VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 15 2015 - 10:58:02 CDT

Hi,
  There was a limitation in older revs of VMD with regard to
alignment of less than 4 atoms. I'm guessing that if you're
having a problem that you must be runnig an older version of
VMD and not VMD 1.9.2 or later.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 15, 2015 at 11:34:25AM -0400, Xing wrote:
> Dear all,
>
> I'm trying to reproduce the step 2 of AMBER A1 tutorial with VMD.
> (http://ambermd.org/tutorials/advanced/tutorial1/section2.htm) because
> Sirius is no longer available. However VMD can never superposition the
> "anchor atoms" and the two structures (linker and dye) cannot be aligned as
> shown in the tutorial. I tried to increase the number of anchor atoms and
> the problem still exists. The script is as
>
> set anc_linker [atomselect 4 "index 5 4 6"]
> set anc_dye [atomselect 3 "index 7 6 4"]
> set linker_to_dye [measure fit $anc_linker $anc_dye]
> set all_linker [atomselect 4 "all"]
> $all_linker move $linker_to_dye
>
> Is there something wrong in the script or VMD just cannot align only a few
> atoms?
>
> --
> Sincerely yours
> Xing 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/