We still have to determine the relative z translation between molecules A and B. The following X-PLOR script file accomplishes this. This is also an example of a translation function with a fixed portion (molecule A). The x,z positions of molecules A and B are known up to a 0.5 translation. Therefore, four translation functions have to be carried out.
The first translation function is successful with a correlation coefficient of 0.45. The corresponding Mathematica plot is shown in Fig.\ 17.5.
Figure 17.5: Translation function.