Fetch IHM entries by 4 character PDB id

[Tom Goddard]

Fix ChimeraX IHM fetch to work with 4-character PDB codes.

It appears PDB has discontinued the fetching of IHM entries by 8-digit codes, it is no longer working in ChimeraX giving

open 18 fromDatabase pdbdev
Fetching url https://pdb-dev.wwpdb.org/cif/PDBDEV_00000018.cif failed:
HTTP Error 404: Not Found

Going to the RCSB web site shows the download link is now

​https://pdb-dev.wwpdb.org/cif/8zzi.cif

using a standard 4 character PDB id code.

[Tom Goddard]

Here is the RCSB announcement of this change

From: Irina Persikova via pdb-l <pdb-l@…>
Subject: pdb-l: PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)
Date: August 14, 2024 at 10:39:29 AM PDT
To: pdb-l@…
Reply-To: Irina Persikova <persikov@…>

Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is issued a PDB ID, reported in the PDBx/mmCIF file in the _database_2 category, and “integrative” method provenance is captured at _struct.pdbx_structure_determination_methodology. Users can access and download IHM structures and associated data at files.wwpdb.org/pub/pdb_ihm/ <​https://files.wwpdb.org/pub/pdb_ihm/>.

Currently, holding files in JSON format, validation reports (summary and full reports) in PDF format, and model files in PDBx/mmCIF format are provided.

• /pdb_ihm/holdings/ (current holdings, released structures last modified dates, unreleased entries)
• /pdb_ihm/data/entries/hash/{PDB_id}/validation_reports/ (includes summary and full validation reports)
• /pdb_ihm/data/entries/hash/{PDB_id}/structures/ (latest version of model files)
• For example, ​https://files.wwpdb.org/pub/pdb_ihm/data/entries/zz/8zz1/structures/8zz1.cif.gz

Data may be expanded in the future based on community needs. In the near future, IHM data will also be available via wwPDB DOI landing pages and wwPDB partner websites.

Questions or feedback? Contact deposit-help@… or pdb-dev@….

--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@…
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[Tom Goddard]

I sent email to RCSB help asking if about their deleting the old IHM entries:

"PDB-Dev entries can no longer be fetched from ChimeraX

I saw that PDB-Dev entries now have 4-character codes like other PDB entries announced on the PDB mailing list (​https://lists.wwpdb.org/empathy/thread/4J6E42RUR67MCGRJSBOZDEFSZGR6AOWS). I discovered that ChimeraX can no longer fetch PDB-Dev entries using the 8-digit PDB-Dev ids. ChimeraX tries to download the file using for example for PDB-Dev 00000018

​https://pdb-dev.wwpdb.org/cif/PDBDEV_00000018.cif

but that file is no longer on the server. Instead it appears there is a file

​https://pdb-dev.wwpdb.org/cif/8zzi.cif

where 8zzi is the new 4-character PDB id code for PDB-Dev 00000018. Was removing the old cif files intentional? That breaks fetching from all current ChimeraX versions. I will make fetching work with the PDB ids available in ChimeraX daily builds but the next ChimeraX release is not until the end of the year.

The PDB-Dev web pages still show the 8-digit id codes and it would probably be nice to allow users to access the files in ChimeraX with that code in addition to the 4-character id. Is there a new way to do that now that the PDBDEV_00000018.cif file is not available?

Thanks,

Tom Goddard
ChimeraX developer"

[Tom Goddard]

I made the ChimeraX fetch from pdbdev handle 4-character PDB id codes and left in the code for 8 digit numeric ids. Will wait to see what the PDB help desk says about fetching by the 8-digit ids before closing this ticket.

[Tom Goddard]

From: Rachel Kramer Green
Subject: Re: [JIRA] (HELP-21446) PDB-Dev entries can no longer be fetched from ChimeraX
Date: August 21, 2024 at 6:12:49 AM PDT
To: Tom Goddard
Cc: Info <info@…>
Reply-To: Info <info@…>

Dear Tom,

The issue you reported below has been addressed. mmCIF and binarycif files are available using both PDB ID and PDB-Dev IDs.

Please let us know if you have any comments or questions.

Best regards,

Rachel

---

RACHEL KRAMER GREEN, PH.D.
Scientific Support & Customer Service Lead
RCSB Protein Data Bank
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854

[Tom Goddard]

Done.

The PDB fixed the problem and fetching by 8-digit ids works again. Also fetching by 4 character ids is working in the ChimeraX daily build.