Hi,
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?
Thanks.