VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 16 2009 - 19:15:00 CDT

Hi,
  You don't want to use measure fit as the means of evaluating
the quality of fit, that command only gives you the transformation
matrix to get you to the best fit that the algorithm was able to
produce. Once you've already got the best fit it can find, you'll
get an identity matrix, though they may not be a perfect fit.
The way to evaluate the _quality_ of the fit is to use the
"measure rmsd" command.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 16, 2009 at 07:09:38PM -0400, Taufik Al-Sarraj wrote:
> >Hi,
> >
> >in the tutorial multiple molecules and scripting,
> >http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html
> >
> >there is a method to color a protein based on distance deviation.
> >
> >lets say i want to output a number for this distance deviation
> >say i have a pre-minimization structure 1DGC and a post minimization
> >structure 1DGC
> >
> >i can load 1DGC as 0 and 1DGCmin as (1), and write
> >
> >set crystal [atomselect 0 "all"]
> >set atomsel1 [atomselect 0 "protein and alpha"]
> >set atomsel2 [atomselect 1 "protein and alpha"]
> >set M [measure fit $atomsel1 $atomsel2]
> >$crystal move $M --this is to get a picture of the alignment
> >and then
> >set Dev [measure fit $atomsel1 $atomsel2] --but this will give me {1.0
> >0.0 0.0 0.0} {0.0 1.0 0.0 0.0} {0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}
> >
> >but, there is actually a slight deviation, it can be seen from the
> >picture, am i using the wrong command?
> >
> >
> >
> > 

-- 
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
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