PEET motive lists represent transformations from reference-centered to particle-centered coordinates. Partly as a result, understanding the correct ordering of fnMOTL1 and fnMOTL2 can be somewhat subtle. A useful rule is to specify them in the order in which they were created. Suppose, for example, that a PEET alignment has been run resulting in an output motive list "MOTL-A.csv", and that individual aligned particles were saved using eTomo's "Save Individual Aligned Particles" option / PEET's "alignedBaseName" parameter. A second PEET run is then performed using these aligned subvolumes as input and resulting in an output motive list "MOTL-B.csv". You now desire to combine these 2 motive lists, so that classification and perhaps further refinement can be done using the original volume(s) rather than the extracted subvolumes. In this case, MOTL-A.csv should be entered as fnMOTL1 and MOTL-B.csv as fnMOTL2 rather than vice-versa.
Considered as transforms from reference to particle coordinates, combineMotiveList will apply the transform in fnMOTL2 first, followed by the one in fnMOTL1. Conversely, if you transforms from particle to reference coordinates, the inverse of fnMOTL1 will be applied first, followed by the inverse of fnMOTL2.