Tim Holy
I can verify this and a test (and hopefully fix) is underway in #909. @KristofferC, is there a better way to search for the extensions associated with a package other...
Since this file was written by VMD, I assume this should be reported to them? @lmiq, can you do that?
If it's true that it violates https://www.wwpdb.org/documentation/file-format (I haven't checked), I'd say that's clearly a problem. It's not OK that there's a workaround. It introduces ambiguities and issues, precisely as...
Given that the format is ambiguous, then perhaps we do need to deal with ambiguity. I don't think this should be open-ended: it's kind of a disaster to take the...
> when part of the system is thousands of water molecules is this part of the issue? That (legacy) PDB only lets you use a single character for encoding the...
So maybe we need a `flavor=:md` mode or something? @jgreener64 would that be acceptable?
I guess my thought is that we decide on concrete flavor-specific behavior and document it. Passing a flavor might require that the entire file be scanned first to identify "occupied"...
Isn't the hierarchy about how you assign bonds? Meaning, you have implicit hierarchy any time you want to link entries in rows together.
> But the "residue number", or "name", "chain", or any other property, are just meaningless labels that help one to draw or select different parts of the structure... > Thus,...
I'd favor strict-by-default and requiring that you pass `renumber=true` to activate that mode, but renumbering seems like a sensible solution.