Outstanding tasks PDB entries in PomBase

[manulera]

A summary of what we discussed today regarding PDB stuff @kimrutherford @ValWood

Best structure

It seems the PDB identifies a "best structure" for a given gene depending on coverage + resolution if there are several entries for the same gene.

Best structures API entrypoint docs https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/#api-SIFTS-GetBestStructures

Best structures for a given entry https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/O74718

Multiple assemblies

However, it seems there may be several assemblies for a single entry. Maybe here is where that best_assembly_id column matters.

https://www.ebi.ac.uk/pdbe/entry/pdb/3h0g/analysis

Highligthing a given chain in the sequence

In the 3D viewer of the pdb of this entry, the protein of interest is highlighted. Perhaps we can find the configuration of molstar from the html or if the code of the pdb website is available somewhere. Then we could do the same for PomBase's structures in a gene page.

https://www.ebi.ac.uk/pdbe/entry/pdb/3h0g/protein/1

[kimrutherford]

It seems the PDB identifies a "best structure" for a given gene depending on coverage + resolution if there are several entries for the same gene.

We're using that API to put the entries in order, with the best structures at the top of the list.

[ValWood]

These touches would be nice for the upcoming update paper, but not critical

[manulera]

This might have already been addressed in a separate issue

[ValWood]

This is a nice example for highlighting the chain in a sequence. https://www.pombase.org/gene/SPBC32H8.05

[ValWood]

Is this any help:

[kimrutherford]

Do you have a link for that?

[ValWood]

No I asked GPC chat, it's probably made up! ;)

[kimrutherford]

Ah, that explains it. I tried to Google search for some of the things a mentioned and couldn't find another. I'll try again soon.