir=${PDB_DIR} --pdb-fasta=${PDB_FASTA} --output pdb-id-list.txt

I've downloaded the PDB-REDO entire DB using the rsync command. My question is how to get the FASTA file. Do you have a link to provide me to continue with the configuration? Or a method to extract the FASTA files from the PDB-REDO DB?

Thanks in advance for your help!

Best regards from Brussels,

mhekkel commented 1 year ago

If you've downloaded the entire pdb-redo databank, you can find the file in the others directory, it is named pdbredo_seqdb.txt

I believe we should add this bit to the documentation.

agdiaz commented 1 year ago

Thanks for the info @mhekkel ! Agree with the idea of adding it to the Readme file 👍