Hi Eric, You are correct about #2 & #3, there would be an ambiguity in the design & coding. what I would propose: If a folder shuts off (hide), all multiple instantiations would be turned off. If a folder turns on (show), it only turns the model on in that folder. If a protein were in to two folders, it would require a third checkbox option of mixed, along with show & hide states. definitely needs more analysis. Initially I would prefer #2 over #3 as for the motivation: each folder would represent a scenario, easy switching between scenes, improved convenience in working with dozens or hundreds of models.
1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder
I think #2 and #3 are in conflict though. Really, I don't think you want #2 -- it's too confusing. Say a model is in two groups: you close one group -- what happens? You hide one group -- what happens? You deactivate one group and move the other -- what happens? Perhaps if you elaborated on the motivation for putting a model in multiple groups then some other alternative could be devised that provides what you need.