Atlantis sits atop pad 39B today awaiting liftoff Thursday to deliver the Joint Airlock to the international space station. Photo: NASA TV/Spaceflight Now

NASA started up its countdown clock today for Thursday's planned launch of space shuttle Atlantis on a mission that aims to complete the first phase of international space station assembly, but stormy weather in Florida could be an obstacle in getting the ship airborne before an imposed deadline next Tuesday.

The shuttle launch team began the three-day countdown on schedule from the T-minus 43 hour point at 8 a.m. EDT in Firing Room 3 of Kennedy Space Center's Complex 39 Launch Control Center. The count includes over 26 hours of planned holds that will lead to liftoff at about 5:04 a.m. EDT on Thursday.

"We've had a real good flow this time and the vehicle is in excellent shape right now," NASA Test Director Jeff Spaulding said. "The flight and ground systems look great...everything is ready to go."

The only hitch could be the weather. Meteorologists are calling for a 40 percent chance that conditions will prohibit liftoff Thursday during the available launch window of 4:59 to 5:09 a.m. EDT. The launch time forecast is iffy because of possible rainshowers in the area and cloud tops from thunderstorms drifting over the Cape.

"Abundant tropical moisture, coupled with disturbances moving from north to south over eastern Florida will bring the threat of coastal precipitation from Thursday into the weekend," said Shuttle Weather Officer Ed Priselac.

In addition to the launch time weather concerns, Priselac says there are also worries about conditions on Wednesday that could stall final pre-flight preparations.

During the day on Wednesday the rotating service gantry at launch pad 39B will be rolled away from Atlantis, exposing the $2 billion shuttle. Since thunderstorms are possible around the Cape, officials will monitor the storms to ensure they don't become too severe and threaten the delicate heat-protection tiles on the ship's skin. If the storms pose a significant risk, retraction of the service structure will be delayed.

The other hurdle NASA faces is having acceptable weather for fueling Atlantis' bullet-shaped external tank with super-cold liquid oxygen and liquid hydrogen. If there is a good chance of thunderstorms or lightning near the pad during the first hour of fueling, the space agency would likely delay tanking.

The three-hour process to load the tank with a half-million gallons of cryogenic propellants is slated to begin around 8 p.m. Spaulding says the operation could be delayed around two hours and still allow Atlantis to launch on time.

Senior NASA managers will meet at 7 p.m. Wednesday night to decide whether or not to proceed with fueling.

Forecasters are calling for good weather at the emergency landing sites in California, New Mexico, Spain and Africa on Thursday.

Should liftoff slip to Friday or Saturday, conditions are expected to worsen as a weak frontal boundary pushes into Central Florida, bringing with it the possibility of thunderstorms over the Cape during launch time. Priselac says there is a 60 percent chance weather will be unacceptable for launch both days.

The weather at abort landing sites still won't be a factor should the launch be delayed 24 or 48 hours.

NASA has only six days to launch Atlantis -- through July 17 -- with the possibility of a squeezing in one more shot on the 18th. After that, the ship can't fly because the Sun's angle on the shuttle once docked to the international space station will be unfavorable, causing systems on Atlantis to overheat.

The so-called Beta Cutout period extends to August 2. Atlantis could launch then, but NASA wants to keep shuttle Discovery's August 7 liftoff on track to ferry the Expedition Three astronauts to the space station and return the Expedition Two crew back to Earth after their five-month mission.

Further complicating matters will be the Eastern Range -- the Air Force-controlled network of tracking, communications and safety systems that is used by all Cape launches including the shuttle. The Range will be out of service from August 18 through September 21, forcing Atlantis to remain grounded through the down time. Liftoff likely would be targeted for around September 27.

Atlantis and crew of five astronauts will deliver the $164 million Joint Airlock, named Quest, to the space station, giving the outpost a new doorway for American and Russian spacewalks.