The purpose of this project is to provide an alternative to rsync to download data from the PDB https://files.wwpdb.org/pub/pdb/data/structures/divided/mmCIF after I had a problem with my university firewall to download the mmCIF database to run AlphaFold locally. Nevertheless, it should work to download other type of data from this same source.
- Basic knowledge of Unix/Linux Shell commands
- Clone repository.
git clone git@github.com:benjaminlozanow/pdb_data_download.git- Run download_pdb.sh in the desired directory.
chmod +x download_pdb.sh./download_pdb.sh "https://files.wwpdb.org/pub/pdb/data/structures/divided/mmCIF"- You will have generated new files, specially list.txt, where URLs are stored (an outdated version of this files is provided for you to try).
You can run this script to only generate the list of URLs or to just download the data comming from those links. In order to do so you just need to comment some lines from the code.
- After the data is downloaded (it could take a while depending on the type of data), run the unzip_flatten.sh with absolute path of the downloaded directory as argument.
chmod +x unzip_flatten.sh./unzip_flatten.sh ~/path_to_data_directoryWhile executing the download_pdb_mmcif.sh I recieved the following error:
rsync: failed to connect to rsync.rcsb.org (128.6.158.70): Connection timed out (110)
rsync error: error in socket IO (code 10) at clientserver.c(127) [Receiver=3.1.3]
Feel free to optimize/modify the code to have better or different results.