VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 22:16:12 CDT

Try using 5 atoms rather than 4 and let me know if you still
have the problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 15, 2007 at 07:16:26PM -0700, Kara Di Giorgio wrote:
> I asked about using VMD to overlay two structures using several atoms
> in each molecule. I got a very nice reply from Mikolai Fajer. I
> really appreciated it. I got it to work at the time. However, I'm
> trying to use it now and I'm getting odd errors.
>
> I select 4 atoms on each molecule using: set base_original [atomselect
> 0 "index 2645 to 2648"] and set base_new [atomselect 1 "index 2 to 5"]
>
> I used set matrix [measure fit $base_new $base_original]
>
> and keep getting told: measure fit: selections must have the same
> number of atoms
>
> I tried to select the atoms one at a time "index 2 3 4 5" etc and get
> the same error.
>
> They do. I'm not sure what the problem is. Does anyone have any
> questions?
>
> Thanks
>
> Kara Di Giorgio
>
> p.s. I'm adding the tkconsole info from my attempt:
>
> loading history file ... 48 events added
> Main console display active (Tcl8.4.2 / Tk8.4.2)
> (research) 49 % set base_original [atomselect 0 "index 2645-2648"]
> atomselect: cannot parse selection text: index 2645-2648
> >Main< (research) 50 % set base_original [atomselect 0 "index 2645 to
> 2648"]
> atomselect0
> >Main< (research) 51 % set base_new [atomselect 1 "index 2 to 5"]
> atomselect1
> >Main< (research) 52 % set matrix [measure fit $base_new $base_original]
> measure fit: selections must have the same number of atoms
> >Main< (research) 53 % set base_ala [atomselect 0 "index 2645 2646 2647
> 2648"]
> atomselect2
> >Main< (research) 54 % set base_pca [atomselect 1 "index 2 3 4 5"]
> atomselect3
> >Main< (research) 55 % set matrix [measure fit $base_ala $base_pca]
> measure fit: selections must have the same number of atoms
> >Main< (research) 56 % 

-- 
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