Ok what i want to do is start to collate and assemble my mmcif notes into a veritable blog post. The first step is to get some inital structure going here so it’s navigable in the quarto ui preview and i don’t have to jump around the markdown notes because this one seems like it might get a bit long with a bunch of dropdowns and annotations and figures and such..

Before we do that though – do u have any suggestions on what to cleanup here? i started this blog (and the directory structure) before CC and it’s a bit of a mess in terms of how i structure shit (artifacts, completed blogposts and the ones that are wip). In particular – i think the “listings” directory is not used at all anymore and i just use one file called “listings.md” which i like better so it’s safe to delete. Then i also don’t have a good mechanism for storing wip posts in the repo without quarto rendering them sometimes as pages at reachable urls… i’d like to keep them as drafts in the repo but never publish them at actual deployment.

Finally, this mmcif monograph will be my first longer post and i’m curious if i can import/separate the monolithic qmd file into sections, each 1-2 pages so we don’t get confused especially with all the embedded shit and such.

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Making a “structure” more of a computational, queryable object, .sqlite db

Big point: version control and DAG connections, how to reconcile scales heterogeneity

add a survey of operations across pdbtbx, ccp4, coot, isolde, chimerax separate ml operations section