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A research assistant and I noticed an error upon searching for PDB IDs listed here using the "Analysis" tool on w3DNA 2.0: [6JVZ, 6JW4, 6JW3, 6JW5, 6JW0, 6JW2, 6JW1, 6JTQ, 6LEW]
Error Message: "ERROR: Empty or invalid ID, please type in a valid one."
These IDs are deposits dated either in 2019 or 2020. I did a search for 2021 deposits with DNA and did another set of 'Analysis' checks and, again, got the same error.
Is there a lag time between when a PDB deposit is made vs. when it's able to be accessed in the web server?
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Thanks for reporting the issues on analyzing new PDB entries on Web 3DNA 2.0.
Is there a lag time between when a PDB deposit is made vs. when it's able to be accessed in the web server?
As mentioned in the Li et al 2019 paper (https://doi.org/10.1093/nar/gkz394)
To facilitate the analysis of nucleic-acid-containing structures from the PDB, a very common user demand, we constructed a database of those entries for w3DNA 2.0. The current database is populated by all PDB entries (with metadata) from the 6 March 2019 release that contain the 3D coordinates, in traditional PDB format, of at least one nucleotide. Gigantic structures, such as the ribosome, that are available only in PDBx/mmCIF format are thus excluded from the database.
No new PDB entries after 2019-03-06 are auto-processed on the current Web 3DNA 2.0 web server. See also the thread "w3dna server update schedule?" (http://forum.x3dna.org/web-3dna/w3dna-server-update-schedule/)
The project is currently out of funding support, and the service is provided AS IS. Things may change/improve in the future, though.
Best regards,
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University