One of the major obstacles to the use of theoretical and computational methods to understand molecular electronics experiments is the fact that the contact geometry between the molecule and the electrodes is usually not very well controlled. However, the electronic properties of molecular wire junctions are very sensitive to the contact configuration, which makes the synchronization of theory and experiment difficult. One type of experiment which allows for greater control over the contact geometry is that in which an STM (scanning tunnelling microscope) tip is used to form one of the electrodes. The imaging capability of the STM enables the investigation of both the electronic and geometric structure of the junction. Here, we present the results of recent calculations and experiments in which a PTCDA molecule is cleaved in a controlled fashion from a Ag(111) substrate, while simultaneously calculating and measuring its electronic transport properties. The results demonstrate that even when the geometry of the junction is well known, DFT based transport calculations are unable to accurately describe such systems. This is due to the failure of approximate exchangecorrelation functionals such as LDA to describe phenomena such as the derivative discontinuity and the Kondo effect.