[R] squashed domains when doing PCA with bio3d

Hi everyone, I have been doing PCA using bio3d. My protein of interest has two domains and there are two crystal structures, one in a closed (domains are close together) and one in an open state (domains are nearly opposite each other). I ran MD simulations on both states and did PCA. When

Re: [R] squashed domains when doing PCA with bio3d

Hi Bianca, If the domains are rotated between the trajectories, the motion cannot be captured by a single linear component. Think of projecting an arc on a straight line. You loose the (deflection) part on the second component. That looks like squashing. I've mentioned this in relation to MD