VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sun Dec 06 2009 - 15:22:06 CST

Hi Dawn,

There is probably a fancy way to do it, but a quick and dirty method that I've used is the following. If you have a series of conformations along the mode, you can have VMD display all frames simultaneously in the 'Trajectory' tab of the Representations GUI. I select the CA atoms and draw them in the VdW representation. Play around with the size of the spheres so that they overlap such that they look like a line or bar along the mode. You can color them by the frame index for clarity. Create another selection where you show the reference structure in whatever representation that you want.

Josh

On Dec 6, 2009, at 2:29 PM, Dawn wrote:

> Hi,
> I want to have porcupine plots for the first principal component PC1(derived from PCA). Would you please tell me if VMD have such function and how to do it?
>
> Thanks a lot!
> Dawn