Questions about structure DBs

[mtnouchi]

Hello,

I would like to use DeepAlign_Search.sh to perform structure search against PDB. However, I have some questions about the database used by DeepAlign:

First, how can I download the DB?

According to the README,

Users can download some protein structure databases from http://raptorx.uchicago.edu/download/ (...) 2. PDB database If databases/pdb_BC100/ does not exist, create one. Copy or link all the .pdb files to databases/pdb_BC100/

But, where can I find pdb_BC100? There are only pdb_BC40_20210204.tar.gz and pdb_Remain_20210204.tar.gz at http://raptorx.uchicago.edu/download/.

Second, how DBs were constructed?

How did you process the raw PDB files to obtain pdb_BC40_20210204.tar.gz? I believe that you normalized the raw PDB files using the tools under util/ and clustered them with >40% identity in some way. Is this correct understanding? If so, where can I refer to for the procedure?

Thanks for answering. Best, mt