From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Mon Mar 16 2009 - 18:09:38 CDT

> 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?
>
>
>
>