Opened 8 years ago

Closed 8 years ago

Last modified 8 years ago

#755 closed defect (fixed)

Fetch mmcif files from rcsb instead of erratic www.pdb.org

Reported by: Tom Goddard Owned by: Tom Goddard
Priority: major Milestone: Alpha2
Component: Input/Output Version:
Keywords: Cc: chimera-programmers@…, meng@…, tef@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

ChimeraX fetches mmCIF files from www.pdb.org. That site is currently down so files cannot be fetched. But RCSB and PDBe are online. I couldn't find documentation from the PDB saying to use "www.pdb.org" for downloads. In fact searching shows online gives "files.rcsb.org" as the download server:

https://www.rcsb.org/pdb/static.do?p=download/http/index.html

It may be that the www.pdb.org site is not well maintained since no one uses it and we should be fetching from RCSB or PDBe. Chimera 1 fetches from www.rcsb.org.

Change History (2)

comment:1 by Tom Goddard, 8 years ago

Resolution: fixed
Status: assignedclosed

Changed fetching of mmCIF and PDB files to use files.rcsb.org instead of www.pdb.org since this is the URL the Protein Databank has documented online:

https://www.rcsb.org/pdb/static.do?p=download/http/index.html

This means that ChimeraX users in Europe will fetch their mmCIF files from RCSB in the US which would be slower than fetching from PDBe. This is what Chimera 1 does so we have accepted this for the last few decades. Possibly the Protein Databank intends to redirect www.pdb.org to the closest site for downloads, but I did not see anything about this online, so I would guess that www.pdb.org is also hosted by RCSB (the whois database lists the domain owner as RCSB).

For EMDB fetch we fetch from RCSB if the hostname ChimeraX is running on ends in ".edu" or ".gov" otherwise we use PDBe. This results in slower map downloads for US ChimeraX users coming from ".com" and other domains (e.g. downloading from home using an IP address provided by an ISP, or downloads by phramaceutical companies).

Possibly ChimeraX was using "www.pdb.org" to allow the Protein Databank to redirect requests to the nearest site. It would be sensible to use that if they documented online their intent to support that url. The www.pdb.org site has been down for a few hours now.

comment:2 by Elaine Meng, 8 years ago

At least the ChimeraX users in Europe have the option of specifying pdbe or pdbe_updated as the source for atomic coordinates.

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