PDB Downloader and PDB Downloader (Source)


I would like to know if there is something wrong with PDB Downloader Nodes?

PDB Connector is ok but I cannot use PDB Downloader anymore.

I face an issue: "ERROR PDB Downloader Execute failed: com.vernalis.io.FileDownloadException: Problem downloading pdb file: null"

I don't know why, before it worked perfectly. Do you have an idea?




Thanks for the report - we also discovered this issue at the same time.  I have a fix which should go live later today. (It is a result of the RCSB PDB changing the URLs for the file downloads)

Also, if you are using the PDBConnector, please be aware of our post yesterday at https://tech.knime.org/forum/cheminformatics/changes-to-rcsb-pdb-queries.

I will reply again when the fix is live.


I asked the same question two days ago. Apparently with the wrong Tag. :)

I was suspecting some RCSB PDB URL changes.

Thanks Emilie.


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We have just uploaded the newly correct version to the nightly build and to the stable builds for version 3.3 and 3.2.

On consequence is that we have just deprecated the current form of these nodes (although they do now work again!), and replaced them with new versions which also allow downloading NMR Shifts and restraints for those structures where that is relevant.

I will put up a new post imminently dealing with the changes....


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