analyzing PCA graph from MD simulation

Hi! I have generated PCA graph from molecular dynamics simulation trajectory files . But I’m having trouble analyzing the graph . I’m confused about the semi-transparent dots in the graph what does they signify?
by semi-transparent dots I mean the dots which seem to appear in the background of this graph

Hello @jahid10,
The PCA tool is built on the Bio3D package. Have a look at the explanation in their tutorial.
Post here If you still struggling to understand the plots. I will assist as much as I can.