I think that "connect" cannot be used between frames, so it seems and of course it makes sense (not for struts, but for bonds in general). As a workaround, you could use "set appendnew false" and "load append", although then you cannot use the /2 model selector, you'll need to keep track of what atoms belong to each molecule
On the other hand, for display you don't need struts, you could use "draw" for example which has no such limitation. Like this: deaw myLine1 diameter 0.8 ( [LYS]40:A.NZ/1 ) ( [HIS]146:B.OXT/2 ); color $myLine1 green;
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