EMDB quicksubmit (database id) to NIH 3D failing: wwpdb mirror missing file

[kristen.browne@…]

When running some EMD quicksubmits, they are failing: NIH3D FATAL ERROR: Could not open 15007 from emdb_us transferMethod https: Fetching url https://files.wwpdb.org/pub/emdb/structures/EMD-15007/map/emd_15007.map.gz failed. File not found
When I open the entry with open emdb:15007 it opens fine.  It's probably that the US site is down, which seems to happen relatively frequently.  Could we write in a fallback that IF emdb_us fails, it should try just emdb instead?  Hopefully they don't often go down at the same time?

Thanks,

K

Kristen Browne, MSc, MscBMC
Contractor - MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, Room 4A60
Rockville, MD 20852
Office 202-253-5228

[Eric Pettersen]

I get File Not Found in both cases. For me, they both go to the same URL: ​https://files.wwpdb.org/pub/emdb/structures/EMD-15007/map/emd_15007.map.gz . Can you try the "open emdb:15007 " with "ignoreCache true"?

[Tom Goddard]

The United States fetch fails for me and the Europe fetch works

open 15007 from emdb_us -> fails using ​https://files.wwpdb.org/pub/emdb/structures/EMD-15007/map/emd_15007.map.gz
open 15007 from emdb_europe -> succeeds using ​ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-15007/map/emd_15007.map.gz

If you use "from emdb" then the site used depends on your host URL with .gov and .edu using the US site, .cn hosts using China, .jp hosts using Japan, and others using Europe.

[Eric Pettersen]

So is the idea that you would want to cycle through all four EMDB providers (US, Europe, Japan, China) before giving up on an entry?

[goddard@…]

I suggest either always use Europe or fallback to just Europe. The home of the EMDB is the Europe site. The other sites just mirror the data. The advantage of using US first is that it will be faster for downloading large maps. 

[kristen.browne@…]

I think we should start with US because it USUALLY works and is faster.  Then try Europe, then give up.  I don't think we need to look at all of them.

Thanks!

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, December 13, 2022 5:01 PM
To: pett@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Cc: goddard@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8165: EMDB quicksubmit (database id) to NIH 3D failing: wwpdb mirror missing file

#8165: EMDB quicksubmit (database id) to NIH 3D failing: wwpdb mirror missing file
---------------------------------------+----------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  feedback
          Priority:  normal            |  Milestone:
         Component:  Input/Output      |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------

Comment (by goddard@...):

 {{{
 I suggest either always use Europe or fallback to just Europe. The home of  the EMDB is the Europe site. The other sites just mirror the data. The  advantage of using US first is that it will be faster for downloading  large maps.
 }}}

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[Eric Pettersen]

Okay, I added a fallback to EMDB Europe and have submitted it as a pull request on the chimerax-preset-failures branch. Though the entry that engendered this (15007) is now working from the US EMDB!