More prominent "supersedes" info

[Elaine Meng]

If it's a pain to implement, however, it may not be worth doing. Reasoning is that supposedly if a person is delving into a particular system, they should already have looked at the PDB website and figured all this out.

The use cases are (1) person has old stale knowledge of the original entry, (2) person types random PDB ID just to "open something" which was my situation.

File as desired.
Elaine

On Apr 21, 2025, at 5:23 PM, Elaine Meng <meng@…> wrote:

I would vote for a dialog for superseded entries with an option to open the new version (instead of the obsolete one, if it's not already open, otherwise, in addition to the obsolete one)... at least if it is reasonably doable from the programmer standpoint.

Elaine

On Apr 17, 2025, at 5:05 PM, Eric Pettersen <pett@…> wrote:

It is the first warning in the log. The problem is that with all the other warnings and the long bogus “non-standard” residue table, you have to scroll back quite a bit to see it. Perhaps a dialog should be raised for superseded entries.

—Eric

On Apr 17, 2025, at 5:01 PM, Elaine Meng <meng@…> wrote:

Ideally, it would be nice if there was a message in the Log saying it was superseded and link to open the new version, or maybe even a warning dialog "entry blah superseded by entry blah - open anyway?" I don't see anything in the Log about its downgraded status.

But maybe that's not possible to know before actually opening the file, if at all. Also maybe not that common of a situation, so not worth the effort to warn people. I don't think I've had that issue with other structures before.

Elaine

On Apr 17, 2025, at 4:51 PM, Greg Couch <gregc@…> wrote:

The 3fxn.cif file says that the METHIONINE entity is a "non-polymer" and consequently doesn't have the full sequence information either. So somewhat expected, garbage in, garbage out.

-- Greg

On 4/17/25 10:15, Eric Pettersen wrote:
Hi Greg,
Is this expected? If I open 3fxn using PDB format it’s fine, though it says the entry has been superseded by 5nll. Opening 5nll in mmCF format works fine.

—Eric

On Apr 17, 2025, at 10:07 AM, Elaine Meng <meng@…> wrote:

Hrm I just opened it randomly and all the residues are disconnected and considered nonstandard! I.e. no ribbon.