Each time I use 3D variability the end result is a map with frames that track changes of volume contouring, as opposed to actual conformational changes. I am using default settings in 3D variability, and I am solving 3 different modes. I have tried masking the variable region as well as the entire molecule and still get the same result. I have also tried using maps generated from different ab-initio classes and I’m still geting the same result.
Are there any parameters that I can change that would favor screening for conformational changes?