PDB Connector - UniprotKB Accession Number(s)

[Emilie_Pihan]

Dear all,

I would like to thank you for the very useful PDB Connector node.

I notice something weird, or maybe I don't put the right ID.

I would like to find all structures corresponding to a particular UniprotID.

For example, P10827.

So I tried to put it in IDs and Keywords tab, as UniprotKB Accession Number(s) but it was unsuccessful.

If I put this ID in Text Search section, there are missing some structures.

Could you please help me?

Regards,

Emilie

[Vernalis]

Dear Emilie,

I just had a quick try searching for P10827 in the UniProtKB Accession Number(s) field, and I got 8 structure hits - the same as I got trying the same ID on the RCSB Advanced Query website (1NAV, 2H77, 2H79, 3HZF, 3ILZ, 3JZB, 4LNW, 4LNX).

There are two things to help see if we can pin this down.

1 - In the node when you have it configured for the UniProtKB Accession Number(s) query, could you go to the 'Query Options' tab, and click on 'Test Query'.  Two things should happen - the 'Messages' box next to the 'Test Query' button should display a message (in my case, 'Query retrieved 8 hits.'), and the 'XML Query String' box should be populated.  In my case, this now shows:

<orgPdbQuery>
	<queryType>org.pdb.query.simple.UpAccessionIdQuery</queryType>
	<accessionIdList>P10827</accessionIdList>
</orgPdbQuery>

If you could try this, and let us know what you get (you can use the 'Copy Query' button after running the 'Test Query')?

2 - Add a copy of the 'PDB Connector (XML Query)' node to your workflow, and paste the above XML into the 'XML Query String' box on the 'Query Options' tab, then try running the node, and see if you get the expected results

If you could try both those things and let us know what happens, that would be really helpful

Yours,

Steve

[Emilie_Pihan]

Dear Steve,

I realized that I didn't install the last version of your nodes.

It works perfectly now!

Regards,

Emilie

[Vernalis]

Dear Emilie,

Thanks - that's great!  I meant to ask which version you had.  If you have the new version, you should now also have the two query views (the XML view which shows the rather cryptic XML version as above, and also the 'Logic' view which hopefully shows something a little more user-friendly.

Best wishes,

Steve