Allow fetching EMDB map given PDB id

[olibclarke@…]

From: Oliver Clarke
Subject: Re: [ChimeraX] #9846: Allow fetching fit PDB models together with EMDB maps
Date: September 29, 2023 at 6:18:46 AM PDT
To: Tom Goddard
Cc: Elaine Meng

I wonder - if the metadata is available - would it be possible to add the reverse operation? E.g. open "pdb_id" maps true? Grabbing the map from the EMDB, if there is a map associated with the entry? I have no idea whether this is trivial or difficult to add, if it’s a lot of work it’s obviously not worth it, but it would be convenient…

Cheers
Oli

[Tom Goddard]

It is not hard to add such an option. But I'm not sure what the option name should be. A user might expect "open 1xyz maps true" to work for the X-ray structure, and it possibly could since ChimeraX already fetches from the electron density server.

Maybe something that would be more widely used would be just to log a link to the EMDB or EDS map fetch when the PDB model is opened so that you don't have to click More Info in the Log. This would make it easier to get at the maps. I'm not sure if the utility of it across all our users justifies making it more visible than its current location in the More Info table.

[olibclarke@…]

Agreed - I didn\u2019t realize it was there in the \u201cmore info\u201d section until Elaine helpfully pointed it out! Now that I do, it is very easy to use. Maybe there is an argument for making it more prominent, but I don\u2019t think it is really needed.

Cheers
Oli

[Eric Pettersen]

Yeah, I put a direct link in the top level of log for EMDB maps, also not realizing it was available through "more info", but after discussion with Tom and Elaine I removed it, leaving just the "more info" link.