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Author Topic: Is there a time lag between PDB deposits and 'Analysis' use?  (Read 1342 times)

Offline ry54451

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Is there a time lag between PDB deposits and 'Analysis' use?
« on: April 16, 2021, 10:16:42 am »
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?

Offline xiangjun

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Re: Is there a time lag between PDB deposits and 'Analysis' use?
« Reply #1 on: April 16, 2021, 12:24:54 pm »
Thanks for reporting the issues on analyzing new PDB entries on Web 3DNA 2.0.

Quote
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)

Quote from: Datasets section of MATERIALS AND METHODS
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?"

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
« Last Edit: April 16, 2021, 12:33:15 pm by xiangjun »

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.