Ask anyone at Harvard and they will say the school's relationship with Boston is better than it has been in years. But University administrators are learning that a good relationship does not necessarily make development any easier in Boston's cramped neighborhoods.

Last Wednesday, Boston Mayor Thomas M. Menino asked Harvard to redesign a proposal for graduate student housing in Allston, after hearing that residents were outraged over the 21-story structure.

"As you know, the Allston community has serious reservations about the design," Menino wrote in a letter to Harvard President Neil L.

Rudenstine. "In view of that, and because inevitably this project is an important signal of Harvard's larger presence in Boston in the years to come...I must request a redesign to occur."

The interaction illustrates the complicated nature of Harvard development at the current time. University administrators are in almost constant communication with city officials and undertake building projects with the city's full support. But in return for their support, city officials are demanding an unprecedented degree of flexibility from Harvard.

And Harvard has no choice but to accede to city demands if it hopes to sustain the relationship.

"We're absolutely going to honor [the mayor's] request," says Paul S.

Grogan, Harvard's vice president for government, community and public affairs. "The result, though, could mean a setback of anywhere between eight months and a year."

Grogan says he believes the development will eventually succeed as a result of the support Harvard has received from the city.

"We accept that it's just very difficult to build in this environment," he says. "But particularly in Boston, there's a kind of 'let's-get-it-done' attitude."

Menino's letter came on the heels of sustained protest from Allston community members who complained that Harvard's plan would create yet another building along the Charles River that is too tall and is oriented with its back toward Allston residents.

"To us, it was very obvious that the building wasn't facing us. It was facing the river," says Paul Berkeley, the president of the Allston Civic Association. "And the height of the building was very objectionable."

Berkeley says that during negotiations, Harvard had already altered their plans, making what he describes as "token gestures," cutting the tower down from 22 to 21 stories and enlarging the entrance on the Allston side. But the changes were not sufficient for Allston residents, and Berkeley says the mayor made the right decision by stepping in.

But like the mayor, Berkeley says he lauds Harvard's improved relationship with the city. He says the recent clash over graduate student housing is only a step toward the developing reciprocal association between the city and the University.

"We have supported pretty much everything Harvard has proposed up to this project," he says. "It's good for us as a community to stay close to Harvard and then to try to influence Harvard to build in ways that we agree with."