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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

rsync download of the PDB-REDO DB not working #26

Closed roger-boop closed 1 year ago

roger-boop commented 1 year ago

I am not 100% sure that this is the right place for asking this, but I am trying to download the PDB-REDO DB for running alphafill. I am using the command on the webpage 'rsync -av rsync://rsync.pdb-redo.eu/db/ pdb-redo/' This are the errors I get: rsync: [Receiver] failed to connect to rsync.pdb-redo.eu (192.87.97.253): Connection timed out (110) rsync error: error in socket IO (code 10) at clientserver.c(137) [Receiver=3.2.3]

I am on ubuntu 22.04.1

If the rsync server is no longer running could you give an alternative to download the DB?

mhekkel commented 1 year ago

That URL should have been rsync://rsync.pdb-redu.eu/pdb-redo/

So the command should be:

rsync -av rsync://rsync.pdb-redo.eu/pdb-redo/ pdb-redo/

I will update the web page. Thanks for reporting

roger-boop commented 1 year ago

Hi again. This URL still gives me the same error, it is possible that I'm doing something wrong? I simply open the terminal, cd to the directory where I want to store the data, and execute the command. Thanks for the fast answer

mhekkel commented 1 year ago

Most likely you are sitting behind a firewall that blocks access to our rsync server. Please contact your local service desk for help since the command given should really work.