From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 09 2009 - 13:34:18 CDT

Hi,
  The "measure fit" command determines the transformation matrix, to
apply it, you would use something along the lines of:
  $sel move $matrix

See the VMD/NAMD tutorials for some examples of how this is done in practice:
  http://www.ks.uiuc.edu/Training/Tutorials/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 09, 2009 at 02:31:17PM -0400, Yi Shang wrote:
> Dear all,
> I have a quick question about "measure fit" command.
> I learned from the mailinglist that this command could be used for
> superimposing two molecules. So I tried it on two PDB structures. From Tcl
> output it seems it's calculating the matrix. But two molecules just stayed
> where there were -- the command is not moving molecules in the display
> window. So I wonder if it's because I need extra plugin/conditions to use
> this command.
> Below is the command I typed in Tcl, and I am using VMD 1.8.6. In VMD main
> window, both molecules are displayed, activated, and not fixed.
> ===========================================================================
> >Main< (VMD) 2 % set sel [atomselect 1 "serial 560 579 598 611 622 629 639
> 2498 2517 2536 2549 2560 2567 2577"]
> atomselect0
> >Main< (VMD) 3 % set ref [atomselect 2 "serial 368 387 406 419 433 440 450
> 1907 1926 1945 1957 1971 1978 1988"]
> atomselect1
> >Main< (VMD) 4 % measure fit $sel $ref
> {-0.309560984373 -0.537274956703 0.784542918205 38.356502533}
> {0.94680505991 -0.0978629440069 0.306566536427 -13.4308233261}
> {-0.0879328325391 0.837710261345 0.538989186287 -17.8832244873} {0.0 0.0
> 0.0 1.0}
> =============================================================================
> Thank you all!
> --
> Miranda

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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