From: Zhaochuan Shen (zcshen_at_gmail.com)
Date: Thu Nov 01 2007 - 16:52:12 CDT

Hi all,

I have two quesiotns:

1) For all the scripts posted on the website and plugins about RMSD, there
are feature about alignment. Why people want to do alignment? How people do
this? The scripts are not very clear. Just "measure fit" and then "move".
2) I have a long trajectory (100000 frames) and want to find out RMSD
for some alpha carbons. The reference is average coordinate. Is there any
standard process? What I did is exprot the trajectory and then use RMSDTT
plugin directly. Do I need to do the alignment? Or anyone can give a
standard process? Thanks!

Wishes,
Zhaochuan