the question is described below since it can be considered a chemistry or physics question: How to translate from one plane to another? originally posted on mathematics SE
I am trying to get Molecule X (from a xyz file which carries x y and z coordinates of X) to be sandwiched between gold electrodes as shown below:
So far I was able, with a python code, to align X using the rotation matrix Rz.
Please not that the images are from VESTA capable of visualization only (otherwise i would not ask the question at all)
I got the following:
So both X and Y have the same orientation but I am not sure how to properly translate or move X to Y position. In other words I need to sandwich Y around the same gold electrodes X was sandwiched. What I can say is that the yellow balls in X and Y should be the same! However i am not sure what mathematical formulation is needed to move the aligned molecule thus I am here asking for assistance.
So in summary I want to go from starting point to ending point as shown below:
Any assistance would be appreciated.