OBSLTE from pdb and cif input about gemmi HOT 6 OPEN

Note that your example has SPRSDE instead of OBSLTE.

I looked at _pdbx_database_PDB_obs_spr in the current PDB database, and unfortunately in a few cases
(namely: 3EZB 5HUZ 3J7O 3J7P 3J7Q 3J7R 1NEW 9PAP 2R2X 1SAF)
it contains a few entries, for example

loop_
_pdbx_database_PDB_obs_spr.id 
_pdbx_database_PDB_obs_spr.date 
_pdbx_database_PDB_obs_spr.pdb_id 
_pdbx_database_PDB_obs_spr.replace_pdb_id 
_pdbx_database_PDB_obs_spr.details 
SPRSDE 1987-01-15 9PAP 8PAP        ? 
SPRSDE 1986-10-24 9PAP '3PAD 8PAP' ?

although in the corresponding PDB it's only one line

SPRSDE     24-OCT-86 9PAP      3PAD 8PAP

I didn't check how it looks in the obsolete PDB entries.

Out of curiosity, what would you use it for?

from gemmi.

Ah, the https://www.rcsb.org human interface by default jumps 1qon to its replacement 6xyu.

I'm being asked to provide the info and choice to users before they do a large calculation when we pull from the web service programmatically(it doesn't auto-switch to the more recent). For example a user sets our software to modeling missing loops and refining a number of loops to see if they now fit the density. When there could be a better model in the rcsb that already has the loops. Or better density or resolution.

pdb 1qon

OBSLTE     15-FEB-23 1QON      6XYU                                             

mmcif 1qon

_pdbx_database_PDB_obs_spr.id               OBSLTE 
_pdbx_database_PDB_obs_spr.date             2023-02-15 
_pdbx_database_PDB_obs_spr.pdb_id           6XYU 
_pdbx_database_PDB_obs_spr.replace_pdb_id   1QON 
_pdbx_database_PDB_obs_spr.details          ? 
# 

from gemmi.

Perhaps the web service that you use can return status of the entry without downloading a file?
Or maybe it'd be more convenient to use the list from:
https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat

from gemmi.

Thanks for pointing out obsolete.dat
I'm using http://files.rcsb.org/download/ which I think mirrors the wwpdb

They want both ways; it happens when you give them options:-)

If a user already has pdb's what we're trying to do is be nice to their budget and not run unless they know about an updated structure

from gemmi.

OK, I'm not against it.
Are there any examples of multi-line OBSLTE?
Or examples when this record has multiple new PDB IDs (in either PDB or mmCIF format)?

from gemmi.

I'll keep an eye out. Will ask those who run large sets for an example

from gemmi.