VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 04 2007 - 13:53:06 CST

Hi,
  It was posted just the other day, but for your convenience
I've attached a copy of it to this email. I'll update the
script library web page with this version since a lot of people
need it these days.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Nov 04, 2007 at 12:46:13PM -0700, Dong Xu wrote:
> Hi John, I remember you mentioned before about the
> bigdcd_wait_until_done script. Could you tell me where I can download
> it from? I have a 50GB trajectory file. bigdcd didn't work well, it
> only processed a few hundreds frame and quit.
>
> Thanks,
> Dong Xu
>
> 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
> > 

-- 
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