Could not find CIFs

[kuixu]

Could not find CIFs

[chesterroh]

Problem might be that running scripts/download_all_data.sh does not download the PDB data. Reason might be that in scripts/download_pdb_mmcif.sh the relevant commands are commented out (?!):

echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
mkdir --parents "${RAW_DIR}"
# rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
#   rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
#   "${RAW_DIR}"

# rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
#   data.pdbj.org::ftp_data/structures/divided/mmCIF/ \
#   "${RAW_DIR}"

I tried to download mmCIF files by uncommenting the former one in the installer file described above. But after having spent several hours of downloading it via rsync, I got to understand why @kuixu commented it out on purpose. It's really really slow. It would take more than a week I guess.

Please try to download it directly from ftp.pdbj.org or other equivalent mirror sites by using 'wget -r' or other recursive download tools. It takes much shorter time.

[kuixu]

Please change the DOWNLOAD_DIR.

# Set to target of scripts/download_all_databases.sh
DOWNLOAD_DIR = '/path/to/database'

# Path to a directory that will store the results.
output_dir = '/path/to/output_dir'

[clemensgrimm]

Same problem here:

$ echo $DOWNLOAD_DIR
/home/clemens/alphafold/parameter/

but:

$ exp/run_local.sh T1050.fasta
[...]
 ValueError: Could not find CIFs in /data01/xukui/alphafold/pdb_mmcif/mmcif_files

[clemensgrimm]

Problem might be that running scripts/download_all_data.sh does not download the PDB data. Reason might be that in scripts/download_pdb_mmcif.sh the relevant commands are commented out (?!):

echo "Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)..."
mkdir --parents "${RAW_DIR}"
# rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
#   rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
#   "${RAW_DIR}"

# rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
#   data.pdbj.org::ftp_data/structures/divided/mmCIF/ \
#   "${RAW_DIR}"