pdb module

[sbliven]

I love the new alphafold feature! Could there also be a gget pdb command for fetching structures from PDB? Combined with gget blast -db pdbaa this could be very powerful for comparing predictions and templates.

[lauraluebbert]

Thank you! Great idea! You are also not the first person to request a gget pdb module. It is on my to-do list (or happy to receive PRs if anybody wants to give it a try). 😊

[lauraluebbert]

Done! You can install gget pdb by updating to the latest gget version (pip install -U gget) (see the ReadMe for a full manual). gget pdb currently only takes PDB IDs as input. However, in the new version, gget info returns all PDB IDs associated with a given Ensembl ID. Please let me know your thoughts! Also, did you already have a use case in mind? If so, would you be willing to share it with me so I can use it as an example (with credit) (e.g. could you show me how you would use gget to compare predictions)?