You can assign attributes across multiple models using a single file.  The atom specs in the file would need to include the model numbers so that they only assigned into the right model (though you could use “#/name=1xyz” instead of “#0” if you didn’t want to use numbers).  If you are using the Define Attribute tool then you would have to make sure that both models are selected in the “Restrict to models” box (drag select, or click one and then control-click the other).  If you are using the defattr command you don’t have to do anything special (well, still need model numbers in the file).

ChimeraX does not yet have any tools/commands for generic attribute assignment, but down the line it will.  The only way to do attribute assignment right now is directly in Python and even then the attributes will only exist in the current session (i.e. will not be preserved through a session save/restore cycle).  Also, there is not yet support in the command syntax for restricting an operation to items with particular attribute values.  So not a lot of help in ChimeraX yet for generic attribute usage.

—Eric