[gmx-users] PCA on secondary structure of protein.

Hi, I plan to perform PCA on a globular protein which I am studying. The simulation for the same is done for 100ns. I have small doubt. Is it appropriate to perform PCA to study the movement in protein on only secondary structure elements (helices in this case). My protein contains long loops

Re: [gmx-users] PCA on secondary structure of protein.

Sure! You'll just be looking at correlations between secondary structure elements, disregarding the role that the loops may play. But it's a sound approach. :) Tsjerk On Tue, Nov 1, 2011 at 3:44 PM, vivek modi modi.vivek2...@gmail.com wrote: Hi, I plan to perform PCA on a globular protein