3D numerical simulations of a horizontal magnetic flux tube emergence with different twist are carried out in a computational domain spanning the upper layers of the convection zone to the lower corona. We use the Oslo Staggered Code to solve the full MHD equations with non-grey and non-LTE radiative transfer and thermal conduction along the magnetic field lines. The emergence of the magnetic flux tube input at the bottom boundary into a weakly magnetized atmosphere is presented. The photospheric and chromospheric response is described with magnetograms, synthetic images and velocity field distributions. The emergence of a magnetic flux tube into such an atmosphere results in varied atmospheric responses. In the photosphere the granular size increases when the flux tube approaches from below. In the convective overshoot region some 200km above the photosphere adiabatic expansion produces cooling, darker regions with the structure of granulation cells. We also find collapsed granulation in the boundaries of the rising flux tube. Once the flux tube has crossed the photosphere, bright points related with concentrated magnetic field, vorticity, high vertical velocities and heating by compressed material are found at heights up to 500km above the photosphere. At greater heights in the magnetized chromosphere, the rising flux tube produces a cool, magnetized bubble that tends to expel the usual chromospheric oscillations. In addition the rising flux tube dramatically increases the chromospheric scale height, pushing the transition region and corona aside such that the chromosphere extends up to 6Mm above the photosphere. The emergence of magnetic flux tubes through the photosphere to the lower corona is a relatively slow process, taking of order 1 hour.
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