In the foreground, 64 floor plans for a museum in Japan; in the background, 3 models of a museum in New York.

In the summer of 2006, Kazuyo Sejima and Ryue Nishizawa added to the American landscape a small, gleaming, one-story museum gallery with curving interior and exterior walls of glass, set in a grove of trees. The layered views and reflections were dazzling, even if the location—Toledo, Ohio—was not. Now, for their second American building, the Japanese architects and designers (working since 1995 under the name SANAA) have had their hands in the hallowed soil of New York City, creating the first contemporary art museum ever to rise from the ground up in downtown Manhattan. I was there when it opened December 1.

An exhibition of SANAA's models, blueprints, and commercial designs organized by the Henry Art Gallery in Seattle—guest curated by Ken Tadashi Oshima, an assistant professor in the University of Washington's department of architecture—is instructive about just how much the new New Museum of Contemporary Art in New York differs from the team's other projects, particularly from what seems to be its most thematically comparable building, the 21st Century Museum of Contemporary Art in Kanazawa, Japan.

As a sculpture perched at the end of Prince Street, the New Museum in New York is a marvel: a twisted stack of six off-kilter boxes like a teetering pile of holiday gifts. (They are even marked with a tag, an artwork by Ugo Rondinone that spells out in rainbow letters, "Hell, yes!") Each box is clad in aluminum mesh. From afar, the mesh makes the building look soft and chic, a digital version of the beefy analog modernism in Marcel Breuer's similarly stacked Whitney Museum of American Art uptown.

Up close, the mesh is more anxious, more revealing about the uncomfortable spot in which the museum finds itself. It appears protective, like a security measure separating the museum from the grimy brick buildings not yet gentrified in the surrounding neighborhood of the Bowery.

The interior of the building is less refined, and maybe a little too self-consciously so. Skylights opened up from the twisting of the boxes change position from floor to floor, and they're a lovely detail. But they're easily overlooked: The dominant light in the galleries comes from overtly ugly industrial-style rows of fluorescent tubes.

The three gallery levels, with 12,000 square feet total, are relatively undifferentiated white boxes of the sort that SANAA typically avoids, and they feel slightly cramped. That's due in part to the building's function (contemporary art needs unencumbered tall spaces), location (the footprint of the building is only 71 feet wide and 112 feet deep), and modest budget ($50 million).

But the overall effect is a contamination of the innocent spirit that marks the architects' style and leavens their minimalist tendencies. Maybe it's a fundamental mismatch of sorts. Self-consciousness and anxiety—the stock in trade of the super-sophisticated downtown museum, and something you feel throughout the galleries—is not a SANAA trait.

By comparison, the 21st Century Museum in Japan, a single story high like the glass gallery at the Toledo Museum of Art, is a circular building wearing a skin of glass. On the inside it is like a pie cut into shapes dictated not by strict ideas of symmetry or form but by the activities of the rooms—SANAA's designs are active designs. At the Henry exhibition there's a grid of all the drafts for the ways the museum's rooms could have been configured inside the circle. They're lined up like petri dishes, each one containing another mutation, and you can match the correct design to the final blueprint, which hangs nearby.

SANAA's connection to the natural world is crucial to their work, and locates them somewhere between disparate shapemakers like the oozy Frank Gehry and the hard-angled Donald Judd. Maybe Cezanne, too? A set of coffee pots and cups SANAA designed for the upscale Italian company Alessi is coated in reflective chrome but modeled from the unusual shapes of skinned fruit. Styrofoam models for the set are cut with squished spots on their surfaces like piled-up grapefruits or body parts pressed against glass.

It's remarkable how alive their work feels even on the small scale of the single-room show at the Henry. In the models (with the exception of the New Museum and a Dior store in Tokyo, where the interiors aren't visible), they take as much care creating interiors as exteriors. Tiny paper furniture is all set and ready; colorful little vinyl clothes hang in the closets. In projects ranging from private homes with gardens in each room to the Zollverein School of Management and Design in Essen, Germany, where the dimensions of the building match the dimensions of the historic coal mine that defined the city, the interpenetration of interior and exterior—their permeable coexistence, not the turning inside out of much postmodern architecture—is of the utmost importance.

That's hard to achieve when a building is neither part of the past of its neighborhood (the old New Museum was in SoHo) nor excited to be identified with a dreaded, monolithic, gentrified future. No wonder the historically iconoclastic New Museum—formed in 1977 by curator Marcia Tucker after she was bounced out of the Whitney Museum for a Richard Tuttle show that was ruled too daring—is conflicted from inside to out. It may not be the best result, but at least we have an idea how it happened. As for why the New Museum's inaugural show, Unmonumental, is less than thrilling, well, there's no good excuse for that. recommended

jgraves@thestranger.com