Now that they've got round to seeing Angels & Demons, the pope's people seem to have decided that it is, after all, harmless. Perhaps they'll now be apologising to director Ron Howard's people for obstructing the shoot. At the very least, let's hope they'll discourage conservative media watchdogs from calling Tom Hanks a "pawn of Satan" for starring in the sequel to The Da Vinci Code.

You can see why the Vatican might have decided to relent. Unlike its Dan Brown predecessor, Angels & Demons doesn't diss Jesus Christ, Mary Magdalene or Opus Dei. Its handling of its most resonant rift, the conflict between religion and modernity, seems sympathetic to Catholicism, at least superficially. The Vatican is portrayed as harbouring reaction and stupidity, but also compassion and insight, and it's the latter that are allowed to prevail.

All in all, Angels & Demons sometimes sounds like an act of penance for The Da Vinci Code that could have been scripted by the Catholic church's PR department. However, its visual impact belies its overt message.

Religion and science are formally declared to be reconcilable, but in cinematic terms they're locked in glorious combat. It's science that emerges as the hands-down winner, and it achieves its victory by stealing religion's clothes.

The mainspring of the action is derived from fact, not faith. At Cern's international laboratories on the outskirts of Geneva, antimatter is being created. This miraculous material has the power to ordain doomsday. The film's villains steal an eighth of a gram of it, all they'll need to bring apocalypse to the Vatican.

The cathedral in which Cern's priesthood conduct their rituals puts St Peter's in the shade. It includes a cavern hundreds of feet underground that could enshrine the nave of Notre Dame. From here, protons hurtle round a 17-mile-diameter underground tunnel at the rate of 11,000 circuits a second. The purpose of this secular sacrament is no less than to discover the truths of creation.

For its own exegesis of those truths, the church can point only to a book. Hanks's character shuffles impatiently through many a fusty tome in search of vital knowledge, but the Vatican's soulless and deoxygenated library lacks the onscreen charisma of Cern's Large Hadron Collider.

On the face of it, Rome, bedecked by some of history's greatest creative figures, ought surely to outshine a suburban laboratory complex. However, it's Cern, with its uncompromisingly functional hardware, that turns out to cast the more imposing spell. Set against its mysteriously purposeful conformations, the eternal city's colonnades, statuary, vestments and chalices seem like kitsch adornments for a creed lacking enough lustre of its own.

Because the Vatican banned location filming, St Peter's Square, complete with its 284 Doric columns and 140 statues of saints, was reconstructed on 20 acres of Hollywood parking lot. Hundreds of costumes were handmade, red for cardinals, magenta for bishops and multicoloured for the Swiss Guard.

It's all extremely convincing, but the institution being depicted still ends up looking tacky. Its paraphernalia summon up thoughts of pantomime and Elton John, not the secrets of the universe with which Cern's sober accoutrements seem rather more in touch.

When Catholicism first embraced spectacle and mystique, it was effectively the sole provider of mass entertainment. In the face of the ascetic challenges of Protestantism, the Enlightenment and science, it chose to cling to showmanship. Because of this, it's found itself confronting rationalism with bells, smells and razzmatazz.

Now, Howard's film-making implicitly suggests, the church is being outclassed in the cinematic terms through which it's chosen to present itself. As a result, it's losing an image war with science. This will do it no favours as it finds itself increasingly at odds with practices enabled by its rival.

If, as seems likely, Angels & Demons attracts a large worldwide audience, it seems bound to colour future perceptions of Catholicism. This won't stop the world's biggest religious institution from continuing to be seen as grand and colourful. It may, however, leave it looking increasingly irrelevant – on the way to becoming more of a global theme park than the shaper of humanity's destiny.