make "info" report metadata; upon opening file, provide "info" execution link in Log instead of citation

[Elaine Meng]

Currently some metadata like citation is automatically given in the Log when an mmCIF is opened.

Rather than picking and choosing which metadata to put in the Log when file is opened (currently mmCIF, but I imagine analogous for EMDB etc.), better to add dataset metadata-reporting to the "info" command, either in the top-level command or as an additional subcommand.

Then upon opening the file, the Log could include a link to execute this command, if the user desires. Maybe something like:

[More information]…

• or more explicitly -

For more information, run [info model]

…where the bracketed text is an execution link to run “info model”.

Personally, I would like for the title to be shown in the Log upon opening the model, but if others disagree, nothing more than the tables we were showing already. The text with the info link could be right after the title.

[Eric Pettersen]

Whenever this is considered "finished" for mmCIF, change the owner to me and I'll get the corresponding information reported for PDB.

--Eric

[Elaine Meng]

The reasoning behind my suggestion to show only structure title with a link to show more:

(1) Structure title is often different and more informative than paper title. A single paper may be associated with multiple structures (different mutants, bound/unbound, different stages of reaction cycle, etc.) and it is impossible to tell which structure is what from the paper title.

Examples:
6G7H,I,K,L paper title: "Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser." structure title of 6G7H, for example: "Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure"

3ND5 structure title "Crystal structure of phosphopantetheine adenylyltransferase (PPAT) from Enterococcus faecalis"
3ND6 structure title "Crystal structure of phosphopantetheine adenylyltransferase (PPAT) in complex with ATP from Enterococcus faecalis"

(2) structure title is shorter than whole citation, so less scrolling up of previous more useful Log contents, like the clickable tables of assemblies and chains

(3) user has the option to see more by clicking the link. What I usually want to see the most:

1. structure title
2. ligands/hetres names
3. resolution, if applicable, otherwise exptl. method (NMR)

[Greg Couch]

Doesn't Scooter's Cytoscape app use the info command to get information about the open models? Will need to coordinate any changes.

[Elaine Meng]

It wouldn’t just be “info” but some appropriate subcommand or option keywords, that might be completely new.  I.e. there wouldn’t necessarily be any change to what Scooter uses.  Of course we can doublecheck what he uses too.
Elaine

[Elaine Meng]

For example, the actual command could be something like “info metadata <model-number>” … and link text in the Log something as simple as “more…” or “more info”  right under the structure title,  but I’m open to whatever we think works/looks best.

[Eric Pettersen]

I have an input-source-neutral scheme in mind for implementing this, so am reassigning it to me.

[Eric Pettersen]

Now uses "log" command instead of "info" command to show this info. Remaining things to do:

1) Change chain table so that left-hand links select and right-hand links show sequence
2) Get PDB to show citations and non-standard residues

[Eric Pettersen]

Chain table changes now implemented, so just #2 in the previous comment (get PDB format to do all the things) left.

[Eric Pettersen]

Okay, #2 implemented, though it only shows the principal citation.