Frequency of movements during PCA

[Akash Pandya]

Hi,

My PC1 corresponds to an "elbow" bending motion of my protein. I wanted to know if there was any way of quantifying the frequency of those movements in Bio3D or another R code? I have attached an mp4 file, if you could kindly guide me to the right direction?

Regards,

Akash

[Xinqiu Yao]

Hi Akash,

The movie you show is not real-time motion. I don't think you can assign a "frequency" to a PCA result and I have never seen anyone does it. If you do normal mode analysis, you may have a physical frequency associated with each mode.

Hope it helps.

[Akash Pandya]

I understand what you mean. Alternatively, say I wanted to plot the magnitude of those motions could this be done?

I know there is residue-wise loading for each PC, but I would like a general quantification of such motions. Sorry, if I'm asking something that is potentially impossible to obtain.

Many thanks,

Akash

[Xinqiu Yao]

For that purpose, you could use the eigenvalue, which represents the variance of structures along the corresponding PC.