The "load library compound" panel seems to operate while an action like wiggle or a recipe is running.
It's a little hard to tell, but "accept compound" seems to actually replace the current ligand. (A lot of the compounds are very similar, but once in a while, one has a distinctive feature, like a sulfur in place of an oxygen.)
Foldit is usually a bit more modal, although that varies. You won't be able to close a cutpoint while wiggle is running, but you may be able to add a band.
With some further testing, "accept compound" seems to do something, but then the ligand bounces back to its previous version. The exact behavior seems inconsistent, or maybe just confusing.
Thanks for the bug report.
My guess is that it's the two different actions fighting each other. The Compound Library panel attempts to substitute in its design, but wiggle/etc. then comes along and replaces the structure with what it has been working on. – I think you're right that we probably should keep the Compound Library panel from doing the substitution while another action is running.
