I did a 3DVA on my trimeric protein with a mask on a flexible domain of one of the subunits. I ran the job with 2 modes. I then opened the output map along with the two components in Chimerax to see if they represent the two variability components. Attached are two images.
component_fit_ref is the correct one. component_fits_mine is the incorrect one.
Both are obtained from the same dataset.
Could someone please explain why the two components do not accurately capture the variability in the incorrect one?