question about figure legend and so on in bio3D

[B Albert]

Hello:

I've some question about the figure legend in bio3d.

In this tutorial http://thegrantlab.org/bio3d/tutorials/trajectory-analysis

Figure 8, what's the meaning of color scale?

In the same page, Figure 9, in the figure legend, it said "Red and blue lines indicate correlated and anti-correlation motions, respectively."

what does it mean correlation? Does it imply that two residues will move in the same direction? what does it mean anti-correlation? Does it imply that two residues will move in the opposite direction?

Thank you very much

[Xinqiu Yao]

Hi,

Your understanding of (anti-) correlation is overall correct. Positive correlation means that two atoms move (with respect to the mean position of each atom) in the same direction, while negative correlation means that they move in the opposite direction. The absolute value of correlation indicates the degree of such parallel movements. For example, +1 correlation means that the two atoms always move in the same direction through entire trajectory, but +0.5 means that sometimes their moving directions are orthogonal, having an angle, or opposite. The definition of correlation here is similar to normal Pearson's correlation coefficient, with random variables being the Cartesian (x, y and z) coordinates of C-alpha atoms.

Hope this can help.