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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: ry54451 on April 16, 2021, 10:16:42 am

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Title: Is there a time lag between PDB deposits and 'Analysis' use?
Post by: ry54451 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?

Title: Re: Is there a time lag between PDB deposits and 'Analysis' use?
Post by: xiangjun 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?" (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

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.