Hi Min,
It is not straight forward to answer the question, because the low SNR of the data causes the component magnitudes to be very similar, even though the first one is always the “largest.” Also, any single particle is described by a combination of all the components, so what one component looks like can’t necessarily give you a “dominant” motion.
Ultimately, you will have to inspect the components and fit them into your understanding of the protein, realizing that all the components are present in the real particles.
When you say you have different motions from two distinct conformers, do you mean that there are two 3DVA components that have very similar conformations at the extremes, but show a different trajectory of changes? That is pretty interesting and could imply that both sets of changes really co-occur in the particles, or alternatively, that they complementary parts of a conformational cycle (e.g. a functional step followed by a reset).
Here’s another thread where we discussed this issue some more: Help understanding/analysing results