VMD-L Mailing List

From: Zhaochuan Shen (zcshen_at_gmail.com)
Date: Mon Nov 05 2007 - 11:41:52 CST

Hi,

My main question is: why do I need alignment? What's the general idea of
alignment?

Thanks
Zhaochuan

On 11/3/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> Luis' RMSDTT plugin can do the both of the alignments you're asking about
> without having to write scripts etc. Please see the documentation for
> it here:
> http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/
>
> Read the section "calculation type", and "reference molecule" in
> particular.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Nov 01, 2007 at 03:52:12PM -0600, Zhaochuan Shen wrote:
> > 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>