VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 09 2004 - 16:48:29 CDT

Sergio,
  The mailing list bounced your post every time you sent it because
you began one of the lines with "sub-" which is a mailing list command...
Anyway, regarding your question, I'm assuming you're referring to the
VMD tutorial section here:
 http://www.ks.uiuc.edu/Research/vmd/current/tutorial/html/node3.html

To work through the tutorial, you'll also need to download the
various matching scripts etc which are provided on the web site in
a separate directory pointed to by the "required tutorial files" link:
  http://www.ks.uiuc.edu/Research/vmd/current/tutorial/vmd-tutorial-files/

Let us know if you need more help.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 09, 2004 at 01:58:01PM -0500, owner-vmd-l_at_ks.uiuc.edu wrote:
> >From johns_at_halifax.ks.uiuc.edu Fri Jul 9 13:58:01 2004
> Received: from itsa.ucsf.edu (itsa.ucsf.edu [128.218.95.23])
> by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i69Iw0Yi011708
> (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
> for <vmd-l_at_ks.uiuc.edu>; Fri, 9 Jul 2004 13:58:01 -0500 (CDT)
> Received: from localhost (localhost [127.0.0.1])
> by itsa.ucsf.edu (Switch-3.1.5/CDR-Switch-3.1.0) with ESMTP id i69Iw7jw006223
> for <vmd-l_at_ks.uiuc.edu>; Fri, 9 Jul 2004 11:58:08 -0700 (PDT)
> Date: Fri, 9 Jul 2004 11:58:07 -0700 (PDT)
> From: "Sergio E. Wong" <swon9_at_itsa.ucsf.edu>
> To: vmd-l_at_ks.uiuc.edu
> Subject: coloring.tlc script
> Message-ID: <Pine.GSO.4.53.0407091157400.4345_at_itsa.ucsf.edu>
> MIME-Version: 1.0
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Hi;
>
> I was looking at the online documentation and in the "Multiple
> Molecules and Scripting" section, "Using Color to Display the Deviation"
> sub-section.. there is mention of a "coloring.tcl" script. However, I've
> had difficulty in finding this script. I'm particularly interested in
> writing out some sort of "local" rmsd and this section appears to be able
> to produce that data. Or perhaps it is produced in the alignment section
> before coloring. Either way, the information is clearly produced and I'd
> like to write it out to a file. Any ideas on where is this script? Or
> how to do this?
>
> Thanks
>
> -Sergio 

-- 
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