Reconstruction by data integration is an emerging trend to reconstruct large protein assemblies, but uncertainties on the input data yield average models whose quantitative interpretation is challenging. This paper presents methods to probe fuzzy models of large assemblies against atomic resolution models of sub-systems. Consider a Toleranced Model (TOM) of a macro-molecular assembly, namely a continuum of nested shapes representing the assembly at multiple scales. Also consider a template namely an atomic resolution 3D model of a sub-system (a complex) of this assembly. We present graph-based algorithms performing a multi-scale assessment of the complexes of the TOM, by comparing the pairwise contacts which appear in the TOM against those of the template. We apply this machinery on TOM derived from an average model of the Nuclear Pore Complex, to explore the connections among members of its well-characterized Y-complex. The software implementing the algorithms of this paper, called GRAPH_MATCHER, is available from the VORATOM suite, see http://team.inria.fr/abs/software/voratom © Proteins 2013;. © 2013 Wiley Periodicals, Inc.