I am having trouble in downloading multiple pdb files using BATCH with shell scripting. I have used following command line :
1. chmod +x batch_download.sh
2. ./batch_download.sh -f nn -p
Here, "nn' is a text file containing PDB IDs separated by comma.
The output on the terminal is as follows
Downloading https://files.rcsb.org/download/2NLS.pdb.gz to ./2NLS.pdb.gz
Failed to download https://files.rcsb.org/download/2NLS.pdb.gz
An image of the terminal is attached.
Please help.
Dear Bondeepa Saikia
You can use the getpdb utility to download multiple PDB files by copy them out of the your local PDB mirror directory, or, if not found, downloading them from the RCSB repository
you can find more info here:
1. https://www.rcsb.org/downloads
2. https://www.rcsb.org/docs/programmatic-access/file-download-services
3. https://www.biostars.org/p/311292/
Kind Regards
Qamar Ul Islam