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Throughout the Star Trek universe, when in battle or trying to protect the ship, persons not on the ship must wait till the threat has left for the ship to safely turn off its shields so transport could be completed.

Why, since the computers in the future are much better than ours, can't the computer momentarily turn off the shields for a fraction of a second to complete a transport, then restore the shields?

With processors as fast as they are now, that seems like it wouldn't take much effort on the computer or operator of the computer to be able to accomplish.

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I'm going to my source for this, one I've cited here before, the Star Trek: The Next Generation Writers' Technical Manual, Fourth Season Edition. This was sent to me directly, in a pitch package by the ST:TNG Script Supervisor Lolita Fatjo. This is one of the Writers' Guides. In other words, it tells the writers what they can and cannot do on screen.

First, see another answer where I posted another excerpt from the same section. That part points out that the molecules from a person or object being transported are stored in the pattern buffer, then we have this:

On page 29, under The Transporter - Once and for All:

From the Pattern Buffer, the molecular stream and the coded instructions pass through a number of subsystems before reaching the emitter. These include the Subspace, Doppler, and Heisenberg Compensators. Each works to insure that the matter stream is being transmitted or received is in the correct phase, frequency, and so on. (sic)

So when they're transporting a person or object, they are actually sending the molecules from one place to another. It's not just a radio signal, it's a stream of molecules traveling (in the annular confinement beam).

The shields stop transport because the matter itself, the stream of molecules, cannot pass through the shield.

(If you need more on this, there's a few more bits addressing the transmission transmission of the matter in the guide.)

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    I think there was an episode where they managed to do this by creating a "hole" in the shields where the matter could go through. – Teknophilia Jan 10 '12 at 18:32
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    There was also the time Miles O'Brian knew the reset cycling timing of the shields on another starship and managed to beam through with the right timing. – Tango Jan 10 '12 at 18:43
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The average transport takes about 2 seconds (per Wikipedia), and if it is difficult (say, because someone is firing at the ship, or it's maneuvering because it's in combat) or something goes wrong with the transport, it could take significantly longer. Leaving the shields down for this amount of time in the middle of a battle would be extremely hazardous.

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If you could beam things onto a ship with shields raised, then why not just beam a kilo of antimatter onto an enemy vessel and end the battle immediately? Or if huge explosions aren't your thing, why not beam 18,000 gallons of seawater and a couple of humpback whales onto their bridge? You get the idea. Transporters can't be used during a fight or they would be the weapon that makes all other weapons obsolete.

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    Beaming explosives onto enemy ships was used in Stargate Atlantis but was quickly countered through some sort of signal scattering/jamming technique. But you're right - the reason for this limitation is more plot-oriented than technical. – Chad Levy Jan 9 '12 at 21:39
  • I can remember Janeway doing that to a Borg scout-ship ones. The Borg were not happy...neither was Janeway... – Bobby Jan 9 '12 at 22:01
  • Yeah, not the best tactic if you want anything to salvage afterward. – Kyle Jones May 31 '12 at 0:24
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There was an episode of TOS in which they beamed some ambassador with the "screens" up. I think it was called "A taste of Armageddon".

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In the Voyager episode The Raven, Tuvok and Paris were chasing Seven's shuttle and Tuvok tells Paris, "See if you can remodulate our transporters to match her shields."

They have the capability but they place highest priority on minimizing risk. There are strict protocols for everything from transporter locks, biofilters, active weapons, signal integrity, etc. VOY - 'Eye of the Needle' Torres says, The phase amplitude of the visual link with the Romulan ship is within just a few megahertz of meeting transporter protocols. This suggests there are protocols about the signal strength required to minimize risk of signal degradation that would affect the party being transported. However, we also have a few instances where they reverted to using uncommon methods when necessary. In 'Scorpion', Torres invented a 'skeletal lock', and in 'Emanations', Chakotay ordered an emergency beam-out. In that emergency situation, Seska used a 'blind beam-out' which means the transporter didn't achieve a lock on the party being transported. A good reason why these instances occur often on Voyager may be because part of the crew is ex-Maquis, who were highly experienced with attempting risky procedures.

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