Use proc from inside another proc on TCL

The problem is that the command created by the atomselect command is being deleted when the procedure returns. I strongly suspect that this is being done using a local variable deletion trace (on some variable that is otherwise unused). When atomselect is run in the global scope, there's no such natural deletion event (unless the global namespace is deleted, and that's an interpreter-ending event) so the trace never gets called and the created command persists indefinitely.

If we rewrite your create like this:

proc create {} {
    global all
    # Double quotes just because of the highlighting here
    set all [uplevel "#0" atomselect top all]
}

then the atomselect runs in the global scope (and the created command should persist) but all the rest of your code is in your procedure.

More properly, it should be done like this:

proc create {} {
    global all
    # Double quotes just because of the highlighting here
    set all [uplevel "#0" [list atomselect top all]]
    # Or this, to better show that we're talking about running a command:
    #   set all [uplevel "#0" [list \
    #       atomselect top all]]
}

This becomes far more important when you pass arguments with spaces (or other metasyntax characters) in, as list not only produces lists, but also substitution-free commands. (In fact, building commands and command fragments is absolutely one of the main uses of the list command; actual lists for ordinary data storage and manipulation tend to be made with some other command.)