Closed kristycarp closed 11 months ago
Hi @kristycarp - thanks for raising the issue and providing the temporary workaround.
I believe seting -mirror
option to either pdbe
or pdbj
can solve this too (these are identical replicates of default rcsb mirror) - at least this was helpful in recent e-mail conversation regarding similar / or same issue.
I'm away now but I'll look into this more thoroughly at the beginning of November and provide a proper fix.
Setting the mirror as pdbe works for me. Thanks.
When updating the localpdb files (with
localpdb_setup -db_path [DB PATH HERE] --update
) , I get the following error:I am fairly certain this is because of the (recent?) PDB change that makes their HTTP downloads available at files.rcsb.org, whereas their FTP downloads are still at ftp.rcsb.org (see https://www.wwpdb.org/ftp/pdb-ftp-sites).
I tried to tweak the
remote_sources.yml
file to reflect these changes, but was only able to successfully update my localpdb files with these very janky changes to the localpdb code:download_proto
within the rcsb mirror fromhttp
toftp
inremote_sources.yml
ftp=True
to any call todownload_url
inPDBDownloader.py
PDBDownloader.py
(I suspect this is a very bad thing to do!)I had to do all of this because 1) simply changing the url of the rcsb mirror in
remote_sources.yml
to files.rcsb.org led to an error saying that ftp://files.rcsb.org is inaccessible and I couldn't figure out how to make it go to http://files.rcsb.org instead; and 2) simply changing the download_proto of the rcsb mirror inremote_sources.yml
to ftp (from http) led to errors with checking versioning that were only fixed by the other tweaks mentioned above.However, I suspect that this is not the smartest of solutions and that myself and other users would benefit from a fix from the localpdb creators that either properly changes the protocol type from HTTP to FTP, or properly updates the HTTP address to files.rcsb.org.